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From: Warren D. <wa...@de...> - 2006-05-31 21:23:46
|
Seth, Please add config_mouse two_button to their pymolrc file. Cheers, Warren -----Original Message----- From: pym...@li... on behalf of Seth Harris Sent: Wed 5/31/2006 2:14 PM To: pym...@li... Subject: [PyMOL] setting for 2 button mouse view mode =20 Hi all, we have a user with a 2 button mouse who would like pymol to start up = that way (i.e. without having to go to the mouse menu and select 2 button = viewing mode every time he starts). I had a look around for a setting we could = put into his pymolrc file, but the only things with promising names didn't = have the desired effect. For instance, "button_mode_name" allows you to = change the text shown on the screen for the mouse mode, but doesn't actually = change the mouse behavior to match the text. Also, changing = "mouse_selection_mode" didn't seem to do the trick. Any ideas on settings we may have = overlooked or improperly implemented? Thanks, Seth |
|
From: Seth H. <se...@gm...> - 2006-05-31 21:07:33
|
Hi all, we have a user with a 2 button mouse who would like pymol to start up that way (i.e. without having to go to the mouse menu and select 2 button viewing mode every time he starts). I had a look around for a setting we could put into his pymolrc file, but the only things with promising names didn't have the desired effect. For instance, "button_mode_name" allows you to change the text shown on the screen for the mouse mode, but doesn't actually change the mouse behavior to match the text. Also, changing "mouse_selection_mode" didn't seem to do the trick. Any ideas on settings we may have overlooked or improperly implemented? Thanks, Seth |
|
From: Savvas S. <Sav...@UG...> - 2006-05-31 19:43:48
|
Dear all,
the problem with installing PyMol under Windows-XP (see message below) ha=
s been
solved. I tried all kinds of tricks (including reinventing the wheel a nu=
mber of
times) but the only effective way to fix the problem was to reinstall the
operating system from scratch, as has also been suggested by Warren.
I am happy to report that PyMol 0.99 runs great on the new DELL Latitude =
620
with a T2400 Centrino-Duo (1.83 GHz), 1GB RAM and the Intel=AE Graphics =
Media
Accelerator 950. This is indeed a very nice system for the mobile structu=
ral
biologist for a very good price, and it only weighs 2 kg. I am already ru=
nning a
number of crystallographic applications (e.g the full CCP4 v6 release for
windows including Coot) alongside my other software applications.
best wishes
Savvas
----- Forwarded message from "Savvas N. Savvides" <savvas.savvides@ugent.=
be>
-----
Date: Mon, 29 May 2006 12:36:08 +0200
From: "Savvas N. Savvides" <sav...@ug...>
Reply-To: sav...@ug...
Subject: [PyMOL] problems with pymol installation
To: pym...@li...
Dear colleagues,
I am trying to install pymol v0.99 on a new laptop running windows XP
but the installer keeps giving an error message that my specified path
does not exist. This is quite striking to me because the extracted files
do indeed have the path that the installer is complaining about! So the
path does exist! Upon restarting the computer hoping to solve the
problem with path recognition, I get a system error about the ntvdm.exe
emulator. Is this a related problem? Would that also be a sign that I
should reinstall the operating system from scratch? I just got the
computer and this may be the most appropriate time to do it.
Thanks in advance for any input
Savvas
-----
Savvas N. Savvides
Professor of Structural Biology
Ghent University
Laboratory for Protein Biochemistry
K.L.Ledeganckstraat 35
9000 Ghent, BELGIUM
Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19
FAX: +32-(0)9-264.53.38
Email: sav...@ug...
----- End forwarded message -----
--
|
|
From: Virgile A. <vir...@es...> - 2006-05-31 16:18:23
|
<html> <body> Hi thibault,<br> you can either try to download and install the full Threader soft from : <a href="http://bioinf.cs.ucl.ac.uk/threader/" eudora="autourl"> " rel="nofollow">http://bioinf.cs.ucl.ac.uk/threader/<br> </a>or alternatively try the on-server version of PSIpred/(m)GenThreader from : <a href="http://bioinf.cs.ucl.ac.uk/psipred/psiform.html" eudora="autourl"> " rel="nofollow">http://bioinf.cs.ucl.ac.uk/psipred/psiform.html</a> but it looks like this last has possibly some problems currently when trying to submit a task.<br><br> Hope this helps<br><br> Virgile<br><br> <br><br> At 17:58 31/05/2006, ge...@em... wrote:<br> <blockquote type=cite class=cite cite="">Hi all ...<br> I'm not sure weather the pymol mailing list is the best place to ask this but<br> anyway ...<br> I would like model a structure of a protein. I have a sequence of interest and I<br> have a related structure which shares a very low sequence identity but is<br> suppose to have a common fold. Do anyone knows how to deal with this ?<br><br> Thanks,<br><br> Tibo<br><br> <br><br> <br> -------------------------------------------------------<br> All the advantages of Linux Managed Hosting--Without the Cost and Risk!<br> Fully trained technicians. The highest number of Red Hat certifications in<br> the hosting industry. Fanatical Support. Click to learn more<br> <a href="http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642" eudora="autourl"> " rel="nofollow">http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642</a> <br> _______________________________________________<br> PyMOL-users mailing list<br> PyM...@li...<br> <a href="https://lists.sourceforge.net/lists/listinfo/pymol-users" eudora="autourl"> " rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users</a></blockquote> <x-sigsep><p></x-sigsep> <hr> <div align="center"><font color="#808080">Virgile Adam (vir...@es...)<br> <b>E</b>uropean <b>S</b>ynchrotron <b>R</b>adiation <b>F</b>acility<br> Office 18.1.07 - Sector 18<br> 6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex 9 France<br> Tel: +33 (0)4 76 88 27 72 / Fax: +33 (0)4 76 88 26 24<br><br> ***<i>Sometimes I think the surest sign that intelligent life exists elsewhere in the universe is that none of it has tried to contact us</i>*** <br> </font></div> </body> </html> |
|
From: <ge...@em...> - 2006-05-31 15:59:46
|
Hi all ... I'm not sure weather the pymol mailing list is the best place to ask this but anyway ... I would like model a structure of a protein. I have a sequence of interest and I have a related structure which shares a very low sequence identity but is suppose to have a common fold. Do anyone knows how to deal with this ? Thanks, Tibo |
|
From: martin w. <Mar...@bi...> - 2006-05-31 15:28:38
|
Hi everybody, is there a way to switch between different models (frames) of a pdb-file containing multiple conformations (e.g. 1arj)? Switching the display between the conformers works fine with cmd.frame(), but atom-coordinates do not change (still the coordinates of first frame / first model). Any ideas? Cheers, Martin |
|
From: Warren D. <wa...@de...> - 2006-05-30 18:19:34
|
Hi Terry, It is much faster to unpack PyLists than PySequences, which is why the = input needs to be a list. However, I just added some code to = automatically convert tuples to lists at the Python API level in future = PyMOL builds. Thanks for pointing out this potential CGO "gotcha"! Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Terry Jones > Sent: Monday, May 29, 2006 5:04 AM > To: pym...@li... > Cc: dj...@ca... > Subject: [PyMOL] Lists vs Tuples inconsistency in cmd.load_cgo() >=20 > I spent quite a bit of time last night chasing down the=20 > following. This: >=20 > cmd.load_cgo([SPHERE, 0.0, 0.0, 0.0, 1.0], 'a') >=20 > puts a sphere on the screen as expected. But this: >=20 > cmd.load_cgo((SPHERE, 0.0, 0.0, 0.0, 1.0), 'a') >=20 > seemingly has no effect at all. I.e., if you pass a tuple=20 > instead of a list, your CGO is not displayed. It's an easy=20 > mistake to make (supposing it should be called a mistake),=20 > and it's not easy to figure out why your CGO does not appear. >=20 > The reason seems to be an if(PyList_Size(pycgo) test on line=20 > 440 of layer2/ObjectCGO.c in the 0.99 release - at least=20 > that's as far as I went in tracing this. >=20 > Is there any reason why a tuple cannot be used here too? >=20 > Regards, > Terry >=20 >=20 > ------------------------------------------------------- > All the advantages of Linux Managed Hosting--Without the Cost=20 > and Risk! > Fully trained technicians. The highest number of Red Hat=20 > certifications in the hosting industry. Fanatical Support.=20 > Click to learn more > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D107521&bid=3D248729& dat=3D121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
|
From: Warren D. <wa...@de...> - 2006-05-30 17:55:35
|
Tsjerk, There is no direct control of the thickness, although adjusting = "ray_trace_gain" (0.001 to 2.0) will have some effect. However, the = most effectively way to control the thickness is to adjust antialiasing = and image size to achieve the desired effect in the final image. =20 By the way, you are not the only one who likes these modes: Leah = Blasiak at MIT used "set ray_trace_mode, 3" to get the cover of the May = 22nd issue of Chemical & Engineering News in relation to her work on the = SyrB2 iron enzyme. <" rel="nofollow">http://pubs.acs.org/cen/currentissue.html> (see = "Recent Issues" image lower right -- Enzymatic Halogenation). Of course, credit where credit is due: David Goodsell = <" rel="nofollow">http://www.scripps.edu/mb/goodsell/> was the obvious source of = inspiration for this recent addition to PyMOL. Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Tsjerk Wassenaar > Sent: Tuesday, May 30, 2006 5:02 AM > To: pymol > Subject: [PyMOL] Edge thickness in ray_trace_mode 2 and 3 >=20 >=20 > Hi Warren et al. >=20 > I really like the ray_trace_modes 2 and 3. However, I'd like=20 > to fiddle around with the thickness of the edges, but can't=20 > find a setting to do so. Am I overlooking something, or isn't=20 > there any (yet)?=20 > By the way, ray_trace_mode 2 is great for making colouring=20 > pictures to get the little ones acquanted with proteins / DNA etc. ;) >=20 > Cheers, >=20 > Tsjerk >=20 > --=20 >=20 > Tsjerk A. Wassenaar, M.Sc. > Groningen Biomolecular Sciences and Biotechnology Institute=20 > (GBB) Dept. of Biophysical Chemistry University of Groningen=20 > Nijenborgh 4 9747AG Groningen, The Netherlands > +31 50 363 4336 >=20 >=20 |
|
From: surendra n. <ne...@ya...> - 2006-05-30 16:50:24
|
Subject: [PyMOL] Superimpoition problem Use first structure for reference and then align rest of them to first one. --- pym...@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. Lists vs Tuples inconsistency in > cmd.load_cgo() (Terry Jones) > 2. problems with pymol installation (Savvas N. > Savvides) > 3. (no subject) (O. J. Ganesh) > 4. Superimpoition problem (chiradip chatterjee) > > --__--__-- > > Message: 1 > Date: Mon, 29 May 2006 10:01:24 +0200 > From: Terry Jones <tc...@ca...> > To: pym...@li... > CC: dj...@ca... > Reply-To: tc...@ca... > Subject: [PyMOL] Lists vs Tuples inconsistency in > cmd.load_cgo() > > I spent quite a bit of time last night chasing down > the following. This: > > cmd.load_cgo([SPHERE, 0.0, 0.0, 0.0, 1.0], 'a') > > puts a sphere on the screen as expected. But this: > > cmd.load_cgo((SPHERE, 0.0, 0.0, 0.0, 1.0), 'a') > > seemingly has no effect at all. I.e., if you pass a > tuple instead of a > list, your CGO is not displayed. It's an easy > mistake to make (supposing it > should be called a mistake), and it's not easy to > figure out why your CGO > does not appear. > > The reason seems to be an if(PyList_Size(pycgo) test > on line 440 of > layer2/ObjectCGO.c in the 0.99 release - at least > that's as far as I went > in tracing this. > > Is there any reason why a tuple cannot be used here > too? > > Regards, > Terry > > > --__--__-- > > Message: 2 > Reply-To: <sav...@ug...> > From: "Savvas N. Savvides" > <sav...@ug...> > To: <pym...@li...> > Date: Mon, 29 May 2006 12:36:08 +0200 > Organization: Ghent University > Subject: [PyMOL] problems with pymol installation > > This is a multi-part message in MIME format. > > ------=_NextPart_000_0036_01C6831C.78CBC160 > Content-Type: text/plain; > charset="us-ascii" > Content-Transfer-Encoding: 7bit > > Dear colleagues, > I am trying to install pymol v0.99 on a new laptop > running windows XP > but the installer keeps giving an error message that > my specified path > does not exist. This is quite striking to me because > the extracted files > do indeed have the path that the installer is > complaining about! So the > path does exist! Upon restarting the computer > hoping to solve the > problem with path recognition, I get a system error > about the ntvdm.exe > emulator. Is this a related problem? Would that also > be a sign that I > should reinstall the operating system from scratch? > I just got the > computer and this may be the most appropriate time > to do it. > > Thanks in advance for any input > Savvas > > ----- > Savvas N. Savvides > Professor of Structural Biology > Ghent University > Laboratory for Protein Biochemistry > K.L.Ledeganckstraat 35 > 9000 Ghent, BELGIUM > Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 > FAX: +32-(0)9-264.53.38 > Email: sav...@ug... > > > ------=_NextPart_000_0036_01C6831C.78CBC160 > Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"> > <HTML> > <HEAD> > <META HTTP-EQUIV=3D"Content-Type" > CONTENT=3D"text/html; = > charset=3Dus-ascii"> > <META NAME=3D"Generator" CONTENT=3D"MS Exchange > Server version = > 6.0.4630.0"> > <TITLE>problems with pymol installation</TITLE> > </HEAD> > <BODY> > <!-- Converted from text/rtf format --> > > <P><FONT SIZE=3D2 FACE=3D"Arial">Dear > colleagues,</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">I am trying to > install pymol v0.99 on = > a new laptop running windows XP but the installer > keeps giving an error = > message that my specified path does not exist. This > is quite striking to = > me because the extracted files do indeed have the > path that the = > installer is complaining about! So the path does > exist! Upon = > restarting the computer hoping to solve the problem > with path = > recognition, I get a system error about the > ntvdm.exe emulator. Is this = > a related problem? Would that also be a sign that I > should reinstall the = > operating system from scratch? I just got the > computer and this may be = > the most appropriate time to do it.</FONT></P> > > <P><FONT SIZE=3D2 FACE=3D"Arial">Thanks in advance > for any input</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">Savvas</FONT> > </P> > > <P><FONT SIZE=3D2 FACE=3D"Arial">-----</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">Savvas N. > Savvides</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">Professor of > Structural Biology</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">Ghent > University</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">Laboratory for > Protein = > Biochemistry</FONT> > > <BR><SPAN LANG=3D"nl"><FONT SIZE=3D2 > FACE=3D"Arial">K.L.Ledeganckstraat = > 35</FONT></SPAN> > > <BR><SPAN LANG=3D"nl"><FONT SIZE=3D2 > FACE=3D"Arial">9000 Ghent, = > BELGIUM</FONT></SPAN> > > <BR><SPAN LANG=3D"nl"><FONT SIZE=3D2 > FACE=3D"Arial">Phone: = > +32-(0)9-264.51.24 ; > +32-(0)472-92.85.19</FONT></SPAN> > > <BR><SPAN LANG=3D"fr"><FONT SIZE=3D2 > FACE=3D"Arial">FAX: = > +32-(0)9-264.53.38</FONT></SPAN> > === message truncated === __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
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From: Tsjerk W. <ts...@gm...> - 2006-05-30 09:56:12
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Hi Warren et al. I really like the ray_trace_modes 2 and 3. However, I'd like to fiddle around with the thickness of the edges, but can't find a setting to do so. Am I overlooking something, or isn't there any (yet)? By the way, ray_trace_mode 2 is great for making colouring pictures to get the little ones acquanted with proteins / DNA etc. ;) Cheers, Tsjerk -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 |
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From: chiradip c. <chi...@ya...> - 2006-05-29 17:50:09
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Hi Pymol Users I want to superimpose three (3) same residue different pdb structures in Pymol. Currently I can do it with two structures. How can I do this? Thanks in advance Chiradip Chatterjee ___________________________________________________________ Try the all-new Yahoo! Mail. "The New Version is radically easier to use" The Wall Street Journal http://uk.docs.yahoo.com/nowyoucan.html |
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From: O. J. G. <ojg...@mb...> - 2006-05-29 17:05:10
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=20 =20 Hey again PyMOL gurus, >* O. J. Ganesh <ojg...@mb...> [2006-05-18 16:09] wrote: >>=20 >> Hey PyMOL gurus: >>=20 >> I have a 'perfect' helix. Is there some way to 'loosen' all of the >> angles in the helix so instead of 3.6 residues per turn, I could >> have, say, 8 residues per turn. My goal is to make the helix more >> 'coil-like'. Is this possible? > >Well, if you know the phi/psi angles you like, then you could just = build >it and specify those angles with my build_seq.py script: > >http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq.py > >You can specify the phi, psi angles on the command line. Alternatively, >you can create a file of resname, phi, psi and build it with: > >http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq_phi_psi.py > >if you don't want the phi/psi angles to be the same for every residue. > >Cheers, >Rob =20 Thanks Robert Campbell, I've actually used the build_seq_phi_psi.py script before, and it is = WONDERFUL! I can (and probably will) use it in this case also. I was = just checking to see if there wasn't an easier way to do this within = PyMOL... Something that would take a selection of a pdb structure and = generally 'loosen' or 'relax' it. (I know it sounds vague.) =20 Thanks again! |
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From: Savvas N. S. <sav...@ug...> - 2006-05-29 10:50:32
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Dear colleagues, I am trying to install pymol v0.99 on a new laptop running windows XP but the installer keeps giving an error message that my specified path does not exist. This is quite striking to me because the extracted files do indeed have the path that the installer is complaining about! So the path does exist! Upon restarting the computer hoping to solve the problem with path recognition, I get a system error about the ntvdm.exe emulator. Is this a related problem? Would that also be a sign that I should reinstall the operating system from scratch? I just got the computer and this may be the most appropriate time to do it. Thanks in advance for any input Savvas ----- Savvas N. Savvides Professor of Structural Biology Ghent University Laboratory for Protein Biochemistry K.L.Ledeganckstraat 35 9000 Ghent, BELGIUM Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 FAX: +32-(0)9-264.53.38 Email: sav...@ug... |
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From: Terry J. <tc...@ca...> - 2006-05-29 08:01:36
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I spent quite a bit of time last night chasing down the following. This: cmd.load_cgo([SPHERE, 0.0, 0.0, 0.0, 1.0], 'a') puts a sphere on the screen as expected. But this: cmd.load_cgo((SPHERE, 0.0, 0.0, 0.0, 1.0), 'a') seemingly has no effect at all. I.e., if you pass a tuple instead of a list, your CGO is not displayed. It's an easy mistake to make (supposing it should be called a mistake), and it's not easy to figure out why your CGO does not appear. The reason seems to be an if(PyList_Size(pycgo) test on line 440 of layer2/ObjectCGO.c in the 0.99 release - at least that's as far as I went in tracing this. Is there any reason why a tuple cannot be used here too? Regards, Terry |
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From: Robert K. D. <rkd...@ea...> - 2006-05-26 23:46:24
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I have two tasks that I have yet to work out in PyMol. 1) I would like to generate a custom isovalue map. I see that the Isomesh command likely provides what I need, but it requires a "map" object. I can't seem to find any explanation of what a map object is or how I might create one for a custom isovalue map. 2) Clipping planes appear to affect all objects in a view. I often want to display a protein's surface, show a few residues of interest, and show a docked/co-crystal ligand. Is it possible to clip through only the surface and leave the ligand and protein residues intact? Or, more generally, attach and detach clipping planes to specific display objects. Thanks for a great tool!! --------------------- Robert Kirk DeLisle, PhD |
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From: EPF \(E. P. Friis\) <EP...@no...> - 2006-05-26 07:12:34
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Hi Zheng You may try to decrease the value of hash_max, which will reduce the memory requirement for ray tracing, at the expenso of longer rendering time. E.g: set hash_max, 50 Cheers, Esben =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Zheng Yang > Sent: 24. maj 2006 05:42 > To: pym...@li... > Subject: [PyMOL] Runtime Error >=20 >=20 > Dear All, >=20 > Does anyone have the same runtime error, by applying the=20 > command, [ray] or [show surface], on big size protein, e.g.=20 > 1AON, etc?=20 >=20 > PyMOL Version: 0.99 > System: Dell 9100 > OS: Windows XP + SP2 > CPU: Intel P4 3.0G > RAM: 1.5G > Video Card: nVidia GeForce 6800, 256M >=20 > Thanks, > Zheng=20 >=20 |
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From: Thorsten M. <Tho...@un...> - 2006-05-26 07:05:47
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Call for Contributions
=====================================================================
LIFE SCIENCE FREE SOFTWARE SESSION
held at CompLife 2006 (http://www.complife.org)
in Cambridge, United Kingdom, on September 27 - 29, 2006
=====================================================================
In the last years more and more free and open source software has been
developed for chemo- and bioinformatics, molecular modelling or other
Life Science applications, but many of the programs are not well
known. During the CompLife 2006 conference we will organize a special
session dedicated to this type of free software. The demo session will
be preceeded by a short session having room for brief introductory
presentations whereas the demo session itself will allow attendees to
see the tools in action. Authors of free software will have the
opportunity to present their program to the CompLife audience which
will consist of researchers and users from computer science, biology,
chemistry and everything in between.
In case you are interested in the free software session, send us an
email to fs...@co... and briefly describe your program and how
you intend to present it at the conference (1-2 pages max - please
include URL to downloadable version where available). The only
restrictions are that the program must be freely available for
everyone or even open source and that it must be related to Life
Science applications. The deadline for these proposals is June, 16th
2006. In mid July we will notify you if your software demo was
accepted.
--
Thorsten Meinl room: Z813
ALTANA Chair for Bioinformatics fax: +49 (0)7531 88-5132
and Information Mining phone: +49 (0)7531 88-5016
Box M712, 78457 Konstanz, Germany
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From: Jacob C. <jc...@uc...> - 2006-05-24 17:11:36
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Hi everyone, On a few structures (some partially-built) I have run into an odd barely-reproducible crash bug with PyMOL 0.99rc6 (once on windows and once on linux). When a "problem" molecule is loaded (sometimes this is a specific combination of molecules, and not a single molecule), mousing-over any file in the File->Open dialog causes pymol to instantly crash. Altering the problem molecule's coordinates (either by rotation/translation in PyMOL or with subsequent rounds of building into density) often causes this problem to go away for that molecule. This issue has bitten me on two occasions, but before I spend time trying to track down a reproducible case, I would like to find out if anyone else has noticed it, or if it's an isolated problem. Jacob -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology jc...@uc... phone: 510-643-8893 fax: 510-643-9290 |
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From: Robert C. <rl...@po...> - 2006-05-24 15:58:12
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Hi, * O. J. Ganesh <ojg...@mb...> [2006-05-18 16:09] wrote: > > Hey PyMOL gurus: > > I have a 'perfect' helix. Is there some way to 'loosen' all of the > angles in the helix so instead of 3.6 residues per turn, I could > have, say, 8 residues per turn. My goal is to make the helix more > 'coil-like'. Is this possible? Well, if you know the phi/psi angles you like, then you could just build it and specify those angles with my build_seq.py script: http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq.py You can specify the phi, psi angles on the command line. Alternatively, you can create a file of resname, phi, psi and build it with: http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq_phi_psi.py if you don't want the phi/psi angles to be the same for every residue. Cheers, Rob -- Robert L. Campbell, Ph.D. <rl...@po...> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 |
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From: Tsjerk W. <ts...@gm...> - 2006-05-24 14:33:39
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Hi Natasja, That should be done with (IIRC) set surface_color,-1 Tsjerk On 5/24/06, Natasja Brooijmans <Br...@wy...> wrote: > > I accidently used the "set surface_color, x" command, and then unset. No= w > the full surface is colored white. Rather, I want the surface to be color= ed > by the color of the underlying residues, but it looks like I can't get it= to > do that after having used the set command. Any way of resetting the surfa= ce > settings back to the default? I tried deleting the object I created for t= he > surface and remaking it, but the settings are "stuck". > > Thanks, > > Natasja > --=20 Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 |
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From: Natasja B. <Br...@wy...> - 2006-05-24 12:44:32
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I accidently used the "set surface_color, x" command, and then unset. Now = the full surface is colored white. Rather, I want the surface to be = colored by the color of the underlying residues, but it looks like I can't = get it to do that after having used the set command. Any way of resetting = the surface settings back to the default? I tried deleting the object I = created for the surface and remaking it, but the settings are "stuck". =20 Thanks, Natasja |
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From: Takatoshi A. <ar...@be...> - 2006-05-24 05:14:54
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Hi All users, I am a PyMOL ver.0.99rc6 (Win and Linux) user. Now I want to label with chain ID ( A, B, G,... for alpha, beta, gamma,...) in Greek letters. I have tried it following http://www.pymolwiki.org/index.php/Label#UTF8_Fonts , but the output corresponds to "\316\261" has not been printed. Please give me some advice about this and tell me any other ways to do. Thank you, Arakawa |
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From: Zheng Y. <pro...@gm...> - 2006-05-24 03:40:11
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Dear All, Does anyone have the same runtime error, by applying the command, [ray] or [show surface], on big size protein, e.g. 1AON, etc? PyMOL Version: 0.99 System: Dell 9100 OS: Windows XP + SP2 CPU: Intel P4 3.0G RAM: 1.5G Video Card: nVidia GeForce 6800, 256M Thanks, Zheng |
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From: Ricardo A. <apa...@iq...> - 2006-05-23 21:23:23
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Dear all, I thought to be worth posting this message for those who experience problems with dual core+quadro FX. It seems that only recently kernel and compatible driver became available. We succeeded installing PyMOL in a AMD64 X2+Quadro FX1300+Fedora5. After installing Fedora 5 (which seems to recognize FX1300 automatically but without working properly), we followed a recipe (2-May-2006) from http://www.fedorafaq.org/ ("Problems and Their Solutions, Q3") We used "yum install kmod-nvidia" ("yum install kmod-nvidia-smp" did not work) Kernel 2.6.16-1.2122_FC5 was installed by this last command line. (21-May-2006 - http://download.fedora.redhat.com/pub/fedora/linux/core/updates/5/i386/) After that, we have followed the rest of the recipe and changed /etc/X11/xorg.conf (Driver "nvidia") PyMOL 0.99 runs beautifully although stereo mode was not tested yet. Kind regards, Ricardo Aparicio http://www.iqm.unicamp.br/profs/aparicio.html |
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From: Robert I. <imm...@gm...> - 2006-05-23 21:20:39
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Tina, A work-around that does something like what you are looking for is: load protein_with_alts.pdb, A load protein_with_alts.pdb, B hide everything, show sticks, A and alt A show sticks, B and alt B set stick_ball, 1, B set stick_overlap, -1.8, B Cheers, -bob On 5/23/06, Nguyen, Tina (GSBS) <Tin...@um...> wrote: > > > > > Hi, > > > > I would like to represent my alternate conformations by showing one resid= ue > in dashed sticks and the other in solid sticks. Can anyone help me with > that? > > > > Tina Nguyen > > > > Graduate Student > > University of Massachusetts Medical School > > |