pymol-users Mailing List for PyMOL Molecular Graphics System

Hello PyMOLers,

A few weeks ago someone asked about drawing CGO circles.  I went ahead and wrote
a script to do just that.

With these scripts, you can get a circle in two ways:
 * specify X,Y,Z, radius, and colors (if you want);
 * just specify some object or selection to draw a circle around and the script
does the math for you.

You can find the code on the PyMOLWiki:
  http://www.pymolwiki.org/index.php/CgoCircle

Hope someone finds this useful,

-- Jason

--

Jason Vertrees, PhD

Boston U. -- ja...@bu...
Dartmouth -- jv...@cs...

HEllo all

I am trying to make a movie , in which i would like to rotate the struture
at X-axis, rather than Y-axis and followed by zoom out of the particular
state of the frame to make more realistic and expalnatory. I looked into
pymol wiki as well as tutorial of the pymol. I could make the rotation ofthe
structure at Y-axis but not at X-axis and simultaneously i am not able to
zoom out the particular state. I am using the educational version of the
pymol1.1. I also tried eMovie. can any  one suggest some ideas. I would be
thankfull.

Thanks in advance

regards
peter

Problem solved... next time I'll do a completely clean install.  Sorry for
the needless email.

Ian

On Mon, Jul 27, 2009 at 11:08 AM, Ian Berke <ian...@ya...> wrote:

> Hi,
>
> I'm getting this error still using a self-compiled version from the latest
> SVN and python 2.6.2.  The error is:
>
> > Alter-Error: Aborting on error. Assignment may be incomplete.
> > File "<string>", line 1
> > formal_charge=0;flags=flags&0x-8388609
>
> In a previous post it was reported to be fixed.  Is anyone still having
> this issue?
>
> Thanks,
> Ian
>
> >Mark,
> >
> >Should be fixed now (in rev 3720).
> >
> >Cheers,
> >Wawrren
>
>
> > -----Original Message-----
> > From: Mark Wehner [mailto:mark.wehner@ru...]
> > Sent: Monday, May 11, 2009 12:11 PM
> > To: pymol-users@li...
> > Subject: [PyMOL] Vacuum electrostatics
> >
> > Hi everyone,
> >
> > in the newer version of pymol I realized it is not possible to
> generate
> > vacuum
> > electrostatics, there's an error while assigning the formal charges.
> The
> > error
> > message is:
> >
> > Alter-Error: Aborting on error. Assignment may be incomplete.
> > File "<string>", line 1
> > formal_charge=0;flags=flags&0x-8388609
> >
> > I build the source code (rev 3719) using Python 2.6.2. Is anyone
> > experiencing
> > similar problems at the moment?
> >
> > Mark
> >
> >
> ------------------------------------------------------------------------
> --
> > ----
> > The NEW KODAK i700 Series Scanners deliver under ANY circumstances!
> Your
> > production scanning environment may not be a perfect world - but
> thanks to
> > Kodak, there's a perfect scanner to get the job done! With the NEW
> KODAK
> > i700
> > Series Scanner you'll get full speed at 300 dpi even with all image
> > processing features enabled. http://p.sf.net/sfu/kodak-com
> > _______________________________________________
> > PyMOL-users mailing list
> > PyMOL-users@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >

Dear Warren,

I just started to work with session files in addition to scripts, so  
maybe, these are known issues. In version 1.2r1 for Mac, I notice a  
strange behavior when saving and re-opening sessions:

(1) the session file apparently doesn't store the "viewport"-setting
(2) when I re-open a session, restore the viewport-setting by hand  
(which results in the same view as when I stored the session) and  
issue a "ray" command with pixel sizes greater than the viewport- 
setting, the resulting image is suddenly cropped at the edges,  
although, in the original session with the same viewport- and ray- 
settings, the image was not cropped

Could you please check and, maybe, correct this?

Best regards,

Dirk.

*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: 	+49-89-2180-76845
Fax: 	+49-89-2180-76999
E-mail:	kos...@ge...
WWW:	www.genzentrum.lmu.de
*******************************************************

Dirk,

"select" doesn't create object, it creates atom selections, which are essentially lists of atoms in actual molecular objects.  Selections have almost no properties, settings, or anything else other than a name (if they are named selections) and a display state (pink dots, on or off).  Performing operations on selections really means operating on selected atoms within one or more molecular objects.

"create" copies atoms into a new object.  The resulting object is independent of the prior copy, and thus, can have different settings, colors, representations, display states (on/off), etc.

Cheers,
Warren

-----Original Message-----
From: Dirk Kostrewa [mailto:kos...@ge...]
Sent: Wed 7/22/2009 6:22 AM
To: PyMOLBB
Subject: [PyMOL] Difference between create and select?
 
Dear Warren & PyMOLers,

I notice that "create" is needed to make objects that can have  
different transparency settings. But what exactly is the difference  
between "create" and "select", since both commands seem to make a new  
object from the atom selection?

Best regards,

Dirk.

*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: 	+49-89-2180-76845
Fax: 	+49-89-2180-76999
E-mail:	kos...@ge...
WWW:	www.genzentrum.lmu.de
*******************************************************

Dear Warren & PyMOLers,

I notice that "create" is needed to make objects that can have  
different transparency settings. But what exactly is the difference  
between "create" and "select", since both commands seem to make a new  
object from the atom selection?

Best regards,

Dirk.

*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: 	+49-89-2180-76845
Fax: 	+49-89-2180-76999
E-mail:	kos...@ge...
WWW:	www.genzentrum.lmu.de
*******************************************************

Paola,
 
True, PyMOL doesn't write secondary structure to PDB files, but it does save the current in both PyMOL sessions as well as in PKL (Python Pickle) files.
 
load $TUT/1hpv.pdb
 
as cartoon
 
alter chain A, ss='S'

alter chain B, ss='H'
 
rebuild
 
save example.pkl, 1hpv
 
delete all
 
load example.pkl

as cartoon

Cheers,
Warren

 

________________________________

	From: Paola Beassoni [mailto:pao...@gm...] 
	Sent: Tuesday, July 21, 2009 12:27 PM
	To: pym...@li...
	Subject: [PyMOL] about secondary structure assignement: help
	
	
	Dear Pymol Users,
	i am working with some pdb files with no secondary structures assignments embedded on it. Then when i try to see my molecules on cartoon diagrams, i see the secondary structure different to another programs, VMD for example.
	I used the command alter (for example alter 10-34/, ss='S'), and i am capable of assign the secondary structure that i want but this is just temporary. If i save the molecule, when i oppen it again it has the original secondary structure and no the altered one.
	Can anyone help me about this??? I really prefer pymol instead other programs for visualization!
	Thanks!
	
	Paola
	-- 
	Paola Beassoni - PhD
	Dpto. Biologia Molecular - FCEFQyN
	Universidad Nacional de Rio Cuarto
	Río Cuarto - Argentina
	00-54-358-4676422
	00-54-358-4676232 (Fax)
	

On Tue, Jul 21, 2009 at 12:23 PM, Paola Beassoni <pao...@gm...>wrote:

> Dear Pymol Users,
> i am working with some pdb files with no secondary structures assignments
> embedded on it. Then when i try to see my molecules on cartoon diagrams, i
> see the secondary structure different to another programs, VMD for example.
> I used the command alter (for example alter 10-34/, ss='S'), and i am
> capable of assign the secondary structure that i want but this is just
> temporary. If i save the molecule, when i oppen it again it has the original
> secondary structure and no the altered one.
> Can anyone help me about this??? I really prefer pymol instead other
> programs for visualization!


The most compatible solution is probably to generate the HELIX and SHEET
records for your PDB file, which PyMOL will read (not sure about
VMD).  There is an open-source program called KSDSSP that will do this:

http://www.cgl.ucsf.edu/Overview/software.html#ksdssp

I haven't used it very much, but it's supposedly a re-implementation of the
original DSSP algorithm, so theoretically very robust.  If you're
continually generating new PDB files (e.g. refining the structure, etc.)
you'll probably need to keep these records in a separate file and paste them
into every new PDB file, since most programs won't retain that information
when writing files.  If you don't like the results, it's fairly simple to
modify the records to suit your taste.

Alternately, you can save a PyMOL script containing the alter commands and
just invoke that every time you load your structure.

-Nat

There are problems in display window of pymol in ubuntu 9.04. The one
that I install from repository completely blocks the CPU. When I
compile the latest one on my machine (version 1.2b6pre), the display
window does not show up most of the time. The commands buttons do not
show up all the time.

Has someone noticed it ?

-- 
Thank you and Regards,

Vivek Ranjan

Dear Pymol Users,
i am working with some pdb files with no secondary structures assignments
embedded on it. Then when i try to see my molecules on cartoon diagrams, i
see the secondary structure different to another programs, VMD for example.
I used the command alter (for example alter 10-34/, ss='S'), and i am
capable of assign the secondary structure that i want but this is just
temporary. If i save the molecule, when i oppen it again it has the original
secondary structure and no the altered one.
Can anyone help me about this??? I really prefer pymol instead other
programs for visualization!
Thanks!

Paola
-- 
Paola Beassoni - PhD
Dpto. Biologia Molecular - FCEFQyN
Universidad Nacional de Rio Cuarto
Río Cuarto - Argentina
00-54-358-4676422
00-54-358-4676232 (Fax)

Hi all,

In case anyone else runs into it, just wanted to let you know that I've 
solved the (possibly Fedora 10-specific) segfault-induced crashing 
described in the email below.  In a nutshell, it required editing the 
module in question (in this case, line 153 of "all_axes_new.py") so that 
it loops over the space group matrices of an sgtbx-returned object 
('mysg') by calling all_ops() to explicitly render the object iterable; 
i.e., loop over mysg.all_ops() rather than plain mysg.  In this case, 
change this:
>   for smx in space_group_info.group():
to this:
>   for smx in space_group_info.group().all_ops():

With best regards,
Cam

-- 
-------------------------------------------------------
 Cameron Mura
 Assistant Professor
 University of Virginia
 Department of Chemistry
 McCormick Road, Box 400319
 Charlottesville, VA 22904-4319
 Email: cm...@vi...
 Web: http://muralab.org
 Tel: 434.924.7824
 Fax: 434.924.3710
-------------------------------------------------------


=== Cameron Mura wrote (on 07/05/2009 03:33 PM): ===
> Hi all,
>
> Apologies for the message to both mailing lists, but perhaps someone 
> on either cctbxbb or pymol-users has had some recent experience with 
> this...
>
> The subject line more-or-less says it all: I'm wondering if anyone has 
> recently used Rob Campbell's draw_symops (or draw_symops_cctbx) Python 
> modules with a relatively recent (within past year) version of the 
> cctbx (particularly the Boost C++ parts) ?  I succeeded in doing this 
> a few years ago to generate images such as the ones near the top of 
> http://muralab.org/~cmura/PyMOL/Sandbox/, but I can't get it to work 
> on my present system (64-bit Fedora 10; Python 2.5.2 with Python 2.6 
> coexisting).
>
> Below is what happens when I...
>
> 1) Initiate a new PyMOL session (using a PyMOL v1.1 that I built 
> in-place from source, so should be compatible with local python, 
> system libs, etc)
>
> 2) load PDB files (tried with a few diff't files; verified that they 
> contain proper CRYST specifications)
>
> 3) do the usual 'run draw_symops_cctbx.py'
>
> 4) call draw_symops() -- either implicitly, or by explicit 
> specification of the u.c. params (i.e., using something like 
> "draw_symops_param((45.2,45.2,70.8,90.,90.,120.),'p3121',0.5,0.1)")
>
> ...which crashes the pymol session and yields the following trace:
>> PyMOL>draw_symops_param((45.2,45.2,70.8,90.,90.,120.),'p3121',0.5,0.1)
>> libc backtrace (48 frames, most recent call last):
>>   /usr/bin/python [0x400649]
>>   /lib64/libc.so.6(__libc_start_main+0xe6) [0x344081e576]
>>   /usr/lib64/libpython2.5.so.1.0(Py_Main+0xb11) [0x34584e7ef1]
>> *<snip>
>> ...
>> ...
>> </snip>*
>>   /usr/lib64/libpython2.5.so.1.0(PyObject_Call+0x13) [0x345843d493]
>>   /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so 
>> [0x7ff19691db16]
>>   
>> /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x9f) 
>> [0x7ff19692a2ef]
>>   /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so 
>> [0x7ff196920b08]
>>   
>> /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::objects::function::call(_object*, 
>> _object*) const+0x125) [0x7ff196920635]
>>   
>> /root/cctbx/working/v4/cctbx_build/lib/cctbx_sgtbx_ext.so(boost::python::detail::caller_arity<2u>::impl<cctbx::sgtbx::rt_mx 
>> (*)(cctbx::sgtbx::space_group const&, unsigned long), 
>> boost::python::default_call_policies, 
>> boost::mpl::vector3<cctbx::sgtbx::rt_mx, cctbx::sgtbx::space_group 
>> const&, unsigned long> >::operator()(_object*, _object*)+0x12a) 
>> [0x7ff18f820a3a]
>>   /root/cctbx/working/v4/cctbx_build/lib/cctbx_sgtbx_ext.so 
>> [0x7ff18f8034cc]
>>   
>> /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::throw_error_already_set()+0xe) 
>> [0x7ff196929dde]
>>   /usr/lib64/libstdc++.so.6(__cxa_allocate_exception+0x2f) [0x3444cc2cdf]
>>   /lib64/libc.so.6 [0x3440832f90]
>> Segmentation fault (libc call stack above)
>>                 This crash may be due to a problem in any imported
>>                 Python module, including modules which are not part
>>                 of the cctbx project. To disable the traps leading
>>                 to this message, define these environment variables
>>                 (e.g. assign the value 1):
>>                     BOOST_ADAPTBX_FPE_DEFAULT
>>                     BOOST_ADAPTBX_SIGNALS_DEFAULT
>>                 This will NOT solve the problem, just mask it, but
>>                 may allow you to proceed in case it is not critical.
>>  PyMOL: abrupt program termination.
> I tried the recommendation of setting the BOOST_ADAPTBX* env vars, but 
> this doesn't remedy the problem.
>
> Also, I tried accomplishing this with many combinations of workflows:
> 1) old cctbx (e.g., 2005_04_29_1615), latest stable release of cctbx 
> (2009_02_15_2320), bleeding-edge cctbx (2009_07_04_0143)
> 2) pre-built cctbx binaries versus building myself from src (for each 
> of the above), insuring, again, optimal match between local system libs...
> 3) cctbx alone, cctbx in the context of Phenix, cctbx +/- its own 
> bundled Python (2.5 and 2.6)
>
> Also, I tried this with different combinations of Rob's scripts -- 
> e.g., the 'symop_axes.dat'-dependent "draw_symops.py", versus  the 
> 'all_axes_new.py'-dependent "draw_symops_cctbx.py".  Interestingly, I 
> found that get_all_axes() from 'all_axes_new.py' works fine for 
> different PDB files.
>
> Investigating the above draw_symops stacktrace led me to this post 
> from Ralf Grosse-Kunstleve to python-dev: 
> http://mail.python.org/pipermail/python-dev/2008-September/082639.html
> It looks like exactly the same problem that's causing the 
> pymol/draw_symops scripts to choke.  Also, I can verify that issuing 
> commands such as in Ralf's post (boost_adaptbx.segmentation_fault, 
> boost_adaptbx.divide_by_zero) result in the same segfaults and errors 
> as in his post, so... I believe this is the crux of it.  Before 
> delving into Boost codebase, cctbx's exception-handling in C++/Python 
> Boost, etc., I'm wondering if anyone else has seen anything like 
> this...? or has advice on how best to proceed? Any tips or suggestions 
> would be most greatly appreciated.
>
> Thanks,
> Cam
> -- 
> -------------------------------------------------------
>  Cameron Mura
>  Assistant Professor
>  University of Virginia
>  Department of Chemistry
>  McCormick Road, Box 400319
>  Charlottesville, VA 22904-4319
>  Email: cm...@vi...
>  Web: http://muralab.org
>  Tel: 434.924.7824
>  Fax: 434.924.3710
> -------------------------------------------------------
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> cctbxbb mailing list
> cc...@ph...
> http://www.phenix-online.org/mailman/listinfo/cctbxbb
>   

Stuart,

 

Sorry, there is no way to do this at present (short of manually editing
text files).  But thank you for the suggestion!


Cheers,

Warren

 

________________________________

From: Stuart Ballard [mailto:srb...@wi...] 
Sent: Saturday, July 18, 2009 1:58 PM
To: pymol-users
Subject: [PyMOL] Getting SCALE record within PyMOL

 

Hello Warren, all,


Is there any way to read the SCALE record from the PDB file of a protein
loaded into PyMOL either within PyMOL or in a script? Alternatively,
even getting the filepath from an object name so that the PDB can be
accessed directly by a script would be sufficient.


Thanks,
Stuart Ballard

Hello Warren, all,


Is there any way to read the SCALE record from the PDB file of a protein
loaded into PyMOL either within PyMOL or in a script? Alternatively, even
getting the filepath from an object name so that the PDB can be accessed
directly by a script would be sufficient.


Thanks,
Stuart Ballard

Minor correction, for geeks who care about technical trivia.  I
previously wrote:

> I don't think [VGA] Modeline timings have any meaning when 
> generating a true digital display signal...

Apparently the modeline timings do still have significance in terms of
digital information transport, which mimicks analog signal timing, but
there is no hard and fast correlation between data transport and what
actually happens on the screen at any moment in time.  A digital display
can in principle update whatever it wants, whenever it wants, once the
information has arrived.  

Cheers,
Warren
 

Malcolm,

 

Yes, a reasonable person might expect it to work...but we have tried on both Mac and Linux, and it doesn't work with either CystalEyes or NuVision hardware.  I don't think Modeline timings have any meaning when generating a true digital display signal, but regardless, the actual sync signal output is not correct.

 

My naïve guess is that this is because the analog sync signal from the Quadro DIN connector is based off of the SVGA vertical blanking interval and has nothing to do with the digital-only display signal required by these displays.  Note that these displays do not accept an analog SVGA signal - they have only a pure-digital DVI-D connector - not DVI-I, and they have no HD15 SVGA input.  They also require a full dual link DVI-D cable with all pins present.  It seems that the dual-link capacity is used to carry the 120 Hz signal (perhaps split over two regions of the display? or with the left 60Hz on one channel and the right 60Hz on the other?). 

 

Furthermore, even if the Quadro sync was correct, the polarization of the old shutter glasses conflicts with that of the liquid crystal.  I also observed that light from the Samsung LCD seems to interfere with the old CrystalEyes sync signal.  Of course, the other problem is that affordable Quadro cards do not even come with a sync connector.

 

So in summary, there seem to be many problems combining modern LCDs with old stereo 3D hardware, which presumably explains in part why nVidia decided to introduce a new USB emitter and glasses for use with these displays.

 

Cheers,

Warren

 

________________________________

From: Davis, Malcolm [mailto:mal...@bm...] 
Sent: Friday, July 17, 2009 2:00 PM
To: pym...@li...
Subject: Re: [PyMOL] WARNING: No Mac or Linux support for 120 HzLCD synchronization

 

Has anyone tried these with the old CrystalEyes glasses?  We are looking to get one of these to try, but it is hard to understand why there should even be a need for a different graphics driver or a newer Quadro card to use it that way.  The FX1100 cards we still have in some of our Linux workstations can be configured to send a 1600x1200@100Hz signal to our old IBM c220p monitors and the 100Hz limit was from the monitor not the graphics card.  So other than needing to specify the Modeline manually in the X config files, why shouldn't this just work?

 

Malcolm

 

 

From: Warren DeLano [mailto:wa...@de...] 
Sent: Friday, July 17, 2009 12:23 PM
To: pym...@li...
Subject: [PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization

 

Just to make sure everyone understands:

 

Stereo 3D support for these awesome new 120 Hz LCD displays is WINDOWS ONLY due to the need of a special USB driver for the 3D Vision sync emitter.  Unfortunately, you cannot sync a digital 120 Hz LCD using the old stereo analog DIN sync connector - it just doesn't work.

 

Please do not waste money right now buying a 120 Hz LCD if you use Linux or Mac OS (even if you have a Quadro card), or if you use a Windows laptop (without a Quadro graphics chip).  You will be disappointed -- the display will not do 3D with your system, and nVidia has not promised support for 120 Hz LCD synchronization on platforms other than Windows.  That may change, but then again, it might not.

 

Accordingly, our recommended stereo 3D solution for Mac, Linux, and for Windows systems without Quadro cards is the Zalman M220W LCD display.  You get fewer pixels for stereo 3D, but it works great with PyMOL on ALL PLATFORMS (including most laptops). No special graphics hardware or drivers are required to use the Zalman with PyMOL.  http://pymol.org/zalman

 

Cheers,

Warren

 

 

 

 

 

 

 

 

________________________________

This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.

> Has anyone tried these with the old CrystalEyes glasses? 

(snip)

> So other than needing to specify the Modeline manually in the X config
files, why shouldn't this just work?

The goggles have a polarizers on the front and back surfaces of each
goggle "lens".   Similarly, the LCD display have polarizers on the front
and back.  When the liquid crystal in each of these devices is in the
right state each will pass light, but in both cases that light is
polarized.  With a user seated in front of the LCD display with the
goggles on, what happens if the polarizers in the goggles are at right
angles to the ones in the LCD display?    (This wasn't an issue with CRT
displays since the light from those wasn't polarized.)

This was exactly the situation for goggles used with my ViewSonic VX922
display.  Stereo was impossible since I could only see the image on the
screen if my head was turned sideways (parallel to the floor). The
goggles don't even need to be on to see this, just hold them up in front
of the LCD screen and rotate them to see which direction will work.

Near as I can tell there is no standard for display polarizers.  I
checked a few displays and found vertical ones, horizontal ones, and
even one from Apple polarized at 45 degrees. 

Regards,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech

Has anyone tried these with the old CrystalEyes glasses?  We are looking to get one of these to try, but it is hard to understand why there should even be a need for a different graphics driver or a newer Quadro card to use it that way.  The FX1100 cards we still have in some of our Linux workstations can be configured to send a 1600x1200@100Hz signal to our old IBM c220p monitors and the 100Hz limit was from the monitor not the graphics card.  So other than needing to specify the Modeline manually in the X config files, why shouldn't this just work?

Malcolm


From: Warren DeLano [mailto:wa...@de...]
Sent: Friday, July 17, 2009 12:23 PM
To: pym...@li...
Subject: [PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization

Just to make sure everyone understands:

Stereo 3D support for these awesome new 120 Hz LCD displays is WINDOWS ONLY due to the need of a special USB driver for the 3D Vision sync emitter.  Unfortunately, you cannot sync a digital 120 Hz LCD using the old stereo analog DIN sync connector - it just doesn't work.

Please do not waste money right now buying a 120 Hz LCD if you use Linux or Mac OS (even if you have a Quadro card), or if you use a Windows laptop (without a Quadro graphics chip).  You will be disappointed -- the display will not do 3D with your system, and nVidia has not promised support for 120 Hz LCD synchronization on platforms other than Windows.  That may change, but then again, it might not.

Accordingly, our recommended stereo 3D solution for Mac, Linux, and for Windows systems without Quadro cards is the Zalman M220W LCD display.  You get fewer pixels for stereo 3D, but it works great with PyMOL on ALL PLATFORMS (including most laptops). No special graphics hardware or drivers are required to use the Zalman with PyMOL.  http://pymol.org/zalman

Cheers,
Warren








________________________________
This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.

Just to make sure everyone understands:

 

Stereo 3D support for these awesome new 120 Hz LCD displays is WINDOWS
ONLY due to the need of a special USB driver for the 3D Vision sync
emitter.  Unfortunately, you cannot sync a digital 120 Hz LCD using the
old stereo analog DIN sync connector - it just doesn't work.

 

Please do not waste money right now buying a 120 Hz LCD if you use Linux
or Mac OS (even if you have a Quadro card), or if you use a Windows
laptop (without a Quadro graphics chip).  You will be disappointed --
the display will not do 3D with your system, and nVidia has not promised
support for 120 Hz LCD synchronization on platforms other than Windows.
That may change, but then again, it might not.

 

Accordingly, our recommended stereo 3D solution for Mac, Linux, and for
Windows systems without Quadro cards is the Zalman M220W LCD display.
You get fewer pixels for stereo 3D, but it works great with PyMOL on ALL
PLATFORMS (including most laptops). No special graphics hardware or
drivers are required to use the Zalman with PyMOL.
http://pymol.org/zalman

 

Cheers,

Warren

 

 

 

 

 

 

 

Continuing coverage...

 

Although GeForce 3D Vision is not officially supported for Windows XP, I
managed to get it to work with PyMOL.   Assuming you have the following
setup:

 

- A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm

 

- A recent Quadro series graphics card such as an FX 380 or 570.

 

- A GeForce 3D Vision hardware kit (an emitter with 3D shutter glasses).

 

- Windows XP 32 bit 

 

You need the 190-series graphics driver for Windows XP:

 

http://www.nvidia.com/object/winxp_190.38_beta.html

 

and the 190-series 3D Vision driver for Windows Vista:

 

http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_190.38.html

 

Instructions:

 

1. Uninstall the existing display drivers, disconnect the USB emitter,
and reboot.

 

2. Run the Window XP graphics driver installer and reboot.

 

3. Launch the Vista 3D Vision driver in order to extract the files you
need, but do not yet click Next on the Welcome page...just leave it open
for now...do not close the installer.

 

4. Plug in the USB emitter.  Windows should throw up the Found New
Hardware Wizard**. Choose "No, not this time" and go to the Next page.
Select "install from a list or specific location" and click Next to
continue.  Choose "Search for the best driver", "include this specific
location...", and click Browse.  Now comes the hard part: you must
select the folder which contains the file "nvstusb.inf".  On my system,
that file was unpacked into c:\Documents and
Settings\Warren~1~000\Locals~1\Temp\pft16~tmp - your copy may be in a
similar location.  You may need to use Windows Search to find the file.
Once you've chosen the correct folder, click Ok and then Next.  You may
then be asked to locate "nvstusb.sys", which should be in the same
folder.  Click Ok once you've found the file, and then Finish.  This
should complete installation of the USB driver.

 

**If Windows doesn't throw up the Found New Hardware Wizard, use the
Device Manager to locate the device and then update the driver for the
device using the same process described above.

 

5. Now allow the 3D Vision Installer to continue.  Since your on XP, not
Vista, it will complain and throw up one warning and one error message,
but it should still complete.  Reboot when prompted.  The rest of the
instructions are basically the same as for Vista:

 

6. Open the NVIDIA Control Panel, and increase the display refresh rate
to 120 Hz using the display resolution tab.  Then go to the 3D Settings
tab and set the Stereo display mode to "Generic active stereo (with
NVIDIA IR Emitter)", click Apply, and then set Stereo - enable mode to
"on", click Apply, and then close the NVIDIA control panel.

 

7. Launch PyMOL 1.2r1 for Windows.  You should get the message: "OpenGL
quad-buffer stereo 3D detected and enabled."

 

8. Now load a PDB file and issue "stereo on".  The emitter should light
up and the glasses should activate.  

 

Congratulations -- you should now be able to view PyMOL molecular
structures in stereo 3D on a 120 Hz LCD using Windows XP!  

 

Cheers,

Warren

 

 

Today nVidia issued their first public beta release of their 190-series
driver.  Although this release is officially for GeForce hardware, it
seems to work fine for Quadro cards as well.  So, if you have the
following hardware setup, then you can at last now use PyMOL in Stereo
3D at full 1680x1050 resolution on a 120 Hz LCD.  Here is what you need:

 

- A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm

 

- A recent Quadro series graphics card such as an FX 380 or 570.

 

- A GeForce 3D Vision hardware kit (an emitter with 3D shutter glasses).

 

- Windows Vista 32 bit or 64 bit

 

- The driver download (warning ~230 MB ZIP file):

 

http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.htm
l
<http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.ht
ml> 

 

I personally confirmed today that this download enables PyMOL to run in
Stereo 3D on a 2233RZ with a Quadro 570 graphics card and GeForce 3D
Vision hardware under Windows Vista 32 bit.  Instructions:

 

1. Uninstall the existing display drivers, disconnect the USB emitter,
and reboot.

 

2. Extract the contents of the downloaded ZIP file.

 

3. Run the enclosed Launch.exe, click the first option to install the
graphics driver, and then reboot when prompted (essential!).

 

5. Again run Launch.exe, click the second option to install the 3D
Vision Software, and connect the USB emitter when prompted. Confirm that
the stereo 3D tests work as expected, then exit the wizard by clicking
Finish.

 

6. Open the NVIDIA Control Panel, and increase the display refresh rate
to 120 Hz using the display resolution tab.  Then go to the 3D Settings
tab and set the Stereo display mode to "Generic active stereo (with
NVIDIA IR Emitter)", click Apply, and then set Stereo - enable mode to
"on", click Apply, and then close the NVIDIA control panel.

 

7. Reboot (again, essential -- OpenGL stereo 3D will not actually work
until after you reboot.)

 

8. Launch PyMOL 1.2r1 for Windows.  You should get the message: "OpenGL
quad-buffer stereo 3D detected and enabled."

 

9. Now load a PDB file and issue "stereo on".  The emitter should light
up and the glasses should activate.  

 

Congratulations -- you should now be able to view PyMOL molecular
structures in stereo 3D on a 120 Hz LCD!  

 

Cheers,

Warren

 

Valentina,

 

PyMOL has been known to work great with the Samsung 2233rz for quite
some time, but nVidia had not publicly released any of the required
190-series drivers until today.  

 

Note that, officially speaking, you will need a Quadro graphics card in
order to do OpenGL-based stereo 3D.  nVidia does not support OpenGL
stereo 3D on GeForce cards, and the required control panel options for
configuring OpenGL stereo 3D will be absent.

 

More details about today's release will be posted soon...

 

Cheers,

Warren

 

________________________________

From: Valentina Corradi [mailto:val...@gm...] 
Sent: Thursday, July 16, 2009 4:25 PM
To: pym...@li...
Subject: 3D visualization and Samsung SyncMaster 2233RZ/Nvidia GeForce
3D Vision Kit

 

Dear PyMOL users,

my research group is interested in using 3D stereo visualization with
PyMOL.
We have a Windows Vista/Linux (Fedora 11) 64 bit system, with Nvidia
GeForce GTX 295 Graphic card and Nvidia GeForce 3D Vision Kit (Samsung
SyncMaster 2233RZ 120Hz monitor).

Dr. Delano's post, dated June 22 (
http://www.mail-archive.com/pym...@li.../msg07014.h
tml ), says that only Zalman monitor can be used with PyMOL for 3D
stereo visualization.

I installed the latest Nvidia 3D Vision drivers (released on June 22)
officially supporting our monitor and I read on PyMOL home page that on
June 30, PyMOL 1.2r0 version supports stereo 3D for Samsung display.
I am wondering if now it is possible to use this PyMOL version or the
latest one (1.2r1) for 3D stereo visualization together with the OS and
Nvidia kit we have.

Thank you in advance for your help,

Valentina Corradi,
University of Calgary

Hello List,

A new PyMol script for coloring two objects by mutual RMS Deviation is
now available on the PyMol wiki:

http://pymolwiki.org/index.php/ColorByRMSD

Hope some of you will find it useful...

Many thanks to Jason Vertrees for help with turning the initial
proof-of-principle into useful code!!

Best,
Shiven


----------------------------------------------------
Shivender Shandilya,
Graduate Student,
Schiffer Lab,
Dept. of Biochemistry & Molecular Pharmacology,
University of Massachusetts Medical School,
Worcester, MA 01604.

Dear PyMOL users,

my research group is interested in using 3D stereo visualization with PyMOL.
We have a Windows Vista/Linux (Fedora 11) 64 bit system, with Nvidia GeForce
GTX 295 Graphic card and Nvidia GeForce 3D Vision Kit (Samsung SyncMaster
2233RZ 120Hz monitor).

Dr. Delano's post, dated June 22 (
http://www.mail-archive.com/pym...@li.../msg07014.html),
says that only Zalman monitor can be used with PyMOL for 3D stereo
visualization.

I installed the latest Nvidia 3D Vision drivers (released on June 22)
officially supporting our monitor and I read on PyMOL home page that on June
30, PyMOL 1.2r0 version supports stereo 3D for Samsung display.
I am wondering if now it is possible to use this PyMOL version or the latest
one (1.2r1) for 3D stereo visualization together with the OS and Nvidia kit
we have.

Thank you in advance for your help,

Valentina Corradi,
University of Calgary

Dear PyMOL users,

my research group is interested in using 3D stereo visualization with PyMOL.
We have a Windows Vista/Linux (Fedora 11) 64 bit system, with Nvidia GeForce
GTX 295 Graphic card and Nvidia GeForce 3D Vision Kit (Samsung SyncMaster
2233RZ 120Hz monitor).

Dr. Delano's post, dated June 22 (
http://www.mail-archive.com/pym...@li.../msg07014.html),
says that only Zalman monitor can be used with PyMOL for 3D stereo
visualization.

I installed the latest Nvidia 3D Vision drivers (released on June 22)
officially supporting our monitor and I read on PyMOL home page that on June
30, PyMOL 1.2r0 version supports stereo 3D for Samsung display.
I am wondering if now it is possible to use this PyMOL version or the latest
one (1.2r1) for 3D stereo visualization together with the OS and Nvidia kit
we have.

Thank you in advance for your help,

Valentina Corradi,
University of Calgary

Stuart,

 

Thank you for the reports, and sorry to hear you're having trouble.
Please allow me to draw your attention to the Bug Reporter link on the
PyMOL main page (www.pymol.org <" rel="nofollow">http://www.pymol.org/> ).  The direct
link is:

 

http://sourceforge.net/tracker/?atid=104546&group_id=4546&func=browse

 

One advantage of using the bug reporter system is that you can submit
accompanying script or data files which reproduce the problem.  

 

With respect to meshes, rendering of meshes is not generally broken in
1.2r1, so there must be something specific about your input which is
triggering the crash.  We may need an example file, or at least a PDB
code with associated commands, to reproduce the problem.  Likewise,
"fetch" is known not to be generally broken, so we may need more
information about reproducing the problem.

 

[For what it's worth, I just confirmed that:

 

fetch 1fjf, async=0

 

show mesh

 

ray

 

runs fine with 1.2r1].

 

As for selector, it is not a supported part of the supported Python
"cmd" API, but rather, an internal module.  In other words, you should
not ever need to be importing it.  Operationally speaking, the Python
cmd. api is defined by the file "modules/pymol/api.py", and virtually
all public symbols should be accessed as methods or submethods of this
module.

 

Cheers,

Warren

 

________________________________

From: Stuart Ballard [mailto:srb...@wi...] 
Sent: Thursday, July 16, 2009 2:14 PM
To: pym...@li...
Subject: [PyMOL] PyMOL 1.2r1 error report

 

Hello all, Warren,


With the new PyMOL version, myself and others at the lab have found an
issue with ray tracing of mesh representations causing memory
utilization errors.

With parameters identical to those used in previous versions of PyMOL,
1.2r1 has crashed when ray tracing isomesh generated isosurface meshes.
A memory allocation error is given, but a lack of memory does not appear
to be the real issue, as PyMOL crashes long before all RAM is consumed,
and the same error is given when we attempt to run this process on a
machine with 12GB of RAM.

There have also been a few minor issues with the fetch command. Namely,
we've seen intermitent inexplicable failure of the fetch command, while
simultaneously using it in another version of PyMOL with no issue.

Also, some older scripts now need more specific import statements to
utilize certain build-in PyMOL functionality. For example, I did not
need to state "from pymol import selector" to use the selector.process()
function in other versions of PyMOL, but this is not the case with the
new version. Does this reflect changes in the cmd API setup?


Regards,
Stuart Ballard

	 

	
	
	
	
----------------------------------------------------------------------
	
	Message: 1
	Date: Thu, 9 Jul 2009 13:34:53 -0700
	From: "Warren DeLano" <wa...@de...>
	Subject: [PyMOL] PyMOL 1.2r1 Released
	To: <pym...@li...>
	Message-ID:
	
<896...@pl...>
	Content-Type: text/plain; charset="us-ascii"
	
	Greetings,
	
	
	
	Mac, Windows, and Linux builds for 1.2r1 were posted early this
morning.
	Current subscribers can download them via
	
	
	
	Direct download: http://delsci.com/ip/12  or via online docs:
	http://delsci.info/dsc/ip
	
	
	
	As usual, I recommend caution with upgrading.  Please don't
upgrade
	right before a major talk or presentation, unless you have time
to test
	everything thoroughly beforehand.  There were many last-minute
changes
	made after the last beta, so some glitches are to be expected.
	
	
	
	Please try loading your important PyMOL session and show files
into the
	new version and report any serious problems.  At least one
additional
	revision of the 1.2 release is anticipated before the end of the
summer.
	
	
	
	Enabling information about the new capabilities of 1.2 will be
	forthcoming over the next month, and will likely consist of a
series of
	screencast demonstrations and tutorials.  There is a lot of new
stuff to
	communicate!
	
	
	
	Cheers,
	
	Warren