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From: Jason V. <jas...@sc...> - 2010-02-27 05:40:40
|
To those who successfully have this working, would you mind please updating the PyMOL wiki and letting us all know what you did. I don't yet have this setup, so your information would be helpful to us all. Thanks! -- Jason On Fri, Feb 26, 2010 at 2:27 AM, <Gre...@mh...> wrote: > Hi Joachim, > > good advice, this just works! > > Thank you and best regards, > > Joachim > ________________________________ > Von: Joachim Reichelt [mailto:Joa...@he...] > Gesendet: Do 2/25/2010 2:58 > An: pym...@li... > Betreff: Re: [PyMOL] Viewsonic VX2268wm confirmed to work in stereo under > Linux > > I > > Am 25.02.2010 14:01, schrieb Gre...@mh...: > > Hi, > > For supporting a wide variety of software I think it would be the best > choice to have an openGL quad buffered stereo device running. > The fact that Harry did have success with a 120 Hz TFT-Monitor, the Quadro > FX3800 (3-Pin Mini-Din) with 195.x drivers and 3D-Vision Glasses under Linux > is due to the fact that he uses a Linux distribution which is related to > RHEL. > > I just tried exactly the same thing with OpenSuSE 11.2 and couldn't get it > to work at all. The reason, at least how I got it after a long, long > discussion with custhelp.nvidia appears to be that some distributions mount > USB devices under /proc/bus/usb/devices (works...) and some under > /dev/bus/usb (doesn't work). In OpenSuSE, which belongs to the latter class, > the driver appears to look under the non existing /proc/bus/usb/devices, > doesn't find the entry for the 3D-Vision emitter and refuses to switch on > stereo. The nvidia guys tested it with RHEL 5, which belongs to the former > class of distributions. Unfortunately the USB Emitter must be recognized for > reasons I do not know by the driver although the sync signal runs via the > 3-Pin Mini-Din. > > This is easy to fix: > put a line in /etc/init.d/boot.local: > mount /proc/bus/usb > > I have 4 systems up runnig openSuse 11.2 > > Another question of concern is wether the chipset on the FX1800 is supported > by the 195.x driver at all. You should look this up with nvidia. > > Regards, > > Joachim > > > -- > Dr. rer. nat. Joachim Greipel > Med. Hochschule Hannover > Biophys. Chem. OE 4350 > Carl-Neuberg-Str. 1 > 30625 Hannover > Germany > > Fon: +49-511-532-3718 > Fax: +49-511-532-8924 > > > > > ________________________________ > Von: Hugo Gutiérrez de Teran [mailto:hug...@us...] > Gesendet: Donnerstag, 25. Februar 2010 13:10 > An: Harry M. Greenblatt > Cc: pym...@li... > Betreff: Re: [PyMOL] Viewsonic VX2268wm confirmed to work in stereo under > Linux > > Dear PyMolers, > > We are on the process of buying a 3D monitor for stereo rendering. The main > software we use for visualization is PyMOL, in Linux (preferably OpenSuse), > so it is mandatory that it works well with Pymol. We might use stereo with > other programs like Maestro (Schrödinger) or MOE (CCG), so if compatible > with this other software, the better. > Graphics Card is a nVidiaGEFORCE QUADRO FX 1800. > > PyMOL official recommendations was the Zalman ZMM220W, but this is not > longer distributed, at least in Europe. So, before going for any of the > solutions like Samgsung or Viewsonic, and getting deep into the nightmare > of finding out the proper X configuration, I would like to receive as much > input as possible from recent experiences of PyMOL community. > > Thanks in advance, > > Hugo > > -- > Hugo G. de Teran, PhD. > "Parga Pondal" Research fellow > Fundación Pública Galega de Medicina Xenómica - SERGAS > Santiago de Compostela (SPAIN) > > Phone +34 981563100 ext 13873 > e-mail:hug...@us... > http://webspersoais.usc.es/persoais/hugo.teran/ > > Harry M. Greenblatt wrote: > > BS"D > Just to let you all know that we have successfully tested a Viewsonic > VX2268wm (I'm guessing that is the version of the VX2265wm sold on this side > of the pond) with an nVidia Quadro 3800 (3pin stereo version) under Fedora > Core 12, with the nVidia 3D vision glasses, and the 195beta version of the > driver. > Very high quality QB stereo under PyMOL and Coot. > By the way, Warren had warned us that the ATI drivers for Linux were not up > to scratch (without even considering stereo). Is that still true? > Thanks > Harry > > > ------------------------------------------------------------------------- > > Harry M. Greenblatt > > Associate Staff Scientist > > Dept of Structural Biology har...@we... > > Weizmann Institute of Science Phone: 972-8-934-3625 > > Rehovot, 76100 Facsimile: 972-8-934-4159 > > Israel > > > ________________________________ > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > > ________________________________ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > -- > Joachim > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
|
From: hari j. <ha...@gm...> - 2010-02-26 17:35:08
|
Sorry for crying wolf. Everything is working fine with svn 3897 . After Justins email I checked that my system python was suddenly set to a different python and things were probably not getting linked up correctly during building. Now I do get : 1) distutils builds fine 2) make , make install also builds fine Thanks again Hari On Fri, Feb 26, 2010 at 12:03 PM, Justin Lecher <j.l...@fz...>wrote: > Hi Hari, > > the distutils based build is fine. > > justin > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
|
From: Justin L. <j.l...@fz...> - 2010-02-26 17:03:45
|
Hi Hari, the distutils based build is fine. justin |
|
From: hari j. <ha...@gm...> - 2010-02-26 16:08:52
|
Hi ,
I generally track trunk on pymol , i.e I keep my Ubuntu 64 bit linux box
updated with the latest subversion build.
While compiling revision 3897.
I had an error during the build while compiling Cmd.h saying it could not
find "ce_types.h"
That file does exist in
trunk/pymol/modules/cealign/src/ce_types.h
And copying it to trunk/pymol/layer4/ does make it compile fully , but then
the built executable fails to launch with another error ( see below)
So I am just wondering if anyone else is seeing this . Thanks for your help.
Hari
# Initial error without include of ce_types.h
Cmd.c:87:21: error: ce_types.h: No such file or directory
Cmd.c: In function ‘CmdCEAlign’:
Cmd.c:8506: error: ‘pcePoint’ undeclared (first use in this function)
Cmd.c:8506: error: (Each undeclared identifier is reported only once
Cmd.c:8506: error: for each function it appears in.)
Cmd.c:8506: error: expected ‘;’ before ‘coordsA’
Cmd.c:8507: error: ‘pathCache’ undeclared (first use in this function)
Cmd.c:8507: error: expected ‘;’ before ‘paths’
Cmd.c:8540: error: ‘coordsA’ undeclared (first use in this function)
Cmd.c:8540: error: expected ‘;’ before ‘getCoords’
Cmd.c:8541: error: ‘coordsB’ undeclared (first use in this function)
Cmd.c:8541: error: expected ‘;’ before ‘getCoords’
Cmd.c:8544: warning: cast to pointer from integer of different size
Cmd.c:8545: warning: cast to pointer from integer of different size
Cmd.c:8548: warning: cast to pointer from integer of different size
Cmd.c:8554: error: ‘paths’ undeclared (first use in this function)
Cmd.c:8554: error: expected ‘;’ before ‘findPath’
Cmd.c:8557: warning: cast to pointer from integer of different size
make[2]: *** [Cmd.lo] Error 1
make[2]: Leaving directory `/home/hari/pymol/trunk/pymol/layer4'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/hari/pymol/trunk/pymol'
make: *** [all] Error 2
# Error on forced compiling after copying ce_types.h into include path
Traceback (most recent call last):
File "/home/hari/pymol/trunk/pymol/modules/launch_pymol.py", line 32, in
<module>
import pymol
File "/home/hari/pymol/trunk/pymol/modules/pymol/__init__.py", line 472,
in <module>
import _cmd
ImportError: /home/hari/pymol/trunk/pymol/modules/pymol/_cmd.so: undefined
symbol: findBest
|
|
From: <Gre...@mh...> - 2010-02-26 07:27:43
|
Hi Joachim, good advice, this just works! Thank you and best regards, Joachim ________________________________ Von: Joachim Reichelt [mailto:Joa...@he...] Gesendet: Do 2/25/2010 2:58 An: pym...@li... Betreff: Re: [PyMOL] Viewsonic VX2268wm confirmed to work in stereo under Linux I Am 25.02.2010 14:01, schrieb Gre...@mh...: Hi, For supporting a wide variety of software I think it would be the best choice to have an openGL quad buffered stereo device running. The fact that Harry did have success with a 120 Hz TFT-Monitor, the Quadro FX3800 (3-Pin Mini-Din) with 195.x drivers and 3D-Vision Glasses under Linux is due to the fact that he uses a Linux distribution which is related to RHEL. I just tried exactly the same thing with OpenSuSE 11.2 and couldn't get it to work at all. The reason, at least how I got it after a long, long discussion with custhelp.nvidia appears to be that some distributions mount USB devices under /proc/bus/usb/devices (works...) and some under /dev/bus/usb (doesn't work). In OpenSuSE, which belongs to the latter class, the driver appears to look under the non existing /proc/bus/usb/devices, doesn't find the entry for the 3D-Vision emitter and refuses to switch on stereo. The nvidia guys tested it with RHEL 5, which belongs to the former class of distributions. Unfortunately the USB Emitter must be recognized for reasons I do not know by the driver although the sync signal runs via the 3-Pin Mini-Din. This is easy to fix: put a line in /etc/init.d/boot.local: mount /proc/bus/usb I have 4 systems up runnig openSuse 11.2 Another question of concern is wether the chipset on the FX1800 is supported by the 195.x driver at all. You should look this up with nvidia. Regards, Joachim -- Dr. rer. nat. Joachim Greipel Med. Hochschule Hannover Biophys. Chem. OE 4350 Carl-Neuberg-Str. 1 30625 Hannover Germany Fon: +49-511-532-3718 Fax: +49-511-532-8924 ________________________________ Von: Hugo Gutiérrez de Teran [mailto:hug...@us...] Gesendet: Donnerstag, 25. Februar 2010 13:10 An: Harry M. Greenblatt Cc: pym...@li... Betreff: Re: [PyMOL] Viewsonic VX2268wm confirmed to work in stereo under Linux Dear PyMolers, We are on the process of buying a 3D monitor for stereo rendering. The main software we use for visualization is PyMOL, in Linux (preferably OpenSuse), so it is mandatory that it works well with Pymol. We might use stereo with other programs like Maestro (Schrödinger) or MOE (CCG), so if compatible with this other software, the better. Graphics Card is a nVidiaGEFORCE QUADRO FX 1800. PyMOL official recommendations was the Zalman ZMM220W, but this is not longer distributed, at least in Europe. So, before going for any of the solutions like Samgsung or Viewsonic, and getting deep into the nightmare of finding out the proper X configuration, I would like to receive as much input as possible from recent experiences of PyMOL community. Thanks in advance, Hugo -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 e-mail:hug...@us... http://webspersoais.usc.es/persoais/hugo.teran/ Harry M. Greenblatt wrote: BS"D Just to let you all know that we have successfully tested a Viewsonic VX2268wm (I'm guessing that is the version of the VX2265wm sold on this side of the pond) with an nVidia Quadro 3800 (3pin stereo version) under Fedora Core 12, with the nVidia 3D vision glasses, and the 195beta version of the driver. Very high quality QB stereo under PyMOL and Coot. By the way, Warren had warned us that the ATI drivers for Linux were not up to scratch (without even considering stereo). Is that still true? Thanks Harry ------------------------------------------------------------------------- Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology har...@we... Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel ________________________________ ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ________________________________ _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... -- Joachim |
|
From: Yorek, M. S <mat...@ui...> - 2010-02-25 14:40:00
|
Please remove me from your mailing list. REMOVE: mat...@ui...<mailto:mat...@ui...> Thanks |
|
From: Jason V. <jas...@sc...> - 2010-02-25 14:32:24
|
Hugo,
I took that out because I got very little response to the "ailgnto"
command. (Do others use it?) I like it, so I might put it back in.
For now, you can restore that functionality by copy/pasting this into
"alignto.py":
def alignto(sel1):
"""Just a quick & dirty multiple structure alignment"""
for x in cmd.get_names(selection="*"):
print "Aligning %s to %s" % (x, sel1)
cmd.cealign( sel1, x )
# Let PyMOL know about the alignto command
cmd.extend("alignto", alignto)
Start up PyMOL and then type
@/path/to/alignto.py
where "path/to" is the path to where you saved the alignto.py file.
'alignto' should now be defined and working.
-- Jason
2010/2/25 Hugo Gutiérrez de Teran <hug...@us...>:
> Hi Jason,
>
> I have compiled the last PyMOL code, and tried to used CEalign. What I
> wanted is to align all proteins using the first entry as reference, as
> it is possible with the CEalign command "alignto" (following
> instructions in
> http://pymolwiki.org/index.php/Cealign#Multiple_Structure_Alignments).
>
> But alignto command is not found ....
>
> I don't know if this is a bug.
> Any help to align all molecules onto the first entry is also appreciated.
>
> Cheers,
> Hugo
> Jason Vertrees wrote:
>> PyMOLers,
>>
>> As promised:
>>
>> * FreeMOL is back up.
>>
>> * CEalign has been built into the PyMOL source code. You can check
>> out the SourceForge code and test it out.
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>
>
> --
> Hugo G. de Teran, PhD.
> "Parga Pondal" Research fellow
> Fundación Pública Galega de Medicina Xenómica - SERGAS
> Santiago de Compostela (SPAIN)
>
> Phone +34 981563100 ext 13873
> e-mail:hug...@us...
> http://webspersoais.usc.es/persoais/hugo.teran/
>
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120
|
|
From: Joachim R. <Joa...@he...> - 2010-02-25 14:14:59
|
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I<br>
<br>
Am 25.02.2010 14:01, schrieb <a class="moz-txt-link-abbreviated" href="mailto:Gre...@mh...:">Gre...@mh...:</a>
<blockquote
cite="mid:35B...@ex..."
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta content="MSHTML 6.00.6000.16981" name="GENERATOR">
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010">Hi,</span></font></div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010"></span></font> </div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010">For supporting a
wide variety of software I think it would be the best choice
to have an openGL quad buffered stereo device running. </span></font></div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010">T</span></font><font
color="#0000ff" face="Arial" size="2"><span
class="851464412-25022010">he fact that Harry did have
success with a 120 Hz TFT-Monitor, the Quadro FX3800 (3-Pin
Mini-Din) with 195.x drivers and 3D-Vision Glasses under
Linux is due to the fact that he uses a Linux distribution
which is related to RHEL. </span></font></div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010"></span></font> </div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010">I just tried exactly
the same thing with OpenSuSE 11.2 and couldn't get it to
work at all. The reason, at least how I got it after a long,
long discussion with custhelp.nvidia appears to be that some
distributions mount USB devices under /proc/bus/usb/devices
(works...) and some under /dev/bus/usb (doesn't work). In
OpenSuSE, which belongs to the latter class, the driver
appears to look under the non existing
/proc/bus/usb/devices, doesn't find the entry for the
3D-Vision emitter and refuses to switch on stereo. The
nvidia guys tested it with RHEL 5, which belongs to the
former class of distributions. Unfortunately the USB Emitter
must be recognized for reasons I do not know by the driver
although the sync signal runs via the 3-Pin Mini-Din.</span></font></div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010"></span></font> <br>
</div>
</blockquote>
This is easy to fix:<br>
put a line in /etc/init.d/boot.local:<br>
mount /proc/bus/usb<br>
<br>
I have 4 systems up runnig openSuse 11.2<br>
<blockquote
cite="mid:35B...@ex..."
type="cite">
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010">Another question of
concern is wether the chipset on the FX1800 is supported by
the 195.x driver at all. You should look this up with
nvidia.</span></font></div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010"></span></font> </div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010">Regards,</span></font></div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010"></span></font> </div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial"
size="2"><span class="851464412-25022010">Joachim</span></font></div>
<div> </div>
<div align="left"> </div>
<div align="left"><font face="Arial" size="2">-</font><font
face="Arial" size="2">-</font></div>
<div align="left"><font face="Arial" size="2">Dr. rer. nat.
Joachim Greipel</font></div>
<div align="left"><font face="Arial" size="2">Med. Hochschule
Hannover</font></div>
<div align="left"><font face="Arial" size="2">Biophys. Chem. OE
4350</font></div>
<div align="left"><font face="Arial" size="2">Carl-Neuberg-Str. 1</font></div>
<div align="left"><font face="Arial" size="2">30625 Hannover</font></div>
<div align="left"><font face="Arial" size="2">Germany</font></div>
<div align="left"> </div>
<div align="left"><font face="Arial" size="2">Fon:
+49-511-532-3718</font></div>
<div align="left"><font face="Arial" size="2">Fax:
+49-511-532-8924</font></div>
<div align="left"> </div>
<div align="left"> </div>
<div> </div>
<br>
<blockquote style="padding-left: 5px; margin-left: 5px;
border-left: 2px solid rgb(0, 0, 255); margin-right: 0px;">
<div class="OutlookMessageHeader" dir="ltr" align="left"
lang="de">
<hr tabindex="-1"> <font face="Tahoma" size="2"><b>Von:</b>
Hugo Gutiérrez de Teran [<a class="moz-txt-link-freetext" href="mailto:hug...@us...">mailto:hug...@us...</a>] <br>
<b>Gesendet:</b> Donnerstag, 25. Februar 2010 13:10<br>
<b>An:</b> Harry M. Greenblatt<br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:pym...@li...">pym...@li...</a><br>
<b>Betreff:</b> Re: [PyMOL] Viewsonic VX2268wm confirmed to
work in stereo under Linux<br>
</font><br>
</div>
Dear PyMolers,<br>
<br>
We are on the process of buying a 3D monitor for stereo
rendering. The main software we use for visualization is PyMOL,
in Linux (preferably OpenSuse), so it is mandatory that it works
well with Pymol. We might use stereo with other programs like
Maestro (Schrödinger) or MOE (CCG), so if compatible with this
other software, the better.<br>
Graphics Card is a nVidiaGEFORCE QUADRO FX 1800.<br>
<br>
PyMOL official recommendations was the Zalman ZMM220W, <b>but
this is not longer distributed, at least in Europe</b>. So,
before going for any of the solutions like Samgsung or
Viewsonic, and getting deep into the nightmare of finding out
the proper X configuration, I would like to receive as much
input as possible from recent experiences of PyMOL community. <br>
<br>
Thanks in advance,<br>
<br>
Hugo<br>
<br>
<pre class="moz-signature" cols="72">--
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundación Pública Galega de Medicina Xenómica - SERGAS
Santiago de Compostela (SPAIN)
Phone +34 981563100 ext 13873
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:e-mail:hug...@us...">e-mail:hug...@us...</a>
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://webspersoais.usc.es/persoais/hugo.teran/" rel="nofollow">http://webspersoais.usc.es/persoais/hugo.teran/">http://webspersoais.usc.es/persoais/hugo.teran/</a> </pre>
<br>
Harry M. Greenblatt wrote:
<blockquote
cite="mid:DED...@we..."
type="cite">BS"D
<div><br>
</div>
<div>Just to let you all know that we have successfully tested
a Viewsonic VX2268wm (I'm guessing that is the version of
the VX2265wm sold on this side of the pond) with an nVidia
Quadro 3800 (3pin stereo version) under Fedora Core 12, with
the nVidia 3D vision glasses, and the 195beta version of the
driver.</div>
<div><br>
</div>
<div>Very high quality QB stereo under PyMOL and Coot.</div>
<div><br>
</div>
<div>By the way, Warren had warned us that the ATI drivers for
Linux were not up to scratch (without even considering
stereo). Is that still true?</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
</div>
<div>Harry</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div><span class="Apple-style-span" style="word-spacing:
0px; font: 16px Helvetica; text-transform: none; color:
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2;"><span class="Apple-style-span"
style="word-spacing: 0px; font: 16px Helvetica;
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orphans: 2; widows: 2;">
<p style="margin: 0px;"><font style="font: 12px
Helvetica;" size="3"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">-------------------------------------------------------------------------</span></span></font></font></p>
<p style="margin: 0px;"><font style="font: 12px
Helvetica;" size="3"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">Harry M.
Greenblatt</span></span></font></font></p>
<p style="margin: 0px;"><font
class="Apple-style-span" face="Courier" size="3"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">Associate Staff
Scientist</span></span></font></p>
<p style="margin: 0px;"><font style="font: 12px
Helvetica;" size="3"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">Dept of
Structural Biology</span></span></font><span
class="Apple-converted-space"><span
class="Apple-converted-tab"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span"
style="font-size: 12px; font-family:
Courier;"><span class="Apple-style-span"
style="font-size: 12px; font-family:
Courier;"> </span></span></font></span></span><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><a
href="mailto:har...@we..."
moz-do-not-send="true">har...@we...</a></span></span></font></font></p>
<p style="margin: 0px;"><font style="font: 12px
Helvetica;" size="3"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">Weizmann
Institute of Science</span></span></font><span
class="Apple-converted-space"><span
class="Apple-converted-tab"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span"
style="font-size: 12px; font-family:
Courier;"><span class="Apple-style-span"
style="font-size: 12px; font-family:
Courier;"> <span
class="Apple-converted-space"> </span></span></span></font></span></span><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">Phone:</span></span></font><span
class="Apple-converted-space"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span"
style="font-size: 12px; font-family:
Courier;"> </span></span></font></span><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">972-8-934-3625</span></span></font></font></p>
<p style="margin: 0px;"><font style="font: 12px
Helvetica;" size="3"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">Rehovot,
76100<span class="Apple-converted-space"> </span></span></span></font><span
class="Apple-converted-space"><span
class="Apple-converted-tab"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span"
style="font-size: 12px; font-family:
Courier;"><span class="Apple-style-span"
style="font-size: 12px; font-family:
Courier;"> </span></span></font></span></span><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">Facsimile:<span
class="Apple-converted-space"> </span></span></span></font><span
class="Apple-converted-space"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span"
style="font-size: 12px; font-family:
Courier;"> <span
class="Apple-converted-space"> </span></span></span></font></span><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">972-8-934-4159</span></span></font></font></p>
<p style="margin: 0px;"><font style="font: 12px
Helvetica;" size="3"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;">Israel</span></span></font><span
class="Apple-converted-space"><font
class="Apple-style-span" face="Courier"><span
class="Apple-style-span" style="font-size:
12px; font-family: Courier;"><span
class="Apple-style-span"
style="font-size: 12px; font-family:
Courier;"> </span></span></font></span></font></p>
<br class="Apple-interchange-newline">
</span></span></span><br
class="Apple-interchange-newline">
</div>
<br>
</div>
<pre wrap=""><hr width="90%" size="4">
------------------------------------------------------------------------------
Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://p.sf.net/sfu/intel-sw-dev" rel="nofollow">http://p.sf.net/sfu/intel-sw-dev">http://p.sf.net/sfu/intel-sw-dev</a></pre>
<pre wrap=""><hr width="90%" size="4">
_______________________________________________
PyMOL-users mailing list (<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:PyM...@li...">PyM...@li...</a>)
Info Page: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/pymol-users" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users">https://lists.sourceforge.net/lists/listinfo/pymol-users</a>
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</blockquote>
<br>
</blockquote>
<pre wrap="">
<fieldset class="mimeAttachmentHeader"></fieldset>
------------------------------------------------------------------------------
Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
<a class="moz-txt-link-freetext" href="http://p.sf.net/sfu/intel-sw-dev" rel="nofollow">http://p.sf.net/sfu/intel-sw-dev">http://p.sf.net/sfu/intel-sw-dev</a></pre>
<pre wrap="">
<fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
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</blockquote>
<br>
<div class="moz-signature">-- <br>
Joachim
</div>
</body>
</html>
|
|
From: Sabuj P. <sa...@gm...> - 2010-02-25 14:01:35
|
> I just tried exactly the same thing with OpenSuSE 11.2 and couldn't get it > to work at all. The reason, at least how I got it after a long, long > discussion with custhelp.nvidia appears to be that some distributions mount > USB devices under /proc/bus/usb/devices (works...) and some under > /dev/bus/usb (doesn't work). In OpenSuSE, which belongs to the latter class, > the driver appears to look under the non existing /proc/bus/usb/devices, > doesn't find the entry for the 3D-Vision emitter and refuses to switch on > stereo. The nvidia guys tested it with RHEL 5, which belongs to the former > class of distributions. Unfortunately the USB Emitter must be recognized for > reasons I do not know by the driver although the sync signal runs via the > 3-Pin Mini-Din. Did you try in /etc/fstab: none /proc/bus/usb usbdevfs defaults 0 0 or were you able to get it work in suse using some other method? > > Another question of concern is wether the chipset on the FX1800 is supported > by the 195.x driver at all. You should look this up with nvidia. You need at least a quadro 3700. |
|
From: Sabuj P. <sa...@gm...> - 2010-02-25 13:26:22
|
On Thu, Feb 25, 2010 at 7:12 AM, Christine Lee <bio...@gm...> wrote: > Dear, > > Based on my personal experience, I do not recommend Acer, It is really > poor hardware. Or give it a try and after some time you will realize > how poor it is. Yeah, I agree. But anyone know of any other 3D laptops? There are these Asus laptops that can use the Nvidia 3D vision kit: http://www.google.com/products?hl=en&q=asus+3d+vision+laptop&um=1&ie=UTF-8&ei=wXmGS-qsL5DsM8mvxL4M&sa=X&oi=product_result_group&ct=title&resnum=3&ved=0CBoQrQQwAg but it has a builtin GEForce card which will only do stereo on Windows for full screen DirectX apps/games. |
|
From: <Gre...@mh...> - 2010-02-25 13:18:54
|
Hi, For supporting a wide variety of software I think it would be the best choice to have an openGL quad buffered stereo device running. The fact that Harry did have success with a 120 Hz TFT-Monitor, the Quadro FX3800 (3-Pin Mini-Din) with 195.x drivers and 3D-Vision Glasses under Linux is due to the fact that he uses a Linux distribution which is related to RHEL. I just tried exactly the same thing with OpenSuSE 11.2 and couldn't get it to work at all. The reason, at least how I got it after a long, long discussion with custhelp.nvidia appears to be that some distributions mount USB devices under /proc/bus/usb/devices (works...) and some under /dev/bus/usb (doesn't work). In OpenSuSE, which belongs to the latter class, the driver appears to look under the non existing /proc/bus/usb/devices, doesn't find the entry for the 3D-Vision emitter and refuses to switch on stereo. The nvidia guys tested it with RHEL 5, which belongs to the former class of distributions. Unfortunately the USB Emitter must be recognized for reasons I do not know by the driver although the sync signal runs via the 3-Pin Mini-Din. Another question of concern is wether the chipset on the FX1800 is supported by the 195.x driver at all. You should look this up with nvidia. Regards, Joachim -- Dr. rer. nat. Joachim Greipel Med. Hochschule Hannover Biophys. Chem. OE 4350 Carl-Neuberg-Str. 1 30625 Hannover Germany Fon: +49-511-532-3718 Fax: +49-511-532-8924 ________________________________ Von: Hugo Gutiérrez de Teran [mailto:hug...@us...] Gesendet: Donnerstag, 25. Februar 2010 13:10 An: Harry M. Greenblatt Cc: pym...@li... Betreff: Re: [PyMOL] Viewsonic VX2268wm confirmed to work in stereo under Linux Dear PyMolers, We are on the process of buying a 3D monitor for stereo rendering. The main software we use for visualization is PyMOL, in Linux (preferably OpenSuse), so it is mandatory that it works well with Pymol. We might use stereo with other programs like Maestro (Schrödinger) or MOE (CCG), so if compatible with this other software, the better. Graphics Card is a nVidiaGEFORCE QUADRO FX 1800. PyMOL official recommendations was the Zalman ZMM220W, but this is not longer distributed, at least in Europe. So, before going for any of the solutions like Samgsung or Viewsonic, and getting deep into the nightmare of finding out the proper X configuration, I would like to receive as much input as possible from recent experiences of PyMOL community. Thanks in advance, Hugo -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 e-mail:hug...@us... http://webspersoais.usc.es/persoais/hugo.teran/ Harry M. Greenblatt wrote: BS"D Just to let you all know that we have successfully tested a Viewsonic VX2268wm (I'm guessing that is the version of the VX2265wm sold on this side of the pond) with an nVidia Quadro 3800 (3pin stereo version) under Fedora Core 12, with the nVidia 3D vision glasses, and the 195beta version of the driver. Very high quality QB stereo under PyMOL and Coot. By the way, Warren had warned us that the ATI drivers for Linux were not up to scratch (without even considering stereo). Is that still true? Thanks Harry ------------------------------------------------------------------------- Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology har...@we... Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel ________________________________ ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ________________________________ _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
|
From: Christine L. <bio...@gm...> - 2010-02-25 13:18:24
|
Dear, Based on my personal experience, I do not recommend Acer, It is really poor hardware. Or give it a try and after some time you will realize how poor it is. Regards Imtiaz On 24 February 2010 15:00, Sabuj Pattanayek <sa...@gm...> wrote: > On Wed, Feb 24, 2010 at 4:50 AM, Stefano Marzi <ma...@ig...> wrote: >> Hi everybody, >> >> Do you have any suggestion about new laptops that can support Active or >> Passive Stereo 3D visualization with Pymol? > > AS5738DG-6165 > > http://us.acer.com/acer/productv.do?LanguageISOCtxParam=en&kcond61e.c2att101=56746&sp=page16e&ctx2.c2att1=25&link=ln438e&CountryISOCtxParam=US&ctx1g.c2att92=447&ctx1.att21k=1&CRC=1856145400 > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
|
From: Harry M. G. <Har...@we...> - 2010-02-25 13:01:46
|
BS"D Dear Hugo > Graphics Card is a nVidiaGEFORCE QUADRO FX 1800. According to the nVidia website your card will only support LCD- based stereo using a USB signal, under Windows, not Linux. You may also need to upgrade the BIOS on your card, according to the nVidia site. So if you want to use a new LCD screen under Linux, current technology requires you to replace your graphics card with one that has a 3-pin stereo timing connector (for example the Quadro FX 3700). Good luck, Harry ------------------------------------------------------------------------ - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology har...@we... Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel |
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From: Sabuj P. <sa...@gm...> - 2010-02-25 12:55:52
|
> Graphics Card is a nVidiaGEFORCE QUADRO FX 1800. See the Active Stereo 3D (High-Refresh) Displays section on this pymol wiki page: http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#Active_Stereo_3D > PyMOL official recommendations was the Zalman ZMM220W, but this is not I don't think MOE, Sybyl, or most other proprietary viz applications support Zalman stereo. |
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From: Hugo G. de T. <hug...@us...> - 2010-02-25 12:10:06
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type"> </head> <body bgcolor="#ffffff" text="#000000"> Dear PyMolers,<br> <br> We are on the process of buying a 3D monitor for stereo rendering. The main software we use for visualization is PyMOL, in Linux (preferably OpenSuse), so it is mandatory that it works well with Pymol. We might use stereo with other programs like Maestro (Schrödinger) or MOE (CCG), so if compatible with this other software, the better.<br> Graphics Card is a nVidiaGEFORCE QUADRO FX 1800.<br> <br> PyMOL official recommendations was the Zalman ZMM220W, <b>but this is not longer distributed, at least in Europe</b>. So, before going for any of the solutions like Samgsung or Viewsonic, and getting deep into the nightmare of finding out the proper X configuration, I would like to receive as much input as possible from recent experiences of PyMOL community. <br> <br> Thanks in advance,<br> <br> Hugo<br> <br> <pre class="moz-signature" cols="72">-- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 <a class="moz-txt-link-abbreviated" href="mailto:e-mail:hug...@us...">e-mail:hug...@us...</a> <a class="moz-txt-link-freetext" href="http://webspersoais.usc.es/persoais/hugo.teran/" rel="nofollow">http://webspersoais.usc.es/persoais/hugo.teran/">http://webspersoais.usc.es/persoais/hugo.teran/</a> </pre> <br> Harry M. Greenblatt wrote: <blockquote cite="mid:DED...@we..." type="cite">BS"D <div><br> </div> <div>Just to let you all know that we have successfully tested a Viewsonic VX2268wm (I'm guessing that is the version of the VX2265wm sold on this side of the pond) with an nVidia Quadro 3800 (3pin stereo version) under Fedora Core 12, with the nVidia 3D vision glasses, and the 195beta version of the driver.</div> <div><br> </div> <div>Very high quality QB stereo under PyMOL and Coot.</div> <div><br> </div> <div>By the way, Warren had warned us that the ATI drivers for Linux were not up to scratch (without even considering stereo). Is that still true?</div> <div><br> </div> <div>Thanks</div> <div><br> </div> <div>Harry</div> <div><br> </div> <div><br> </div> <div><br> <div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"> <p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; font-size-adjust: none; font-stretch: normal; font-size: 12px;" size="3"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">-------------------------------------------------------------------------</span></span></font></font></p> <p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; font-size-adjust: none; font-stretch: normal; font-size: 12px;" size="3"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">Harry M. Greenblatt</span></span></font></font></p> <p style="margin: 0px;"><font class="Apple-style-span" face="Courier" size="3"><span class="Apple-style-span" style="font-size: 12px; font-family: Courier;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">Associate Staff Scientist</span></span></font></p> <p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; font-size-adjust: none; font-stretch: normal; font-size: 12px;" size="3"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">Dept of Structural Biology</span></span></font><span class="Apple-converted-space"><span class="Apple-converted-tab"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"> </span></span></font></span></span><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><a moz-do-not-send="true" href="mailto:har...@we...">har...@we...</a></span></span></font></font></p> <p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; font-size-adjust: none; font-stretch: normal; font-size: 12px;" size="3"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">Weizmann Institute of Science</span></span></font><span class="Apple-converted-space"><span class="Apple-converted-tab"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"> <span class="Apple-converted-space"> </span></span></span></font></span></span><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">Phone:</span></span></font><span class="Apple-converted-space"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"> </span></span></font></span><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">972-8-934-3625</span></span></font></font></p> <p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; font-size-adjust: none; font-stretch: normal; font-size: 12px;" size="3"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">Rehovot, 76100<span class="Apple-converted-space"> </span></span></span></font><span class="Apple-converted-space"><span class="Apple-converted-tab"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"> </span></span></font></span></span><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">Facsimile:<span class="Apple-converted-space"> </span></span></span></font><span class="Apple-converted-space"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"> <span class="Apple-converted-space"> </span></span></span></font></span><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">972-8-934-4159</span></span></font></font></p> <p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; font-size-adjust: none; font-stretch: normal; font-size: 12px;" size="3"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;">Israel</span></span></font><span class="Apple-converted-space"><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"><span class="Apple-style-span" style="font-family: Courier; font-size: 12px;"> </span></span></font></span></font></p> <br class="Apple-interchange-newline"> </span></span></span><br class="Apple-interchange-newline"> </div> <br> </div> <pre wrap=""> <hr size="4" width="90%"> ------------------------------------------------------------------------------ Download Intel&#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. <a class="moz-txt-link-freetext" href="http://p.sf.net/sfu/intel-sw-dev" rel="nofollow">http://p.sf.net/sfu/intel-sw-dev">http://p.sf.net/sfu/intel-sw-dev</a></pre> <pre wrap=""> <hr size="4" width="90%"> _______________________________________________ PyMOL-users mailing list (<a class="moz-txt-link-abbreviated" href="mailto:PyM...@li...">PyM...@li...</a>) Info Page: <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/pymol-users" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users">https://lists.sourceforge.net/lists/listinfo/pymol-users</a> Archives: <a class="moz-txt-link-freetext" href="http://www.mail-archive.com/pym...@li..." rel="nofollow">http://www.mail-archive.com/pym...@li...">http://www.mail-archive.com/pym...@li...</a></pre> </blockquote> <br> </body> </html> |
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From: Harry M. G. <Har...@we...> - 2010-02-25 11:01:06
|
BS"D Just to let you all know that we have successfully tested a Viewsonic VX2268wm (I'm guessing that is the version of the VX2265wm sold on this side of the pond) with an nVidia Quadro 3800 (3pin stereo version) under Fedora Core 12, with the nVidia 3D vision glasses, and the 195beta version of the driver. Very high quality QB stereo under PyMOL and Coot. By the way, Warren had warned us that the ATI drivers for Linux were not up to scratch (without even considering stereo). Is that still true? Thanks Harry ------------------------------------------------------------------------ - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology har...@we... Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel |
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From: Hugo G. de T. <hug...@us...> - 2010-02-25 08:59:49
|
Hi Jason, I have compiled the last PyMOL code, and tried to used CEalign. What I wanted is to align all proteins using the first entry as reference, as it is possible with the CEalign command "alignto" (following instructions in http://pymolwiki.org/index.php/Cealign#Multiple_Structure_Alignments). But alignto command is not found .... I don't know if this is a bug. Any help to align all molecules onto the first entry is also appreciated. Cheers, Hugo Jason Vertrees wrote: > PyMOLers, > > As promised: > > * FreeMOL is back up. > > * CEalign has been built into the PyMOL source code. You can check > out the SourceForge code and test it out. > > Cheers, > > -- Jason > > -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 e-mail:hug...@us... http://webspersoais.usc.es/persoais/hugo.teran/ |
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From: Jason V. <jas...@sc...> - 2010-02-25 05:45:15
|
Zach,
I remember my grad-school days hacking away at PyMOL movies. It can
be fun, but sometimes frustrating. I used to love to watch the
audience while they watched a really cool molecular movie.
I rescripted your movie to perform the trna movements and also rotate
around the scene as the movie plays. The key concept you were missing
is that a "scene" stores the camera position. So, when you made your
360 scenes--we'll talk about that in a second--you inadvertently
stored the camera position, too. That's why the camera was "frozen".
What you can do, instead is use the "mdo" command. Next, scenes takes
up lots of memory, especially as PyMOL likes to interpolate between
them as well as store camera, color and object representations. So,
better than that is to script a small command per frame; hence, the
mdo command, or better yet, take advantage of the interpolations.
Check out the PyMOLWiki for the difference between a 'scene', 'frame'
and 'state'. Those must be absolutely clear before you get good at
complex movies.
Here's the working (but mediocre) script. Copy and paste it into
PyMOL. There are a couple other ways you could reproduce this.
#
# BEGIN
#
reinit
# position molecule & view
fetch 1yfg, trna, async=0
orient
rotate z, 60, trna
python
for x in range(6):
n = "trna_%s" % x
cmd.create( n, "trna", 1, 1)
cmd.hide("everything", "trna")
cmd.translate( [0, -60, 0], "trna" )
cmd.origin("trna")
for x in range(6):
n = "trna_%s" % x
cmd.rotate( "z", 60. * x, n)
cmd.show_as("cartoon", n)
cmd.origin("trna")
cmd.zoom()
python end
mset 1x360
python
for x in range(1,361):
cmd.mdo( x, "rotate y, 1.0, object=trna_0; rotate [-1.4,1.,0.], 1.0,
object=trna_1; rotate [-1.4, -1., 0.], 1.0, object=trna_2; rotate y,
1.0, object=trna_3; rotate [-1.4, 1., 0.], 1.0, object=trna_4; rotate
[1.4,1.,0.], 1.0, object=trna_5; ")
python end
frame 1
orient vis
mview store
python
for f in [120,240,360]:
cmd.frame(f)
cmd.turn('y', 60)
cmd.mview(action="store", linear=1)
python end
frame 1
mplay
#
# END
#
Last, this can be improved by making the 360 mdos into 2 rotates (per
trna and camera). Can you figure out how? Think about it and play
around. The answer is on my PyMOLWiki User Page:
http://www.pymolwiki.org/index.php/User:Inchoate#tRNA_hairball.
Cheers,
-- Jason
On Wed, Feb 24, 2010 at 9:29 PM, Zach Charlop-Powers
<zac...@ms...> wrote:
> Hello Pymol-ers,
> I am trying to script pymol to make some movies. I would like to:
> 1) move the molecules around and save their states somehow (as a state or
> scene or something to that effect). After that, I would like to be able to
> 2) move the camera around independently of the molecules to give a nice
> effect.
> You can see below that I am able to do the first part of this. However when
> i use either "scene" command (in use) or the "mview" command (commented out)
> I run into the same problems: My camera position seems to be locked so i
> can no longer use the positioning and interpolation functions that Warren
> and others worked so hard to put together. I have been playing with this for
> a while and can't figure out a solution. I am hoping someone may have some
> hints on how to proceed.
>
> thanks,
> zach cp
> grad student
> mount sinai school of medicine.
>
> # setup PyMOL for movies
> reinitialize
> set movie_auto_interpolate, off
> set matrix_mode, 1
> set movie_panel, 1
> set scene_buttons, 1
> set cache_frames, 1
> config_mouse three_button_motions, 1
>
> # download the complex and set it up
> fetch 1yfg.pdb, trna
> orient
> rotate z,60, trna
> # make an array of the molecules
> python
> s = range(1,7)
> for x in s:
> cmd.copy("trna%s" %x, "trna")
> cmd.hide("lines", "trna")
> cmd.translate("[0,-60,0]", "trna")
> cmd.origin("trna")
> s = range(1,7)
> for x in s:
> cmd.rotate("z", "%d" %(60*x), "trna%s" %x)
> cmd.hide("lines" ,"trna%s" %x)
> cmd.show("cartoon" ,"trna%s" %x)
> cmd.origin("trna")
> cmd.zoom()
> python end
>
> # overview of the scene
> frame 1
> mview store
> orient
>
> python
> for x in range(360):
> cmd.madd("1 x1"); cmd.frame(1000);
> cmd.rotate("y", 1.0, object="trna1")
> cmd.rotate("[-1.4,1,0]", 1.0, object="trna2")
> cmd.rotate("[-1.4,-1,0]", 1.0, object="trna3")
> cmd.rotate("y", 1.0, object="trna4")
> cmd.rotate("[1.4,-1,0]", 1.0, object="trna5")
> cmd.rotate("[1.4,1,0]", 1.0, object="trna6")
> #cmd.mview("store", object="trna1")
> #cmd.mview("store", object="trna2")
> #cmd.mview("store", object="trna3")
> #cmd.mview("store", object="trna4")
> #cmd.mview("store", object="trna5")
> #cmd.mview("store", object="trna6")
> #cmd.mview("reinterpolate")
> cmd.scene("new","store")
> python end
> frame 180
> set_view (\
> 0.769429266, -0.001453266, 0.638730288,\
> -0.483805567, 0.651568949, 0.584285855,\
> -0.417025983, -0.758588016, 0.500633180,\
> 0.000000000, 0.000000000, -635.205078125,\
> -42.521865845, 33.457977295, 19.863151550,\
> 530.689270020, 739.720764160, -20.000000000 )
> mview store
> mview interpolate
> mview reinterpolate
>
> mplay
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120
|
|
From: Zach Charlop-P. <zac...@ms...> - 2010-02-25 02:29:35
|
Hello Pymol-ers,
I am trying to script pymol to make some movies. I would like to:
1) move the molecules around and save their states somehow (as a state or
scene or something to that effect). After that, I would like to be able to
2) move the camera around independently of the molecules to give a nice
effect.
You can see below that I am able to do the first part of this. However when
i use either "scene" command (in use) or the "mview" command (commented out)
I run into the same problems: My camera position seems to be locked so i
can no longer use the positioning and interpolation functions that Warren
and others worked so hard to put together. I have been playing with this for
a while and can't figure out a solution. I am hoping someone may have some
hints on how to proceed.
thanks,
zach cp
grad student
mount sinai school of medicine.
# setup PyMOL for movies
reinitialize
set movie_auto_interpolate, off
set matrix_mode, 1
set movie_panel, 1
set scene_buttons, 1
set cache_frames, 1
config_mouse three_button_motions, 1
# download the complex and set it up
fetch 1yfg.pdb, trna
orient
rotate z,60, trna
# make an array of the molecules
python
s = range(1,7)
for x in s:
cmd.copy("trna%s" %x, "trna")
cmd.hide("lines", "trna")
cmd.translate("[0,-60,0]", "trna")
cmd.origin("trna")
s = range(1,7)
for x in s:
cmd.rotate("z", "%d" %(60*x), "trna%s" %x)
cmd.hide("lines" ,"trna%s" %x)
cmd.show("cartoon" ,"trna%s" %x)
cmd.origin("trna")
cmd.zoom()
python end
# overview of the scene
frame 1
mview store
orient
python
for x in range(360):
cmd.madd("1 x1"); cmd.frame(1000);
cmd.rotate("y", 1.0, object="trna1")
cmd.rotate("[-1.4,1,0]", 1.0, object="trna2")
cmd.rotate("[-1.4,-1,0]", 1.0, object="trna3")
cmd.rotate("y", 1.0, object="trna4")
cmd.rotate("[1.4,-1,0]", 1.0, object="trna5")
cmd.rotate("[1.4,1,0]", 1.0, object="trna6")
#cmd.mview("store", object="trna1")
#cmd.mview("store", object="trna2")
#cmd.mview("store", object="trna3")
#cmd.mview("store", object="trna4")
#cmd.mview("store", object="trna5")
#cmd.mview("store", object="trna6")
#cmd.mview("reinterpolate")
cmd.scene("new","store")
python end
frame 180
set_view (\
0.769429266, -0.001453266, 0.638730288,\
-0.483805567, 0.651568949, 0.584285855,\
-0.417025983, -0.758588016, 0.500633180,\
0.000000000, 0.000000000, -635.205078125,\
-42.521865845, 33.457977295, 19.863151550,\
530.689270020, 739.720764160, -20.000000000 )
mview store
mview interpolate
mview reinterpolate
mplay
|
|
From: Kin S. S. L. <si...@ch...> - 2010-02-24 18:52:26
|
Hello, I have gone through the tutorial and follow every single step. The plugin said it successfully generate the receptor pdbqt file. However, when I get to the docking, it still cannot detect the receptor so I cannot run any autogrid or autodock. Is there any reason for that? Thank you very much! Sing On Feb 19, 2010, at 11:41 AM, Shiven Shandilya wrote: > Hello Sing, > > Perhaps going over the basic tutorial will help make things clear: > > http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html > > > Best, > Shiven > > > > On Fri, Feb 19, 2010 at 1:13 PM, Kin Sing Stephen Lee > <si...@ch...> wrote: >> Dear all, >> >> Sorry I fixed the prepare_ligand4.py problem. However, when I try to >> do the autodock in the plugin, the plugin cannot recognize the >> receptor so there is no choice available in the receptor in the >> docking page. If I click autogrid or autodock, the program shows no >> response. Is there any setting I could check and fix it? >> >> Thank you very much >> >> Sing >> >> On Feb 19, 2010, at 9:33 AM, pymol-users- >> re...@li... >> wrote: >> >>> Send PyMOL-users mailing list submissions to >>> pym...@li... >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>> or, via email, send a message with subject or body 'help' to >>> pym...@li... >>> >>> You can reach the person managing the list at >>> pym...@li... >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of PyMOL-users digest..." >>> >>> >>> Today's Topics: >>> >>> 1. Re: coordinate systems of pymol and povray (Tsjerk Wassenaar) >>> 2. FreeMOL (Jason Vertrees) >>> 3. Re: PyMOL-users Digest, Vol 45, Issue 9 (Kin Sing Stephen Lee) >>> 4. Save movie not working (Kent Rossman) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Thu, 18 Feb 2010 21:42:39 +0100 >>> From: Tsjerk Wassenaar <ts...@gm...> >>> Subject: Re: [PyMOL] coordinate systems of pymol and povray >>> To: Gab...@al..., pymol-users >>> <pym...@li...> >>> Message-ID: >>> <8ff...@ma...> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Hi Gabriela, >>> >>> If you only want to get the molecule back in view and rotate/ >>> translate >>> it to your liking, you can use commands like: >>> >>> #declare Protein = union { #include "protein.inc" } >>> #declare Center = (min_extent(Protein)+max_extent(Protein))/2; >>> object { Protein translate -Center } >>> >>> If you want to preserve the view you had in Pymol, you'll need >>> something more. For this purpose I wrote a set of POV-Ray macros, >>> which are attached. For this to work, you have to save the view from >>> get_view(). If you used the (better ;)) second version of make_pov >>> from the wiki, the view is already saved in the pov-ray file. Place >>> the macro file somewhere where POV-Ray can find it, and uncomment >>> the >>> section in the .pov file starting with "Uncomment the following >>> lines" :) Now, if you want to add objects to your scene that you >>> have >>> defined based on the coordinates in the pdb file, you can use >>> something like: >>> >>> // This draws a sphere of radius 1 at the origin of your .pdb >>> coordinate system >>> sphere { 0, 1 SET_PYMOL_VIEW( PYMOL_VIEW )) } >>> >>> For more extensive information, read the first section of the >>> file. If >>> things are still unclear, feel free to contact me. And if you find >>> that you've managed to do really cool stuff with it, please let me >>> know :) >>> >>> >>> Hope it helps, >>> >>> Tsjerk >>> >>> On Wed, Feb 17, 2010 at 5:07 PM, Gabriela Schlau-Cohen >>> <gs...@ho...> wrote: >>>> Hi all, >>>> >>>> I am trying to load a pymol graphic into povray and then add on >>>> geometric >>>> objects.? I exported and loaded the molecular model from pymol >>>> successfully >>>> using the make_pov.py script from the wiki. ?I can then copy and >>>> paste that >>>> file into povray to generate the molecules through povray. ?Then, >>>> when I >>>> save the object in pymol to get the molecular coordinates, the >>>> coordinates >>>> are in a different system. >>>> Can someone tell me how to get the molecular coordinates and a >>>> povray file >>>> in the same coordinate system? >>>> Thanks, >>>> Gabriela >>>> ________________________________ >>>> Hotmail: Trusted email with powerful SPAM protection. Sign up now. >>>> ------------------------------------------------------------------------------ >>>> Download Intel? Parallel Studio Eval >>>> Try the new software tools for yourself. Speed compiling, find bugs >>>> proactively, and fine-tune applications for parallel performance. >>>> See why Intel Parallel Studio got high marks during beta. >>>> http://p.sf.net/sfu/intel-sw-dev >>>> _______________________________________________ >>>> PyMOL-users mailing list (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>> >>> >>> >>> -- >>> Tsjerk A. Wassenaar, Ph.D. >>> >>> Computational Chemist >>> Medicinal Chemist >>> Neuropharmacologist >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: pymolmacro.inc.gz >>> Type: application/x-gzip >>> Size: 2390 bytes >>> Desc: not available >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Thu, 18 Feb 2010 16:36:40 -0500 >>> From: Jason Vertrees <jas...@sc...> >>> Subject: [PyMOL] FreeMOL >>> To: pym...@li... >>> Message-ID: >>> <795...@ma...> >>> Content-Type: text/plain; charset=ISO-8859-1 >>> >>> PyMOLers, >>> >>> The FreeMOL website is back up as it was before (http:// >>> freemol.org). >>> FreeMOL is still open-source, based off the original bioinformatics >>> project. The only difference is the location of the webserver: it >>> is >>> now running from a Schrodinger server to give me better access >>> (again, >>> Warren's servers only had FTP access, we now have ssh). >>> >>> Please let me know if anything's missing. >>> >>> Thanks for being patient, >>> >>> -- Jason >>> >>> -- >>> Jason Vertrees, PhD >>> PyMOL Product Manager >>> Schrodinger, LLC >>> >>> (e) Jas...@sc... >>> (o) +1 (603) 374-7120 >>> >>> >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Fri, 19 Feb 2010 01:37:24 -0800 >>> From: Kin Sing Stephen Lee <le...@ms...> >>> Subject: Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 9 >>> To: pym...@li... >>> Message-ID: <23B...@ms...> >>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >>> >>> Thank you Daniel, >>> >>> I finally found the Autodock tool path in Mac however, i got another >>> error message: "ImportError: No module named MolKit" Is there any >>> solution for this in Mac? >>> >>> Thank you very much >>> >>> Sing >>> >>> On Feb 18, 2010, at 10:56 AM, pymol-users- >>> re...@li... wrote: >>> >>>> Send PyMOL-users mailing list submissions to >>>> pym...@li... >>>> >>>> To subscribe or unsubscribe via the World Wide Web, visit >>>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> or, via email, send a message with subject or body 'help' to >>>> pym...@li... >>>> >>>> You can reach the person managing the list at >>>> pym...@li... >>>> >>>> When replying, please edit your Subject line so it is more specific >>>> than "Re: Contents of PyMOL-users digest..." >>>> >>>> >>>> Today's Topics: >>>> >>>> 1. Autodock plugin (Kin Sing Stephen Lee) >>>> 2. Re: Autodock plugin (Daniel Seeliger) >>>> 3. Update & Submitting Bugs (Jason Vertrees) >>>> 4. Re: Update & Submitting Bugs (Christoph Gohlke) >>>> 5. Re: Update & Submitting Bugs (Jason Vertrees) >>>> 6. Re: Update & Submitting Bugs (Christoph Gohlke) >>>> 7. Regarding the Control panel in pymol (phani ghanakota) >>>> 8. Re: Regarding the Control panel in pymol (Jason Vertrees) >>>> 9. coordinate systems of pymol and povray (Gabriela Schlau-Cohen) >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Tue, 16 Feb 2010 11:06:40 -0800 >>>> From: Kin Sing Stephen Lee <le...@ms...> >>>> Subject: [PyMOL] Autodock plugin >>>> To: "pym...@li..." >>>> <pym...@li...> >>>> Message-ID: <333...@ms...> >>>> Content-Type: text/plain; charset=US-ASCII; format=flowed; >>>> delsp=yes >>>> >>>> Dear all, >>>> >>>> This is the first time for me to use the autodock plugin and I have >>>> some simple questions. I'm using Macbook Pro (OS X v 10.5 - >>>> leopard). Autodock and autodock tools run fine in the X11 >>>> terminal. >>>> In the autodock plugin, I need to put in the autodock tool program >>>> path,so I put in the path where I installed the autodock tool >>>> (under >>>> applications folder). When I tried to prepare my receptor and >>>> ligand >>>> file, the plugin cannot find the autodock tools >>>> (prepare_receptor4.py >>>> as well as prepare_ligand4.py) so I am wondering where I can find >>>> the >>>> autodock tools program path or is it possible to use the plugin in >>>> mac? >>>> >>>> Thank you very much >>>> >>>> Sing >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 2 >>>> Date: Tue, 16 Feb 2010 20:26:00 +0100 >>>> From: Daniel Seeliger <ds...@gw...> >>>> Subject: Re: [PyMOL] Autodock plugin >>>> To: pym...@li... >>>> Message-ID: <201...@gw...> >>>> Content-Type: Text/Plain; charset="iso-8859-1" >>>> >>>> Hi Sing, >>>> >>>> take a look into >>>> ~/.ADplugin/pymol_autodock_plugin.conf >>>> and set the path to the autodocktools scripts correctly. Then the >>>> plugin >>>> should find them. >>>> >>>> Cheers, >>>> Daniel >>>> >>>> On Tuesday 16 February 2010 08:06:40 pm Kin Sing Stephen Lee wrote: >>>>> Dear all, >>>>> >>>>> This is the first time for me to use the autodock plugin and I >>>>> have >>>>> some simple questions. I'm using Macbook Pro (OS X v 10.5 - >>>>> leopard). Autodock and autodock tools run fine in the X11 >>>>> terminal. >>>>> In the autodock plugin, I need to put in the autodock tool program >>>>> path,so I put in the path where I installed the autodock tool >>>>> (under >>>>> applications folder). When I tried to prepare my receptor and >>>>> ligand >>>>> file, the plugin cannot find the autodock tools >>>>> (prepare_receptor4.py >>>>> as well as prepare_ligand4.py) so I am wondering where I can find >>>>> the >>>>> autodock tools program path or is it possible to use the plugin in >>>>> mac? >>>>> >>>>> Thank you very much >>>>> >>>>> Sing >>>>> >>>>> >>>>> --------------------------------------------------------------------------- >>>>> --- SOLARIS 10 is the OS for Data Centers - provides features such >>>>> as >>>>> DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris >>>>> 10 NOW >>>>> http://p.sf.net/sfu/solaris-dev2dev >>>>> _______________________________________________ >>>>> PyMOL-users mailing list (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol- >>>>> users >>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>> >>>> >>>> -- >>>> Dr. Daniel Seeliger >>>> Computational Biomolecular Dynamics Group >>>> Max-Planck-Institute for Biophysical Chemistry >>>> Tel. +49 (0) 551-201-2310 >>>> http://wwwuser.gwdg.de/~dseelig >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 3 >>>> Date: Wed, 17 Feb 2010 14:35:13 -0500 >>>> From: Jason Vertrees <jas...@sc...> >>>> Subject: [PyMOL] Update & Submitting Bugs >>>> To: pym...@li... >>>> Message-ID: >>>> <795...@ma...> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> PyMOLers, >>>> >>>> * In order to keep all bugs in one place please email your bugs to >>>> he...@sc... instead of using the SourceForge tracker. >>>> Schrodinger has a very nice bug tracker that we use; and, in the >>>> end >>>> it's just better to not duplicate effort. >>>> >>>> * I started pushing small changes into the open-source code and >>>> more >>>> are coming. Please file bugs to the aforementioned address. >>>> >>>> * CEAlign is working on all my versions of PyMOL, so I'll be >>>> pushing >>>> that to the open-source soon. >>>> >>>> * We now have another server for FreeMOL (which maps right back to >>>> http://freemol.org/) and we also have control over the FreeMOL >>>> project. When I get back to my office (where the files live) I'll >>>> update FreeMOL. >>>> >>>> Thanks, >>>> >>>> -- Jason >>>> >>>> -- >>>> Jason Vertrees, PhD >>>> PyMOL Product Manager >>>> Schrodinger, LLC >>>> >>>> (e) Jas...@sc... >>>> (o) +1 (603) 374-7120 >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 4 >>>> Date: Wed, 17 Feb 2010 21:15:06 -0800 >>>> From: Christoph Gohlke <cg...@uc...> >>>> Subject: Re: [PyMOL] Update & Submitting Bugs >>>> To: pym...@li... >>>> Message-ID: <4B7...@uc...> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> What is the URL of the Schrodinger bug tracker? The PyMOL >>>> SourceForge >>>> tracker is disabled. >>>> >>>> Thanks, >>>> >>>> Christoph >>>> >>>> >>>> On 2/17/2010 11:35 AM, Jason Vertrees wrote: >>>>> PyMOLers, >>>>> >>>>> * In order to keep all bugs in one place please email your bugs to >>>>> he...@sc... instead of using the SourceForge tracker. >>>>> Schrodinger has a very nice bug tracker that we use; and, in the >>>>> end >>>>> it's just better to not duplicate effort. >>>>> >>>>> * I started pushing small changes into the open-source code and >>>>> more >>>>> are coming. Please file bugs to the aforementioned address. >>>>> >>>>> * CEAlign is working on all my versions of PyMOL, so I'll be >>>>> pushing >>>>> that to the open-source soon. >>>>> >>>>> * We now have another server for FreeMOL (which maps right back to >>>>> http://freemol.org/) and we also have control over the FreeMOL >>>>> project. When I get back to my office (where the files live) I'll >>>>> update FreeMOL. >>>>> >>>>> Thanks, >>>>> >>>>> -- Jason >>>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 5 >>>> Date: Thu, 18 Feb 2010 00:30:49 -0500 >>>> From: Jason Vertrees <jas...@sc...> >>>> Subject: Re: [PyMOL] Update & Submitting Bugs >>>> To: Christoph Gohlke <cg...@uc...> >>>> Cc: pym...@li... >>>> Message-ID: >>>> <795...@ma...> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> Christoph, >>>> >>>> Schrodinger's tracker is internal only. To submit a bug, just >>>> email >>>> your bugs to he...@sc... (for faster turnaround put >>>> something >>>> like "PyMOL Bug" in the title). They are immediately filed and >>>> assigned to me. >>>> >>>> I chose to turn off the SourceForge tracker because I do not want >>>> to >>>> miss bugs or spend my time duplicating tracking efforts, as I was. >>>> >>>> Thanks, >>>> >>>> -- Jason >>>> >>>> On Thu, Feb 18, 2010 at 12:15 AM, Christoph Gohlke >>>> <cg...@uc...> >>>> wrote: >>>>> What is the URL of the Schrodinger bug tracker? The PyMOL >>>>> SourceForge >>>>> tracker is disabled. >>>>> >>>>> Thanks, >>>>> >>>>> Christoph >>>>> >>>>> >>>>> On 2/17/2010 11:35 AM, Jason Vertrees wrote: >>>>>> PyMOLers, >>>>>> >>>>>> * In order to keep all bugs in one place please email your bugs >>>>>> to >>>>>> he...@sc... instead of using the SourceForge tracker. >>>>>> Schrodinger has a very nice bug tracker that we use; and, in the >>>>>> end >>>>>> it's just better to not duplicate effort. >>>>>> >>>>>> * I started pushing small changes into the open-source code and >>>>>> more >>>>>> are coming. ?Please file bugs to the aforementioned address. >>>>>> >>>>>> * CEAlign is working on all my versions of PyMOL, so I'll be >>>>>> pushing >>>>>> that to the open-source soon. >>>>>> >>>>>> * We now have another server for FreeMOL (which maps right back >>>>>> to >>>>>> http://freemol.org/) and we also have control over the FreeMOL >>>>>> project. ?When I get back to my office (where the files live) >>>>>> I'll >>>>>> update FreeMOL. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> -- Jason >>>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Download Intel® Parallel Studio Eval >>>>> Try the new software tools for yourself. Speed compiling, find >>>>> bugs >>>>> proactively, and fine-tune applications for parallel performance. >>>>> See why Intel Parallel Studio got high marks during beta. >>>>> http://p.sf.net/sfu/intel-sw-dev >>>>> _______________________________________________ >>>>> PyMOL-users mailing list (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol- >>>>> users >>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>> >>>> >>>> >>>> >>>> -- >>>> Jason Vertrees, PhD >>>> PyMOL Product Manager >>>> Schrodinger, LLC >>>> >>>> (e) Jas...@sc... >>>> (o) +1 (603) 374-7120 >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 6 >>>> Date: Wed, 17 Feb 2010 23:23:26 -0800 >>>> From: Christoph Gohlke <cg...@uc...> >>>> Subject: Re: [PyMOL] Update & Submitting Bugs >>>> To: Jason Vertrees <jas...@sc...> >>>> Cc: pym...@li... >>>> Message-ID: <4B7...@uc...> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> Good. Thanks for keeping PyMOL development going. >>>> >>>> Christoph >>>> >>>> On 2/17/2010 9:30 PM, Jason Vertrees wrote: >>>>> Christoph, >>>>> >>>>> Schrodinger's tracker is internal only. To submit a bug, just >>>>> email >>>>> your bugs to he...@sc... (for faster turnaround put >>>>> something >>>>> like "PyMOL Bug" in the title). They are immediately filed and >>>>> assigned to me. >>>>> >>>>> I chose to turn off the SourceForge tracker because I do not >>>>> want to >>>>> miss bugs or spend my time duplicating tracking efforts, as I was. >>>>> >>>>> Thanks, >>>>> >>>>> -- Jason >>>>> >>>>> On Thu, Feb 18, 2010 at 12:15 AM, Christoph Gohlke >>>>> <cg...@uc...> wrote: >>>>>> What is the URL of the Schrodinger bug tracker? The PyMOL >>>>>> SourceForge >>>>>> tracker is disabled. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Christoph >>>>>> >>>>>> >>>>>> On 2/17/2010 11:35 AM, Jason Vertrees wrote: >>>>>>> PyMOLers, >>>>>>> >>>>>>> * In order to keep all bugs in one place please email your >>>>>>> bugs to >>>>>>> he...@sc... instead of using the SourceForge tracker. >>>>>>> Schrodinger has a very nice bug tracker that we use; and, in the >>>>>>> end >>>>>>> it's just better to not duplicate effort. >>>>>>> >>>>>>> * I started pushing small changes into the open-source code and >>>>>>> more >>>>>>> are coming. Please file bugs to the aforementioned address. >>>>>>> >>>>>>> * CEAlign is working on all my versions of PyMOL, so I'll be >>>>>>> pushing >>>>>>> that to the open-source soon. >>>>>>> >>>>>>> * We now have another server for FreeMOL (which maps right >>>>>>> back to >>>>>>> http://freemol.org/) and we also have control over the FreeMOL >>>>>>> project. When I get back to my office (where the files live) >>>>>>> I'll >>>>>>> update FreeMOL. >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> -- Jason >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 7 >>>> Date: Thu, 18 Feb 2010 09:30:34 -0800 (PST) >>>> From: phani ghanakota <gph...@ya...> >>>> Subject: [PyMOL] Regarding the Control panel in pymol >>>> To: pym...@li... >>>> Message-ID: <820...@we...> >>>> Content-Type: text/plain; charset="us-ascii" >>>> >>>> Hi, >>>> >>>> Is there a way to toggle on and off the control panel using a >>>> command. So that viewing in the full screen mode would be more >>>> pleasant. >>>> >>>> Thanks in advance. >>>> >>>> >>>> >>>> >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> >>>> ------------------------------ >>>> >>>> Message: 8 >>>> Date: Thu, 18 Feb 2010 13:54:40 -0500 >>>> From: Jason Vertrees <jas...@sc...> >>>> Subject: Re: [PyMOL] Regarding the Control panel in pymol >>>> To: phani ghanakota <gph...@ya...> >>>> Cc: pym...@li... >>>> Message-ID: >>>> <795...@ma...> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> On Thu, Feb 18, 2010 at 12:30 PM, phani ghanakota >>>> <gph...@ya...> wrote: >>>>> Is there a way to toggle on and off the control panel using a >>>>> command. So that viewing in the full screen mode would be more >>>>> pleasant. >>>> >>>> Phani, >>>> >>>> # turns off the internal UI >>>> set internal_gui, 0 >>>> >>>> # make PyMOL fullscreen; works on Windows and Mac; some issues on >>>> Linux >>>> fullscreen >>>> >>>> -- Jason >>>> >>>> -- >>>> Jason Vertrees, PhD >>>> PyMOL Product Manager >>>> Schrodinger, LLC >>>> >>>> (e) Jas...@sc... >>>> (o) +1 (603) 374-7120 >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 9 >>>> Date: Wed, 17 Feb 2010 16:07:05 +0000 >>>> From: Gabriela Schlau-Cohen <gs...@ho...> >>>> Subject: [PyMOL] coordinate systems of pymol and povray >>>> To: <pym...@li...> >>>> Message-ID: <SNT...@ph...> >>>> Content-Type: text/plain; charset="iso-8859-1" >>>> >>>> >>>> Hi all, >>>> >>>> I am trying to load a pymol graphic into povray and then add on >>>> geometric objects. I exported and loaded the molecular model from >>>> pymol successfully using the make_pov.py script from the wiki. I >>>> can then copy and paste that file into povray to generate the >>>> molecules through povray. Then, when I save the object in pymol to >>>> get the molecular coordinates, the coordinates are in a different >>>> system. >>>> Can someone tell me how to get the molecular coordinates and a >>>> povray file in the same coordinate system? >>>> Thanks,Gabriela >>>> _________________________________________________________________ >>>> Hotmail: Trusted email with powerful SPAM protection. >>>> http://clk.atdmt.com/GBL/go/201469227/direct/01/ >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> >>>> ------------------------------ >>>> >>>> ------------------------------------------------------------------------------ >>>> Download Intel® Parallel Studio Eval >>>> Try the new software tools for yourself. Speed compiling, find bugs >>>> proactively, and fine-tune applications for parallel performance. >>>> See why Intel Parallel Studio got high marks during beta. >>>> http://p.sf.net/sfu/intel-sw-dev >>>> >>>> ------------------------------ >>>> >>>> _______________________________________________ >>>> PyMOL-users mailing list >>>> PyM...@li... >>>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> >>>> >>>> End of PyMOL-users Digest, Vol 45, Issue 9 >>>> ****************************************** >>>> >>> >>> >>> >>> >>> ------------------------------ >>> >>> Message: 4 >>> Date: Thu, 18 Feb 2010 22:33:14 -0500 >>> From: "Kent Rossman" <kro...@me...> >>> Subject: [PyMOL] Save movie not working >>> To: pym...@li... >>> Message-ID: <4B7...@me...> >>> Content-Type: text/plain; charset=iso-8859-1; format=flowed >>> >>> Hi Delano, >>> >>> When I try to save an MPEG from the save movie menu, pymol works on >>> writing out the movie, then i get an error that says mpeg_encode.exe >>> has >>> encounteres a problem and has to close. A file is written with 0 >>> bytes. There was also an error that mpeg_encode was being used by >>> another file/program...I think. Can you help? >>> >>> Thanks, >>> kr >>> >>> -- >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> Kent Rossman, Ph.D. >>> Research Assistant Professor >>> Department of Pharmacology >>> Lineberger Comprehensive Cancer Center >>> UNC-Chapel Hill, CB 7295 >>> Chapel Hill, NC 27599 >>> >>> Tel: 919-962-1057 >>> Fax: 919-966-0162 >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> >>> >>> >>> >>> >>> >>> ------------------------------ >>> >>> ------------------------------------------------------------------------------ >>> Download Intel® Parallel Studio Eval >>> Try the new software tools for yourself. Speed compiling, find bugs >>> proactively, and fine-tune applications for parallel performance. >>> See why Intel Parallel Studio got high marks during beta. >>> http://p.sf.net/sfu/intel-sw-dev >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> PyMOL-users mailing list >>> PyM...@li... >>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>> >>> >>> End of PyMOL-users Digest, Vol 45, Issue 10 >>> ******************************************* >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> |
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From: David H. <li...@co...> - 2010-02-24 17:44:09
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If you would like to use a server for protein-protein docking, you can check out the nice list on the wikipedia page for CAPRI. http://en.wikipedia.org/wiki/Critical_Assessment_of_PRediction_of_Interactions#List_of_predictions_servers_participating_in_CAPRI If you're looking for actual pieces of software or more manual approaches, you can look at the recent series of posts on the Rosetta Design Group's blog that summarizes many of the talks from the CAPRI assessment meeting in December. http://rosettadesigngroup.com/blog/tag/capri/ Aslo, http://dx.doi.org/10.1016/j.sbi.2009.02.008 has a nice summary of the various approaches. -David On Wed, Feb 24, 2010 at 7:36 AM, mohan raj <moh...@gm...> wrote: > hi all: > > i am a new to pymol. could some one tell me more about the programs > involved in ligand interaction..... > > could i do protein protein interaction simulateions using pymol??? > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
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From: Sanishvili, R. <rsa...@an...> - 2010-02-24 16:01:30
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Dear Colleagues, Building on the success of the past 2 years, we are pleased to announce the third annual CCP4 workshop at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2010/ Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 10 to 17. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The workshop content: First two days of the workshop will be dedicated to beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. The workshop will feature authors and experts of many modern crystallographic software packages. It will be organized in three Sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 9. Application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2010/ Fees: there will be a $250 contribution towards lodging paid directly to Argonne Guest House. All other local expenses (rest of the hotel bill, meals and refreshments) will be covered by the workshop. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsa...@an... |
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From: Sabuj P. <sa...@gm...> - 2010-02-24 15:00:22
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On Wed, Feb 24, 2010 at 4:50 AM, Stefano Marzi <ma...@ig...> wrote: > Hi everybody, > > Do you have any suggestion about new laptops that can support Active or > Passive Stereo 3D visualization with Pymol? AS5738DG-6165 http://us.acer.com/acer/productv.do?LanguageISOCtxParam=en&kcond61e.c2att101=56746&sp=page16e&ctx2.c2att1=25&link=ln438e&CountryISOCtxParam=US&ctx1g.c2att92=447&ctx1.att21k=1&CRC=1856145400 |
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From: Tsjerk W. <ts...@gm...> - 2010-02-24 14:53:19
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Hi Mohan Raj, >From the description it is clear that Pymol is a *visualization* program. So, no, it can not do simulations of any sort. Cheers, Tsjerk On Wed, Feb 24, 2010 at 1:36 PM, mohan raj <moh...@gm...> wrote: > hi all: > > i am a new to pymol. could some one tell me more about the programs > involved in ligand interaction..... > > could i do protein protein interaction simulateions using pymol??? > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist |
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From: <se...@un...> - 2010-02-24 14:30:21
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Hi Stefano, in principle intel graphic should not work properly for some molecular graphic packages. I heard from some mailing list. ciao ciao, Marco Def. Quota "Stefano Marzi" <ma...@ig...>: > Hi everybody, > > Do you have any suggestion about new laptops that can support Active or > Passive Stereo 3D visualization with Pymol? > > Thank you, > > Best, > > Stefano > > -- > Dr. Stefano MARZI > UPR 9002 CNRS-ARN > Université De Strasbourg > IBMC > 15 Rue René Descartes > 67084 Strasbourg-France > Phone +33 (0)3 88417051 > Fax: +33 (0)3 88602218 > E-mail: s....@ib... > http://www-ibmc.u-strasbg.fr/arn/Romby/ > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: se...@un... e-mail: m7...@ya... Tel.: +39-0672594424 Fax: +39-0672594328 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
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