pymol-users Mailing List for PyMOL Molecular Graphics System

Björn,

set seq_view, off, object-name

for the pseudoatom object.

As for why they're visible, the sequence viewer has at least two purposes:
(a) showing alignments and (b) providing a convenient linear way of
selecting, zooming, modifying or otherwise transforming atoms that may be
present in the system but not necessarily visible in the 3D viewer.

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Björn Kauppi 
> Sent: Monday, March 31, 2008 5:05 AM
> To: pym...@li...
> Subject: [PyMOL] pseudoatoms and alignment
> 
> Hi
> 
> 
> 
> I use the pseudoatom command to put labels at specific 
> coordinates in space. How can I remove the pseudoatom object 
> show up in the sequence alignment?
> 
> 
> 
> I can not see any reason pseudoatoms should be in the alignment or?
> 
> 
> 
> Björn
> 
> 
> 
> 
> 
> 
> **************************************************************
> *************
> This e-mail may contain confidential information proprietary 
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Hi



I use the pseudoatom command to put labels at specific coordinates in space. How can I remove the pseudoatom object show up in the sequence alignment?



I can not see any reason pseudoatoms should be in the alignment or?



Björn






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Hi all,

Just want to know if there are only per user pymolrc files at ~/.pymolrc 
or could there be a system wide configuration e.g. /etc/pymolrc. or 
somewhere else?

Thanks,
justin

pseudoatom tmp, pos=[X, Y, Z]
show sticks, tmp expand R
delete tmp

Working example:

load $TUT/1hpv.pdb
pseudoatom tmp, pos=[10.0, 17.0, -3.0]
show sticks, tmp expand 6
delete tmp

But like Tsjerk says, you might want to do something more like:

delete all
load $TUT/1hpv.pdb
show sticks, byres (organic expand 5)
color yellow, organic and elem c

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Horacio Emilio Pérez Sánchez
> Sent: Friday, March 28, 2008 1:42 PM
> To: pym...@li...
> Subject: [PyMOL] Show sticks till a certain radius
> 
> Hi,
> 
> Given a receptor in cartoon representation and a ligand 
> (sticks) in its cavity, center of mass x, y, z, I wonder how 
> could I get the sticks representation of the protein (in 
> addition to cartoon) but only in a region limited by a sphere 
> of radius "R", with center at x, y, z.
> 
> Thanks in advance
> 
> Horacio
> 
> 
> 
> 
> --------------------------------------------------------------
> -----------
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Hi Horacio,

Do you really need a sphere around (x,y,z)? That's tough. But I'd
reckon it's more meaningful to select all residues within a certain
distance from any atom of the ligand anyway, which is easy:

show sticks, byres protein within 3.5 of ligand

Without 'byres' only the atoms actually within the 3.5 A distance will
be shown as sticks. The 3.5 approximately corresponds to H-bonding
distance, but of course you can change it to whatever value you like.
If you insist on showing sticks within a sphere around the center of
mass, you can use the 'pseudoatom' command in the >1.0 version of
Pymol to first create an atom placed at the center of mass of the
ligand and show the sticks based on the distance to that atom.

Hope it helps,

Tsjerk

On Fri, Mar 28, 2008 at 9:41 PM, Horacio Emilio Pérez Sánchez
<hor...@in...> wrote:
> Hi,
>
>  Given a receptor in cartoon representation and a ligand (sticks) in its
>  cavity, center of mass x, y, z, I wonder how could I get the sticks
>  representation of the protein (in addition to cartoon) but only in a
>  region limited by a sphere of radius "R", with center at x, y, z.
>
>  Thanks in advance
>
>  Horacio
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi,

Given a receptor in cartoon representation and a ligand (sticks) in its 
cavity, center of mass x, y, z, I wonder how could I get the sticks 
representation of the protein (in addition to cartoon) but only in a 
region limited by a sphere of radius "R", with center at x, y, z.

Thanks in advance

Horacio

Dear All,

OS is CentOS 4.5. I checked out Pymol revision 3252 via
subversion and downloaded ext-0_99rc1-src.tgz for external
dependencies. Compilation apparently went smoothly.


When starting Pymol I get the following error:


[ediths@botsun2 pymol]$ ./pymol
  PyMOL(TM) Molecular Graphics System, Version 1.1beta4pre.
  Copyright (C) 2007 by DeLano Scientific LLC.
  All Rights Reserved.

     Created by Warren L. DeLano, Ph.D.

     Other Major Authors and Contributors:

        Ralf W. Grosse-Kunstleve, Ph.D.

     PyMOL is user-supported open-source software.  Although some versions
     are freely available, PyMOL is not in the public domain.

     If PyMOL is helpful in your work or study, then please volunteer
     support for our ongoing efforts to create open and affordable 
scientific
     software by purchasing a PyMOL Maintenance and/or Support 
subscription.

     More information can be found at "http://www.pymol.org".

     Enter "help" for a list of commands.
     Enter "help <command-name>" for information on a specific command.

  Hit ESC anytime to toggle between text and graphics.

  OpenGL graphics engine:
   GL_VENDOR: VA Linux Systems, Inc.
   GL_RENDERER: Mesa GLX Indirect
   GL_VERSION: 1.2 Mesa 3.4.2
python: Objects/object.c:1397: PyObject_GenericGetAttr: Assertion `mro != 
((void *)0)' failed.
./pymol: line 2: 31502 Aborted                 /usr/bin/python 
/usr/lib/python2.3/site-packages/pymol/__init__.py $*



Thanks for your help,
best regards,

Edith






******************************************
Dr Edith Schlagenhauf
Bioinformatics
Institute of Plant Biology
University of Zurich
Zollikerstrasse 107
CH-8008 Zurich
SWITZERLAND

e-mail: ediths AT botinst DOT uzh DOT ch
Tel.:   +41 44 634 82 78
Fax :   +41 44 634 82 04
******************************************

Sirano,
 
The phrasing is a bit confusing, but the point is that one of the roles of
the external gui window is to provide a place where
operating-system-provided copy and paste functions can work.  They cannot
work in the internal GUI window because as far as the operating system is
concerned, the internal GUI is just an OpenGL context (graphics only).
 
Sorry for the inconvenience!
 
Warren
 
  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Sirano
Dhe-Paganon
Sent: Saturday, March 22, 2008 8:07 AM
To: pym...@li...
Subject: [PyMOL] cut and paste internal


Hi,
 
It is stated in: 
 
http://pymol.sourceforge.net/newman/user/S0200start.html
 
that "One important advantage of the external GUI window is that standard
"cut and paste" functions for text will only work within the External GUI,
and not within in the PyMOL Viewer. "
 
 
 
But this is clear a DISADVANTAGE for me, as I currently cannot directly
paste into the viewer window, which is exactly what I'd like to do.
 
Can I edit some parameter so that I might be able to directly paste into the
viewer window?
 
Sirano
(416)946-3876
sir...@ut...
 
 

Hi,
 
It is stated in: 
 
http://pymol.sourceforge.net/newman/user/S0200start.html
 
that "One important advantage of the external GUI window is that standard
"cut and paste" functions for text will only work within the External GUI,
and not within in the PyMOL Viewer. "
 
 
 
But this is clear a DISADVANTAGE for me, as I currently cannot directly
paste into the viewer window, which is exactly what I'd like to do.
 
Can I edit some parameter so that I might be able to directly paste into the
viewer window?
 
Sirano
(416)946-3876
sir...@ut...
 
 

Thanks to Carsten and Mauricio.

Following approaches work:

1) set stick_transparency, 0.4, molecule4

Useful if you are drawing multiple selections from Mol4 and want it transparent

2) Individual objects

create M223Dser, /mol4//D/MET`223 and !mc
show sticks, M223Dser
set stick_transparency=0.9, M223Dser

Here you still have to specific the type of transparency - for sticks 
- since its not a global object transparency, which mesed me up.


>Mark,
>
>as far as I know, transparency is supported for sufaces and sticks 
>or cartoons. Filter the settings menu for transparency to get a 
>better idea. To set transparency for an object
>
>set transparency = 0.5, <object>
>
>should work
>
>	Carsten
>


Lets say:

pymol> load molecule1.pdb
pymol> load molecule2.pdb
pymol> hide lines
pymol> set sphere_transparency, 0.4, molecule1
pymol> set sphere_transparency, 0, molecule2
pymol> show spheres

Cheers,

>Mauricio
>


-- 

Mark,

you need to set

set stick_transparency=0.9, M223Dser

> -----Original Message-----
> From: Dr. Mark Mayer [mailto:ma...@ma...]
> Sent: Thursday, March 20, 2008 5:22 PM
> To: Schubert, Carsten [PRDUS]
> Cc: pym...@li...
> Subject: RE: [PyMOL] Transparency in individual molecules/objects?
> 
> 
> Hi Carsten,
> 
> Thanks for response - I Just tried following and its still drawn as 
> solid object. Did I mess up or should this have worked?
> 
> create M223Dser, /mol4//D/MET`223 and !mc
> show sticks, M223Dser
> set transparency=0.9, M223Dser
> 
> 
> >Mark,
> >
> >as far as I know, transparency is supported for sufaces and sticks 
> >or cartoons. Filter the settings menu for transparency to get a 
> >better idea. To set transparency for an object
> >
> >set transparency = 0.5, <object>
> >
> >should work
> >
> >	Carsten
> >
> >>  -----Original Message-----
> >>  From: pym...@li...
> >>  [mailto:pym...@li...]On Behalf
> >>  Of Dr. Mark
> >>  Mayer
> >>  Sent: Thursday, March 20, 2008 4:46 PM
> >>  To: PyM...@li...
> >>  Subject: [PyMOL] Transparency in individual molecules/objects?
> >>
> >>
> >>  Hi All,'
> >>
> >>  If I have a PyMol script with multiple molecules loaded, 
> is there a
> >>  way to set transparency (say for sticks or spheres), on a by
> >>  molecule, or even better on an object by object case. 
> Used to be able
> >>  to do this in molscript/raster3d, but for PyMol I've only 
> figured out
> >>  how to set sphere and stick transparency as global variables
> >>
> >>  Thanks
> >>
> >>  --
> >  > Mark Mayer Ph.D.
> >
> 
> 
> -- 
> 
> 
> 
> 

Hi Carsten,

Thanks for response - I Just tried following and its still drawn as 
solid object. Did I mess up or should this have worked?

create M223Dser, /mol4//D/MET`223 and !mc
show sticks, M223Dser
set transparency=0.9, M223Dser


>Mark,
>
>as far as I know, transparency is supported for sufaces and sticks 
>or cartoons. Filter the settings menu for transparency to get a 
>better idea. To set transparency for an object
>
>set transparency = 0.5, <object>
>
>should work
>
>	Carsten
>
>>  -----Original Message-----
>>  From: pym...@li...
>>  [mailto:pym...@li...]On Behalf
>>  Of Dr. Mark
>>  Mayer
>>  Sent: Thursday, March 20, 2008 4:46 PM
>>  To: PyM...@li...
>>  Subject: [PyMOL] Transparency in individual molecules/objects?
>>
>>
>>  Hi All,'
>>
>>  If I have a PyMol script with multiple molecules loaded, is there a
>>  way to set transparency (say for sticks or spheres), on a by
>>  molecule, or even better on an object by object case. Used to be able
>>  to do this in molscript/raster3d, but for PyMol I've only figured out
>>  how to set sphere and stick transparency as global variables
>>
>>  Thanks
>>
>>  --
>  > Mark Mayer Ph.D.
>


-- 

Hi All,'

If I have a PyMol script with multiple molecules loaded, is there a 
way to set transparency (say for sticks or spheres), on a by 
molecule, or even better on an object by object case. Used to be able 
to do this in molscript/raster3d, but for PyMol I've only figured out 
how to set sphere and stick transparency as global variables

Thanks

-- 
Mark Mayer Ph.D.
LCMN NICHD NIH DHHS
Bldg 35, Room 3B 1002 MSC 3712
35 Lincoln Drive
Bethesda MD 20892 3712
Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
Lab web site: http://mayerlab.nichd.nih.gov

Send packages, Fedex and anything requiring a signature to:

Bldg 35, Room 3B 1004
35 Lincoln Drive
Bethesda MD 20892

or if B' is residues M to N in prot1 and B'' is residues L to K in prot2,
its as simple as

load prot1.pdb
load prot2.pdb

align prot1 and i. M-N, prot2 and i. L-K

look at "help selections" and you can try to align any two selections..

cheers,
Abhi.

On Thu, Mar 20, 2008 at 12:34 PM, DeLano Scientific <de...@de...>
wrote:

> Carlo,
>
> If B is the chain ID for the matched seguments, then it should be as
> simple
> as:
>
> load file1.pdb
> load file2.pdb
>
> align file1//B//CA, file2//B//CA
>
> Cheers,
> Warren
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:de...@de...
>
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf
> > Of Carlo Zambonelli
> > Sent: Thursday, March 20, 2008 11:37 AM
> > To: pym...@li...
> > Subject: [PyMOL] partial alignment (super?)
> >
> > Hi,
> > I have 2 pdb files corresponding to 2 partially overlapping proteins:
> > AB' and B"C. B' and B" have similar but not identical
> > structures. I want to align B' and B" so to obtain ABC. Can I
> > select to align only portions of molecules? Another
> > possibility is to create 2 new pdb files corresponding to B'
> > and B", do the alignment and then attach back A and C, even
> > though I'm not completely sure after importing A and C in the
> > B'-B" alignment session, how I would correctly position A and
> > C with their original orientations relative to B' and B".
> > Thank you for your help!
> > Carlo
> >
> >
> > --------------------------------------------------------------
> > -----------
> > This SF.net email is sponsored by: Microsoft Defy all
> > challenges. Microsoft(R) Visual Studio 2008.
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> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
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>



-- 
Abhianv Verma
Research Associate,
Daggett Lab,
Benjamin Hall Interdisciplinary Research Building
University of Washington
Box 355013
Seattle, WA 98195-5013

Carlo,

If B is the chain ID for the matched seguments, then it should be as simple
as:

load file1.pdb
load file2.pdb

align file1//B//CA, file2//B//CA

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Carlo Zambonelli
> Sent: Thursday, March 20, 2008 11:37 AM
> To: pym...@li...
> Subject: [PyMOL] partial alignment (super?)
> 
> Hi,
> I have 2 pdb files corresponding to 2 partially overlapping proteins:
> AB' and B"C. B' and B" have similar but not identical 
> structures. I want to align B' and B" so to obtain ABC. Can I 
> select to align only portions of molecules? Another 
> possibility is to create 2 new pdb files corresponding to B' 
> and B", do the alignment and then attach back A and C, even 
> though I'm not completely sure after importing A and C in the 
> B'-B" alignment session, how I would correctly position A and 
> C with their original orientations relative to B' and B".
> Thank you for your help!
> Carlo
> 
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Microsoft Defy all 
> challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi,
I have 2 pdb files corresponding to 2 partially overlapping proteins:
AB' and B"C. B' and B" have similar but not identical structures. I want
to align B' and B" so to obtain ABC. Can I select to align only portions
of molecules? Another possibility is to create 2 new pdb files
corresponding to B' and B", do the alignment and then attach back A and
C, even though I'm not completely sure after importing A and C in the
B'-B" alignment session, how I would correctly position A and C with
their original orientations relative to B' and B".
Thank you for your help!
Carlo

I have had a difficult time getting hardware stereo configured using 
CrystalEyes glasses and I thought I'd share the solution with other 
pymol users.  I've just set up a new system with an Intel motherboard 
and quad-core processor and an Nvidia quadro fx1300 video card.  The 
operating system is Fedora 8.  I'm using my old SGI IR emitter with 
an adaptor that provides 12VDC power in place of the 5VDC the video 
card delivers. RealD has a diagram of the necessary cable here: 
http://www.reald-corporate.com/scientific/pdf/Sgi-retro-VESA-REV-B.pdf

My problem was that stereo mode would fail with no message on all the 
applications I tried: Pymol, Chimera and VMD.  It was difficult to 
tell whether the problem was with hardware, driver or improperly 
configured software.  In the end the solution was lurking in my 
/var/log/Xorg.0.log file:

(WW) NVIDIA(0): UBB is incompatible with the Composite extension.  Disabling
(WW) NVIDIA(0):     UBB.
(WW) NVIDIA(0): Stereo is incompatible with the Composite extension.
(II) NVIDIA(0): Disabling stereo.

Commenting out the Option "Composite" "Enable" line in the extensions 
section of my xorg.conf file didn't fix the problem.  Apparently the 
Composite extension is enabled by default.  Changing to:
   Option "Composite" "Disable"
fixed the problem.  I added the following to my device section for 
good measure:
   Option      "AddARGBGLXVisuals" "False"
because ARGB GLX visuals require the Composite extension.

In the end, the relevant section of my xorg.conf file looks like this:

Section "Monitor"
	Identifier   "Monitor0"
	VendorName   "Unknown"
	ModelName    "Unknown"
	HorizSync    30.0 - 110.0
	VertRefresh  50.0 - 150.0
# 1440x1050 Stereo @ 100 Hz
	ModeLine "1440x1050_100" 212.76 1440 1504 1824 1952 1050 1051 1054 1103
	Option	    "DPMS"
EndSection

Section "Device"
	Identifier  "Videocard0"
	Driver      "nvidia"
	Option      "UBB" "True"
	Option	    "Stereo" "3"
# ARGB GLX visuals require Composite extension which is incompatible 
with stereo
	Option      "AddARGBGLXVisuals" "False"
EndSection

Section "Screen"
	Identifier "Screen0"
	Device     "Videocard0"
	Monitor    "Monitor0"
	DefaultDepth     24
	SubSection "Display"
		Viewport   0 0
		Depth     24
		Modes     "1440x1050_100"
	EndSubSection
EndSection

Section "Extensions"
# UBB and Stereo are incompatible with the Composite extension
	Option	    "Composite" "Disable"
EndSection


Stereo mode now works beautifully in all applications.  Rendering on 
large complexes, even without stereo, is slower with the Composite 
extension disabled though.  Anyway, I hope this is helpful to other 
Pymol users.

Chad

Dear Pymol-users,
  Can anybody tell me if it's possible to view gaps in the sequence viewer?  I've got pdb files that are renumbered according to an alignment and I would like to preserve the alignment in the sequence viewer.

thanks!

-Louis
 
Louis Clark, Ph.D.
lou...@co...

On 07.03.2008, at 23:04, DeLano Scientific wrote:

> My view is that the obvious low-hanging fruit for Open-Source PyMOL is
> integration with other open-source code.  Since that mostly  
> involves work at
> the Python level, such projects are well within the reach of students,
> especially if they have experience with both packages.
>
> So from where I sit, the obvious open-source candidates are:

...

> MMTK (molecular mechanics -- Python/flexible)

If anyone wishes to tackle PyMOL-MMTK interfacing, he/she can  
certainly count on my help.

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hi...@cn...
---------------------------------------------------------------------

This is almost certainly a problem with the SIS OpenGL drivers, which aren't
up to the high standards currently being set by nVidia.  

Again, the only useful advice one can offer is to update video drivers, if
possible.  Otherwise, it may be time to look for new or used laptop with an
nVidia (best), ATI (good), or Intel (acceptable) graphics chip.  

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Horacio Emilio Pérez Sánchez
> Sent: Wednesday, March 12, 2008 7:28 AM
> To: pym...@li...
> Subject: [PyMOL] SISGL video memory error
> 
> Hi,
> 
> I have a 1G memory laptop with a sis650 graphics card runnign 
> windows xp. I use pymol a lot and sometimes I get the 
> following error message:
> 
> Warning: can't create a new surface
> Out of video memory
> This program will exit
> 
> And the only solution for use pymol again is to reboot the computer.
> 
> Is it there another way to get rid out of this error message ?
> 
> Thanks
> 
> Horacio
> 
> 
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Microsoft Defy all 
> challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Joris,

We used to experience this problem occasionally on Linux, but not anymore.

Your best bet is to update to the latest drivers.  If that does not work,
then this may be an unsolvable hardware issue on older cards.

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Joris Beld
> Sent: Wednesday, March 12, 2008 1:44 AM
> To: PyM...@li...
> Subject: [PyMOL] hardware stereo problem
> 
> Dear Pymol users,
> 
> We have a problem with one of our hardware stereo equipped PCs.
> 
> For some reason, hardware stereo works fine for about 30sec 
> but than switches to an inverted 3D image. And it keeps 
> switching back and forth between the 'normal' 3D image and 
> the inverted one, every 30sec. This is pretty annoying and 
> even after reinstalling winXP, the right nvidia driver and 
> playing around with all possible nvidia settings, we cannot 
> find the problem. The problem is not Pymol specific, having 
> the same problem in DSviewer. Does anybody recognize this problem?
> 
> The PC (AMD X2, 4GB, Nvidia quadro4 980XGL) is running winXP 
> and one of the latest pymol builds (1.0r2).
> The monitor is a high-end 21" (EIZO Flexscan T966) and we are 
> using a stereographics emitter.
> 
> Thanks a lot in advance.
> Best,
> 
> Joris Beld
> ETH Zürich
> Switzerland
> 
> --------------------------------------------------------------
> -----------
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Jong,
 
Based on ChangeLog, draggable labels should be present in 0.99 and above.
Control-left-click-and-drag on the label while in edit mode.
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Jong Yu
Sent: Wednesday, March 12, 2008 1:21 AM
To: pym...@li...
Subject: [PyMOL] generating a labeled stereo image


Dear Pymol Users,
 
I'm having a very difficult time moving labels/text in Pymol - to eventually
generate a stereo image. I've read the manuals, searched online, and tried
the obvious stuff with no success: 1) under edit_mode, I can't move any
labels!!  2)  I've also briefly attempted the pseudoatom approach, and the
command doesn't seem to work.
 
By what I've read online, this should work.  Am I missing something?  Is
this a function of the version I am working with?  Are there other options
to get labels in the figure?
 
Thanks for any help,
 
Jong 
 
 



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HDtDypao8Wcj9tAcJ> it now.

Hi,

I have a 1G memory laptop with a sis650 graphics card runnign windows 
xp. I use pymol a lot and sometimes I get the following error message:

Warning: can't create a new surface
Out of video memory
This program will exit

And the only solution for use pymol again is to reboot the computer.

Is it there another way to get rid out of this error message ?

Thanks

Horacio

Joris:

There is a thread (at least one, anyway) at the nvidia support forum,
that may address this problem:

  http://www.nvnews.net/vbulletin/showthread.php?t=85807

Note, however, that the problem the thread addresses is under linux,
not windows.

--
Steve Lane
System, Network and Security Administrator
Doudna Lab
Biomolecular Structure and Mechanism Group
UC Berkeley


On Wed, Mar 12, 2008 at 08:46:02AM -0400, Schubert, Carsten [PRDUS] wrote:
> Joris,
> 
> This is a well known problem with the NVIDIA cards.  It gets better
> with the newer highend cards but does not go away completely. You may
> want to invest in such a card and play around with different drivers.
> 
> Carsten
> 
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...]On Behalf Of Joris
> > Beld
> > Sent: Wednesday, March 12, 2008 4:44 AM
> > To: PyM...@li...
> > Subject: [PyMOL] hardware stereo problem
> > 
> > 
> > Dear Pymol users,
> > 
> > We have a problem with one of our hardware stereo equipped PCs.
> > 
> > For some reason, hardware stereo works fine for about 30sec but than 
> > switches to an inverted 3D image. And it keeps switching back 
> > and forth 
> > between the 'normal' 3D image and the inverted one, every 
> > 30sec. This is 
> > pretty annoying and even after reinstalling winXP, the right nvidia 
> > driver and playing around with all possible nvidia settings, 
> > we cannot 
> > find the problem. The problem is not Pymol specific, having the same 
> > problem in DSviewer. Does anybody recognize this problem?
> > 
> > The PC (AMD X2, 4GB, Nvidia quadro4 980XGL) is running winXP 
> > and one of 
> > the latest pymol builds (1.0r2).
> > The monitor is a high-end 21" (EIZO Flexscan T966) and we are using a 
> > stereographics emitter.
> > 
> > Thanks a lot in advance.
> > Best,
> > 
> > Joris Beld
> > ETH Z?rich
> > Switzerland
> > 
> > --------------------------------------------------------------
> > -----------
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio 2008.
> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users

Joris,

this is a well known problem with the NVIDIA cards. It gets better with the newer highend cards but does not go away completely. You may want to invest in such a card and play around with different drivers.

Carsten

> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...]On Behalf Of Joris
> Beld
> Sent: Wednesday, March 12, 2008 4:44 AM
> To: PyM...@li...
> Subject: [PyMOL] hardware stereo problem
> 
> 
> Dear Pymol users,
> 
> We have a problem with one of our hardware stereo equipped PCs.
> 
> For some reason, hardware stereo works fine for about 30sec but than 
> switches to an inverted 3D image. And it keeps switching back 
> and forth 
> between the 'normal' 3D image and the inverted one, every 
> 30sec. This is 
> pretty annoying and even after reinstalling winXP, the right nvidia 
> driver and playing around with all possible nvidia settings, 
> we cannot 
> find the problem. The problem is not Pymol specific, having the same 
> problem in DSviewer. Does anybody recognize this problem?
> 
> The PC (AMD X2, 4GB, Nvidia quadro4 980XGL) is running winXP 
> and one of 
> the latest pymol builds (1.0r2).
> The monitor is a high-end 21" (EIZO Flexscan T966) and we are using a 
> stereographics emitter.
> 
> Thanks a lot in advance.
> Best,
> 
> Joris Beld
> ETH Zürich
> Switzerland
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
>