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From: S. S. S. R. <ra...@ya...> - 2008-10-31 03:46:20
|
Its also available in Ubuntu 8.10 and macintel (pymol-py25) --- On Thu, 10/30/08, Tim Fenn <fe...@st...> wrote: From: Tim Fenn <fe...@st...> Subject: [PyMOL] pymol for fedora To: pym...@li... Date: Thursday, October 30, 2008, 1:09 PM Just as a quick FYI, pymol is available in the official fedora 9 updates, and will be part of the fedora 10 release. If you have fedora 9 or will be installing fedora 10, you can just do yum install pymol and you should be all set. The rpm is based on the b11 branch, SVN tag 3468. -Tim -- CAPS LOCK IS THE CRUISE CONTROL OF AWESOMNESS ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
|
From: aaron b. <br...@wi...> - 2008-10-30 22:15:17
|
Are their any plans to improve checkerboard stereo support for 3D DLP hdtvs any time soon in the incentive builds. for more info look at: http://www.dlp.com/hdtv/3-d_dlp_hdtv.aspx thanks, aaron bryden |
|
From: Tim F. <fe...@st...> - 2008-10-30 17:10:06
|
Just as a quick FYI, pymol is available in the official fedora 9 updates, and will be part of the fedora 10 release. If you have fedora 9 or will be installing fedora 10, you can just do yum install pymol and you should be all set. The rpm is based on the b11 branch, SVN tag 3468. -Tim -- CAPS LOCK IS THE CRUISE CONTROL OF AWESOMNESS |
|
From: froschkoenig05 <fro...@gm...> - 2008-10-29 21:15:00
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Thanks Tsjerk, this was very helpful!<br>
<br>
Cheers,<br>
Tanja<br>
<br>
Tsjerk Wassenaar wrote:
<blockquote
cite="mid:8ff...@ma..."
type="cite">
<pre wrap="">Hi Tanja,
Try:
pymol -qcd 'cmd.help("launching")' > pymol_launching.txt
and examine the resulting file :)
Cheers,
Tsjerk
On Wed, Oct 29, 2008 at 7:48 PM, Tanja Mittag <a class="moz-txt-link-rfc2396E" href="mailto:Tan...@gm..."><Tan...@gm...></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi!
I would like to run pymol scripts on the command line only without
invoking the x-window because there is no need to display the structures
involved (and also no way because I will run this on a Linux computer
cluster). I am only interested in the pymol text output that can be
piped into an output file. For example like this:
Pymol.com script.pml > log.out
I just want to avoid the x-window coming up (and possible errors if it
cannot).
Thanks for your input!
Cheers,
Tanja
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
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_______________________________________________
PyMOL-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:PyM...@li...">PyM...@li...</a>
<a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/pymol-users" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users">https://lists.sourceforge.net/lists/listinfo/pymol-users</a>
</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
<br>
</body>
</html>
|
|
From: gilleain t. <gil...@gm...> - 2008-10-29 20:49:18
|
Hmmm.
I'm probably over-complicating matters, but:
def before_load():
cmd.delete("all")
def after_load():
cmd.as("cartoon")
cmd.hide("nonbonded")
def wrapped_load(filename):
before_load()
cmd.load(filename)
after_load()
cmd.extend("wrapped_load", wrapped_load)
gilleain
On Wed, Oct 29, 2008 at 7:26 PM, Nathaniel Echols
<nat...@gm...> wrote:
> On Wed, Oct 29, 2008 at 11:39 AM, Thomas S. Leyh, Ph. D. <le...@ae...>
> wrote:
>>
>> Every once in a while, I try to show a metal ion as a tranparent
>> sphere and inevetiably get stuck trying to make the tiny cartesian
>> coordinate system that appears at the center of the sphere disappear so it
>> doesn't "show through". Suggestions?
>
> I think you want "hide nonbonded".
> I have a related question: is there a way (or could there be) to control the
> default appearance of molecules upon loading? Personally, when I use PyMOL
> I almost always want to look at cartoons, without nonbonded atoms.
> Something as simple as a few new settings that I could throw in ~/.pymolrc
> would be fine.
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
|
|
From: Tsjerk W. <ts...@gm...> - 2008-10-29 20:47:20
|
Hi Tanja,
Try:
pymol -qcd 'cmd.help("launching")' > pymol_launching.txt
and examine the resulting file :)
Cheers,
Tsjerk
On Wed, Oct 29, 2008 at 7:48 PM, Tanja Mittag <Tan...@gm...> wrote:
> Hi!
>
> I would like to run pymol scripts on the command line only without
> invoking the x-window because there is no need to display the structures
> involved (and also no way because I will run this on a Linux computer
> cluster). I am only interested in the pymol text output that can be
> piped into an output file. For example like this:
>
> Pymol.com script.pml > log.out
>
> I just want to avoid the x-window coming up (and possible errors if it
> cannot).
>
> Thanks for your input!
>
> Cheers,
> Tanja
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
--
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
|
|
From: Nathaniel E. <nat...@gm...> - 2008-10-29 19:26:11
|
On Wed, Oct 29, 2008 at 11:39 AM, Thomas S. Leyh, Ph. D. <le...@ae...>wrote: > Every once in a while, I try to show a metal ion as a tranparent > sphere and inevetiably get stuck trying to make the tiny cartesian > coordinate system that appears at the center of the sphere disappear so it > doesn't "show through". Suggestions? > I think you want "hide nonbonded". I have a related question: is there a way (or could there be) to control the default appearance of molecules upon loading? Personally, when I use PyMOL I almost always want to look at cartoons, without nonbonded atoms. Something as simple as a few new settings that I could throw in ~/.pymolrc would be fine. |
|
From: Schubert, C. [PRDUS] <CSC...@it...> - 2008-10-29 19:23:40
|
Tom,
you need to hide the 'nonbonded' representation of your ion, which shows up as a little coordinate system i.e.
hide nonbonded, chain I #if your ion is in chain I
show spheres, chain I
set sphere_transparency=0.5, chain I
Cheers,
Carsten
-----Original Message-----
From: Thomas S. Leyh, Ph. D. [mailto:le...@ae...]
Sent: Wednesday, October 29, 2008 2:39 PM
To: pym...@li...
Subject: [PyMOL] remove cartesian coordinate from w/in transparent metal ions
Every once in a while, I try to show a metal ion as a tranparent sphere and inevetiably get stuck trying to make the tiny cartesian coordinate system that appears at the center of the sphere disappear so it doesn't "show through". Suggestions?
Tom Leyh
|
|
From: Tanja M. <Tan...@gm...> - 2008-10-29 18:48:36
|
Hi! I would like to run pymol scripts on the command line only without invoking the x-window because there is no need to display the structures involved (and also no way because I will run this on a Linux computer cluster). I am only interested in the pymol text output that can be piped into an output file. For example like this: Pymol.com script.pml > log.out I just want to avoid the x-window coming up (and possible errors if it cannot). Thanks for your input! Cheers, Tanja |
|
From: Sean S. <sea...@go...> - 2008-10-26 22:38:53
|
Hi, I would like to make a movie in PyMol based on "mset 1 x60" followed by "mdo 1: turn x,3; turn y,5;" but whereas this makes a rotating molecule on-screen, exporting to PNG files yields only a single file. Is this normal? Thanks, Sean |
|
From: Joonghyun R. <jh...@vo...> - 2008-10-26 12:06:21
|
Dear Warren
Thank you for your information.
It works fine.
Joonghyun
-----Original Message-----
From: DeLano Scientific [mailto:de...@de...]
Sent: Sunday, October 26, 2008 3:25 AM
To: 'Joonghyun Ryu'; pym...@li...
Subject: RE: [PyMOL] question about checking the performance of PyMOL
Joonghyun,
To optimize performance and responsiveness, PyMOL tends to defer
compute-intensive tasks until their results are actually needed. Thus,
cmd.show("surface")
Doesn't actually show a surface, it only sets the surface visibility flag on
the atoms present (for future reference). An actual surface won't be
computed until PyMOL is asked to refresh or render the display. When
running a script, you can force an update by calling:
cmd.refresh()
After cmd.show.
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...
-----Original Message-----
From: Joonghyun Ryu [mailto:jh...@vo...]
Sent: Friday, October 24, 2008 10:39 PM
To: pym...@li...
Subject: [PyMOL] question about checking the performance of PyMOL
Hi, all
I am sending this email for asking you about checking the performance of
PyMOL.
I tried to check the elapsed time for the computation of a molecular surface
as follows.
--
import os
import cmd
import pymol
cmd.set("surface_quality", "2")
start = time.time()
cmd.show("surface")
end = time.time()
elapsedTime = (end - start)
print "Elapsed time: ", elapsedTime, "sec."
--
The result always shows 0 sec. for any sized PDB file. For example, it takes
about 10 sec. for 1L7A.pdb (by my watch) which contains about 5000 atoms.
However, if I run the above codes in PyMOL command-line mode, it shows
Elapsed time: 0 sec.
Currently, I am using PyMOL 1.1b4edu (May 2008) on Windows XP.
Should I use other APIs for checking the performance?
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great
prizes Grand prize is a trip for two to an Open Source event anywhere in the
world http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users
|
|
From: DeLano S. <de...@de...> - 2008-10-25 18:25:00
|
Joonghyun,
To optimize performance and responsiveness, PyMOL tends to defer
compute-intensive tasks until their results are actually needed. Thus,
cmd.show("surface")
Doesn't actually show a surface, it only sets the surface visibility flag on
the atoms present (for future reference). An actual surface won't be
computed until PyMOL is asked to refresh or render the display. When
running a script, you can force an update by calling:
cmd.refresh()
After cmd.show.
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...
-----Original Message-----
From: Joonghyun Ryu [mailto:jh...@vo...]
Sent: Friday, October 24, 2008 10:39 PM
To: pym...@li...
Subject: [PyMOL] question about checking the performance of PyMOL
Hi, all
I am sending this email for asking you about checking the performance of
PyMOL.
I tried to check the elapsed time for the computation of a molecular surface
as follows.
--
import os
import cmd
import pymol
cmd.set("surface_quality", "2")
start = time.time()
cmd.show("surface")
end = time.time()
elapsedTime = (end - start)
print "Elapsed time: ", elapsedTime, "sec."
--
The result always shows 0 sec. for any sized PDB file. For example, it takes
about 10 sec. for 1L7A.pdb (by my watch) which contains about 5000 atoms.
However, if I run the above codes in PyMOL command-line mode, it shows
Elapsed time: 0 sec.
Currently, I am using PyMOL 1.1b4edu (May 2008) on Windows XP.
Should I use other APIs for checking the performance?
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great
prizes Grand prize is a trip for two to an Open Source event anywhere in the
world http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users
|
|
From: Joonghyun R. <jh...@vo...> - 2008-10-25 05:52:26
|
Hi, all
I am sending this email for asking you about checking the performance of
PyMOL.
I tried to check the elapsed time for the computation of a molecular surface
as follows.
--
import os
import cmd
import pymol
cmd.set("surface_quality", "2")
start = time.time()
cmd.show("surface")
end = time.time()
elapsedTime = (end - start)
print "Elapsed time: ", elapsedTime, "sec."
--
The result always shows 0 sec. for any sized PDB file. For example, it takes
about 10 sec. for 1L7A.pdb (by my watch)
which contains about 5000 atoms. However, if I run the above codes in PyMOL
command-line mode,
it shows Elapsed time: 0 sec.
Currently, I am using PyMOL 1.1b4edu (May 2008) on Windows XP.
Should I use other APIs for checking the performance?
|
|
From: Tsjerk W. <ts...@gm...> - 2008-10-24 20:40:54
|
Hi Florian, Check the selection stuff in Pymol: help selections > For example displaying all residues not farer away than 6 A from any > ligand Atom? > If ligand is your ligand selection and protein the protein part, this is done simply (intuitively) with: show sticks, byres protein within 6 of ligand Cheers, Tsjerk -- 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 |
|
From: Florian K. <for...@tu...> - 2008-10-22 16:07:22
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Hi Folks! Is there any possibility (or a plugin doin that) to display only the binding pocket of a ligand-receptor complex? For example displaying all residues not farer away than 6 A from any ligand Atom? (Ligand of corse non covalently bound?) Thanx alot! |
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From: Pete M. <pa...@mc...> - 2008-10-20 18:44:55
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Odds are you've heard back from the mapman people by now. But if you haven't, if you've got a map that mapman says is too large you need to increase (or set) the MAPSIZE environmental variable. aka $ mapman MAPSIZE 20000000 instead of $ mapman Pete Vahdati N. wrote: > Dear Pymol users, > > Is it possible to export/save surface files from within pymol? > > I am loading a binary ccp4 volume/surface file into pymol and would like to export it as another format or simply the same format but in alphanumeric. This is because I am interested in knowing the coordinates of the centre or origin of my volume to use in my follow up analysis. > > I don't seem to be able to use MAPMAN which seems to be the usual tool to convert map file formats. I think this is due to the size of the file but I am seeking clarification on that from the MAPMAN developers. > > Thank you in advance for any comments. > > Nadia Vahdati > Postgraduate research student > Prof. J. W. Essex Group > University of Southampton > UK. > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
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From: DeLano S. <de...@de...> - 2008-10-20 17:59:53
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Vahdati, The short answer to this is no. However, for the application you describe, try: zoom print cmd.get_position() Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:su...@de... -----Original Message----- From: Vahdati N. [mailto:na...@so...] Sent: Sunday, October 19, 2008 12:11 PM To: pym...@li... Subject: [PyMOL] export surface Dear Pymol users, Is it possible to export/save surface files from within pymol? I am loading a binary ccp4 volume/surface file into pymol and would like to export it as another format or simply the same format but in alphanumeric. This is because I am interested in knowing the coordinates of the centre or origin of my volume to use in my follow up analysis. I don't seem to be able to use MAPMAN which seems to be the usual tool to convert map file formats. I think this is due to the size of the file but I am seeking clarification on that from the MAPMAN developers. Thank you in advance for any comments. Nadia Vahdati Postgraduate research student Prof. J. W. Essex Group University of Southampton UK. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
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From: Jason V. <jv...@cs...> - 2008-10-20 15:24:19
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PyMOLers, Normally I don't announce new scripts to the PyMOLWiki, but I just finished one small utility script I find very useful. I hope someone out there can benefit from it too. The script, loadDir, loads ALL the files (you specify the type) in a directory (you provide the path). It can also group them all, helping keep your data organized in PyMOL. The script can be downloaded from the PyMOLWiki: http://www.pymolwiki.org/index.php/LoadDir If you're interested, here are some details: On startup you can issue something like, pymol dataDir/*.pdb and PyMOL will load all the PDB files in dataDir. But, once in PyMOL it's more difficult and involves some Python scripting (which I just finished). Here's some example uses: (1) Load all PDBs in the current directory loadDir ., *.pdb The defaults are to load all pdbs from ".", so the above can also be done through loadDir (2) Load all the SD files in /tmp. # all 4 do the same thing; gives you flexibility loadDir /tmp, sdf loadDir /tmp, .sdf loadDir /tmp, *.sdf loadDir /tmp, fileName.sdf (3) Let's say you have a directory tree like: # ./receptors # - classA # - classB # - classE # - classF # # ./nonBinders # - classC We can load all the files in the subdirs of receptors and group them into one group called "rec" loadDir receptors/*, *.pdb, group=rec Likewise we can load classC by name or glob into the group "nonBind" # these two commands do the same thing, in this example loadDir nonBinders/*, *.pdb, group=nonBind loadDir nonBinders/classC, *.pdb, group=nonBind Cheers! -- Jason -- Jason Vertrees, PhD Dartmouth College : jv...@cs... Boston University : ja...@bu... PyMOLWiki : http://www.pymolwiki.org/ |
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From: Vahdati N. <na...@so...> - 2008-10-19 19:11:14
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Dear Pymol users, Is it possible to export/save surface files from within pymol? I am loading a binary ccp4 volume/surface file into pymol and would like to export it as another format or simply the same format but in alphanumeric. This is because I am interested in knowing the coordinates of the centre or origin of my volume to use in my follow up analysis. I don't seem to be able to use MAPMAN which seems to be the usual tool to convert map file formats. I think this is due to the size of the file but I am seeking clarification on that from the MAPMAN developers. Thank you in advance for any comments. Nadia Vahdati Postgraduate research student Prof. J. W. Essex Group University of Southampton UK. |
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From: Christian S. <cse...@bp...> - 2008-10-14 05:06:46
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Thanks for our answer. set defer_builds_mode, 3 fixed my problem. Greets, Christian. On Sun, 2008-10-12 at 09:18 -0700, DeLano Scientific wrote: > Christian, > > PyMOL's default behavior is to pre-compute and cache molecular geometry in > RAM. Although this provides optimal performance for small numbers of > molecular states, due to RAM usage, it is an unworkable approach for viewing > long MD simulations. So, > > set defer_builds_mode, 3 > > before loading your trajectory in order to force PyMOL to only cache the > current frame in RAM. > > In the current open-source build (and future builds 1.2+), you can also > > set defer_builds_mode, 5 > > to obtain VMD-like playback speed for lines, spheres, and nonbonded > representations (immediate mode rendering -- geometry never touches RAM). > > Cheers, > Warren > > -----Original Message----- > From: Christian Seifert [mailto:cse...@bp...] > Sent: Sunday, October 12, 2008 1:03 AM > To: pym...@li... > Subject: [PyMOL] System freezes in cause of memory abuse > > Hi! > > I'm working with big structures and even bigger trajectories. When I try > to load a trajectory, pymol takes the full 2GB RAM and freezes my PC > (ubuntu 7.10/gnome/core 2 duo/2 GB RAM). The only way out is pulling the > plug. :-( > > My Question: > Is there a possibility to reduce the memory used by pymol? > The "nice" command did not work, because it just reduces the available > CPU time for pymol and not the available memory. > > Greetings > Christian. > -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: cse...@bp... Web: http://www.bph.rub.de |
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From: Folmer F. <fo...@gm...> - 2008-10-13 06:22:27
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Hi Massimo 2008/10/13 Massimo Heitor <mas...@gm...>: > I am looking at the residue sequence for a protein that I'm studying for a > class and I have a few questions. > I understand the regular amino acid codes (CYS, ARG, LEU, etc...). > What is NAG? I see one sequence "NAG NAG NAG NAG" (resisting off-topic joke) If you have access to wikipedia a quick search would indicate that you might be looking at N-Acetylglucosamine (http://en.wikipedia.org/wiki/N-Acetylglucosamine). > What is HOH? I see about 107 "HOH" elements in a row. They are all colored > red. What is that? Ok, I'm going to ask a question. What molecule has to "H" atoms and one "O"? > On the sequence number bar, I see one break represented as "//", and one gap > in the numbering. 130-133 is "NAG NAG NAG NAG", and 140-246 is all HOH, but > there is seemingly nothing at positions 134-139. Why is that? What is the > difference between a "//" break and a numbering sequence gap? I don't use the sequence bar myself so I'll have to pass an that question. > Thanks! Hope this helps! > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > |
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From: Massimo H. <mas...@gm...> - 2008-10-13 05:26:53
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I am looking at the residue sequence for a protein that I'm studying for a class and I have a few questions. I understand the regular amino acid codes (CYS, ARG, LEU, etc...). What is NAG? I see one sequence "NAG NAG NAG NAG" (resisting off-topic joke) What is HOH? I see about 107 "HOH" elements in a row. They are all colored red. What is that? On the sequence number bar, I see one break represented as "//", and one gap in the numbering. 130-133 is "NAG NAG NAG NAG", and 140-246 is all HOH, but there is seemingly nothing at positions 134-139. Why is that? What is the difference between a "//" break and a numbering sequence gap? Thanks! |
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From: DeLano S. <de...@de...> - 2008-10-12 16:18:48
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Christian, PyMOL's default behavior is to pre-compute and cache molecular geometry in RAM. Although this provides optimal performance for small numbers of molecular states, due to RAM usage, it is an unworkable approach for viewing long MD simulations. So, set defer_builds_mode, 3 before loading your trajectory in order to force PyMOL to only cache the current frame in RAM. In the current open-source build (and future builds 1.2+), you can also set defer_builds_mode, 5 to obtain VMD-like playback speed for lines, spheres, and nonbonded representations (immediate mode rendering -- geometry never touches RAM). Cheers, Warren -----Original Message----- From: Christian Seifert [mailto:cse...@bp...] Sent: Sunday, October 12, 2008 1:03 AM To: pym...@li... Subject: [PyMOL] System freezes in cause of memory abuse Hi! I'm working with big structures and even bigger trajectories. When I try to load a trajectory, pymol takes the full 2GB RAM and freezes my PC (ubuntu 7.10/gnome/core 2 duo/2 GB RAM). The only way out is pulling the plug. :-( My Question: Is there a possibility to reduce the memory used by pymol? The "nice" command did not work, because it just reduces the available CPU time for pymol and not the available memory. Greetings Christian. -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: cse...@bp... Web: http://www.bph.rub.de ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
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From: Martin H. <mar...@gm...> - 2008-10-12 10:42:41
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Am Sonntag, 12. Oktober 2008 schrieb Christian Seifert: > Hi! > > I'm working with big structures and even bigger trajectories. When I try > to load a trajectory, pymol takes the full 2GB RAM and freezes my PC > (ubuntu 7.10/gnome/core 2 duo/2 GB RAM). The only way out is pulling the > plug. :-( > > My Question: > Is there a possibility to reduce the memory used by pymol? > The "nice" command did not work, because it just reduces the available > CPU time for pymol and not the available memory. On linux systems, you could try ulimit to limit the maximum available memory for current shell and all spawned processes. ulimit -a shows current setup ulimit -v SizeInKB allows setting of a limit in current shell. Best Martin -- Tip of the Day: "Nur Vollidioten tun Vollquoten!" (Markus Schaber in de.rec.sf.babylon5) |
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From: Christian S. <cse...@bp...> - 2008-10-12 09:04:50
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Hi! I'm working with big structures and even bigger trajectories. When I try to load a trajectory, pymol takes the full 2GB RAM and freezes my PC (ubuntu 7.10/gnome/core 2 duo/2 GB RAM). The only way out is pulling the plug. :-( My Question: Is there a possibility to reduce the memory used by pymol? The "nice" command did not work, because it just reduces the available CPU time for pymol and not the available memory. Greetings Christian. -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: cse...@bp... Web: http://www.bph.rub.de |
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