Re: [PyMOL] Windows PDB file for debugging pymol C extension?

Try to turn on heap verification for python.exe using the following registration key and then start pymol with `python.exe -m pymol` [HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image File Execution Options\python.exe] "GlobalFlag"="0x0200"

Re: [PyMOL] Windows PDB file for debugging pymol C extension?

Thanks -- unfortunately it seems to be heap corruption. I can see where it's detected: ntdll.dll!RtlpLogHeapFailure () Unknown ntdll.dll!RtlFreeHeap() Unknown ucrtbase.dll!_free_base() Unknown _cmd.cp36-win_amd64.pyd!VLAFree(void * ptr) Line 222 C++

Re: [PyMOL] Windows PDB file for debugging pymol C extension?

I put a VS2015 build of svn rev 4189 including debug information files for the pymol source at Hope this helps. Christoph On 5/9/2018 7:34 AM, Gary Oberbrunner wrote: Hi; I'm running into a crash in Windows pymol, in the C

[PyMOL] Windows PDB file for debugging pymol C extension?

Hi; I'm running into a crash in Windows pymol, in the C extension part (_cmd.cp36-win_amd64.pyd) using pymol open source 2.1.0. I'd like to debug it; is there a symbol file (.pdb) available anywhere? Or failing that, can I rebuild the C extension from source and create a pdb? -- Gary Oberbrunner

Re: [PyMOL] Editing PDB to remove flexible loop

Hi Ahmad, there are a number of pymol tutorials online that should be helpful. From the first page of a Google search, some that look helpful include: https://www.mrc-lmb.cam.ac.uk/rlw/text/MacPyMOL_tutorial.html

[PyMOL] Editing PDB to remove flexible loop

Hello, Is there a way to keep the sequence of structure, but remove the modelling of some flexible loop? Meaning, Pymol should show the entire sequence, but the strcuture should not show this sequence. A side question, how else can I compare two structures in Pymol besides aligning them and

Re: [PyMOL] on PDB

Hi Smith, It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture. Shane Shane Caldwell McGill University On Fri,

Re: [PyMOL] on PDB

Dear All, Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the

Re: [PyMOL] on PDB

try running find ~/ -name “newpdb.pdb” > On Nov 27, 2015, at 9:08 PM, Smith Liu wrote: > > > Dear All, > > Osvaldo is new here for this question, so I repeat it a little. By pymol I > open a pdb and orient it and I want to save the oriented pdb. First I input >

Re: [PyMOL] on PDB

Dear Shane, get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb? Smith At 2015-11-26 03:54:32, "Shane Caldwell" wrote: Hi Smith, You can type >get_view and copy the output into a txt

Re: [PyMOL] on PDB

Hi Smith, You can type >get_view and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings Shane Shane Caldwell McGill University On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu wrote: > Dear All, > >

Re: [PyMOL] on PDB

http://pymolwiki.org/index.php/Save ?? -David > On Nov 24, 2015, at 9:45 PM, Smith Liu wrote: > > Dear All, > > Suppose the original PDB was not oriented. Once we have it oriented by pymol, > is any way we can save the new PDB oriented? > > Smith > > > > >

Re: [PyMOL] on PDB

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures Andreas On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu wrote: > Dear Shane, > > get_view is a nice command. Is any way to change the original PDB based on > what we get by set_view to get the new pdb? > >

Re: [PyMOL] on PDB

Dear All, For get view, we get something like set_view (\ 0.999876618, -0.000452542, -0.015699286,\ 0.000446742,0.99821, -0.000372844,\ 0.015699454,0.000365782,0.999876678,\ 0.0,0.0, -150.258514404,\ 11.842411041,

[PyMOL] on PDB

Dear All, Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented? Smith-- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users

Re: [PyMOL] on PDB display and calculation

Hi Smith, are you looking to visualize symmetrie axes? Then this might be a starting point: http://www.pymolwiki.org/index.php/SuperSym Cheers, Julian On Mon, Nov 23, 2015 at 4:15 PM, Smith Liu <smith_liu...@163.com> wrote: > Dear All, > > Once I have displayed a tetramer PDB b

Re: [PyMOL] on PDB display and calculation

t Department of Biochemistry and Molecular Biophysics Columbia University > On Nov 23, 2015, at 12:15 AM, Smith Liu <smith_liu...@163.com> wrote: > > Dear All, > > Once I have displayed a tetramer PDB by pymol, is any way I can get the > central axis of the tetramer and display i

[PyMOL] on PDB display and calculation

Dear All, Once I have displayed a tetramer PDB by pymol, is any way I can get the central axis of the tetramer and display it? Is any way I can get the cross-section of the tetramer (perpendicular to the central axis) and display it? If the tetramer is asymmetric, then how to get the central

Re: [PyMOL] Multiple pdb simulation data

Hi Tsjerk, Thanks you for your reply. Sorry for my late response, for some reasons the mail went to the spam folder. This is my log.pml file which I am trying to use to load all the simulation generated pdb files. for i in range(251,1000,100): cmd.load(prod_%d.pdb%i,traj) hide all show cartoon

[PyMOL] Multiple pdb simulation data

Dear All, I have around 1000 PDB files generated from the MD simulation. Each file is around 32 MB in size. What I am trying to do: a) Load every 100th pdb file automatically and analyze the data. b) I am also trying to customize the load list, for example from 100 to say 50 or 25 or 10 like

Re: [PyMOL] Multiple pdb simulation data

Hi Ritesh, Assuming you want the PDB files to end up in one object and they are numbered like file0.pdb .. file1000.pdb for i in range(0,1000,100): cmd.load(file%d.pdb%i,traj) You can set the step size from 100 to 50, 25, ... One thing that you may want to ask yourself is whether you need all

[PyMOL] sorting pdb ensembles based on rmsd

Dear PyMol users! I have a set of conformations extracted from the MD trajectory (on the equal time-steps). After loading of all that pdb's into pymol (each conformer= separate pdb file) I want to sort that structures based on the RMSD relative to the reference conformer (e.g step0.pdb ) in the

[PyMOL] Verify PDB format

Dear PyMOL users Does anybody know a script to verify that a file contains valid a valid PDB formatted structure? The file extension alone obviously does not provide sufficient validation. Thanks for any feedback. Martin

Re: [PyMOL] Verify PDB format

would help! Joel -Original Message- From: Martin Hediger [mailto:ma@bluewin.ch] Sent: Wednesday, 27 June 2012 10:01 p.m. To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Verify PDB format Dear PyMOL users Does anybody know a script to verify that a file contains valid a valid PDB

Re: [PyMOL] save pdb with headers

Hi Osvaldo, Sorry for the delay. Mobile PyMOL development is taking up most of my time now. There is no easy way. You'd need to wrap the save function. It would look something like (warning untested code follows): def my_save(file,object,header): # make sure there's a newline after the

[PyMOL] save pdb with headers

Hi, There is an easy way to save a pdb adding custom headers using PyMol? Thanks. -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app

Re: [PyMOL] Open .pdb / .pml files in ubuntu/mint

I had exactly the same problem but under Gentoo Linux 64bits using KDE 4.7.4. In my case, I solved it by re-installing the package for chemical-mime-data (sci-chemistry/chemical-mime-data), which was missing since the removal of some Gnome chemical packages with all their dependencies I

[PyMOL] Open .pdb / .pml files in ubuntu/mint

Hi guys. Ehh. I have a newly installed Mint 12 box with gnome 3. I have that annoying thing, that when I click a text .pdb files, it opens with gedit. Then I can right click and select .pdb files to open with pymol. But when I then click a .txt file, it opens it with pymol. Grrr... I know its

Re: [PyMOL] Open .pdb / .pml files in ubuntu/mint

Hmm, Have you tried putting a .txt and .pdb file on your desktop. Right click either one and click Properties. There is an Open With tab. It should say Open this file and other .txt files with and then you can select gedit. Conversely do the same for .pdb files. Jordan On Jan 29, 2012, at

Re: [PyMOL] Open .pdb / .pml files in ubuntu/mint

Oh duh, You are saying the .pdb is read as a plain text file You would then have to add a new mime type .pdb to the source XML file that gnome reads in /usr/share/mime/packages/freedesktop.org.xml http://library.gnome.org/admin/system-admin-guide/stable/mimetypes-source-xml.html.en Sorry for

Re: [PyMOL] creating PDB structure

Hi James. Look here for windows: http://www.pymolwiki.org/index.php/Windows_Install#Pre-compiled_PyMOL Basically: You can make a pymolrc.pym file, and put it under C:\Users\YOU. In the file you can write the following listed. This folder is now in your PyMOL search path, so you can put pymol

[PyMOL] creating PDB structure

Dear PyMol Users! I wounder to know about possible ways of creation of the peptide structures via PyMol Builder module. In particular I need create a linear structure of my protein ( with fixed phi and psi angles) for futher folding molecular dynamics simulation of that peptide. But in builder

Re: [PyMOL] creating PDB structure

On 11/23/2011 01:18 PM, James Starlight wrote: Thanks Thomas! Those scripts works fine. Could you tell me if there any way to install all of those scripts as the pymol plugins ( that I need not to load this scripts every time when I sttart pymol de novo )? James Hi James Jason Vertrees

Re: [PyMOL] creating PDB structure

Hi James, C could not find if all those scripts are able to make CAPS on the residues but if it's not possible Iwant to add some CAP group ( e.g ACE to the N term) via builder module. So I've chose ACE residue from that module and obtained message pick location to attach ace how now

Re: [PyMOL] creating PDB structure

If you are in the PyMOL Viewer and in Edit mode, you can hit ALT+{a,g,d,e,...} to build up a linear polypeptide, where the single letters correspond to the amino acide identifiers. Is this useful to you? Am 23.11.11 11:43, schrieb James Starlight: Dear PyMol Users! I wounder to know

[PyMOL] Model pdb section support

Have pdb file with pseudobeads: MODEL 2 HETATM1 O24.000 46.000 39.000 HETATM2 O24.000 47.000 39.000 HETATM3 O24.000 47.000 38.000 HETATM4 O25.000 47.000 38.000 HETATM5 O25.000

Re: [PyMOL] Model pdb section support

Hi Sergey, If I understand you correctly, you want the following: set all_states then load your file. Cheers, -- Jason On Mon, Jan 10, 2011 at 10:38 AM, Sergey Ivanov icegood1...@gmail.com wrote: Have pdb file with pseudobeads: MODEL     2 HETATM    1   O                24.000  46.000  

Re: [PyMOL] Model pdb section support

Dear Sergey, From looking at your PDB file, I don't think PyMOL supports exactly what you want. I believe that in order for all_states to show atoms properly, they have to be in all of the states (all MODELs). So, you could do something like the following, but it feels a little clunky to me.

Re: [PyMOL] Model pdb section support

Hello Sergey, On Mon, 10 Jan 2011 16:38:52 +0100 Sergey Ivanov icegood1...@gmail.com wrote: Have pdb file with pseudobeads: MODEL 2 HETATM1 O24.000 46.000 39.000 HETATM2 O24.000 47.000 39.000 etc. I displayed this file using Nathan's

Re: [PyMOL] Displaying PDB files that were determined via fiber diffraction

Hi Chad, Good question. The PDB header to 1rmv tells us we can generate the biological unit using REMARK 350 from the PDB. Recently a script was added to the PyMOLWiki that creates just such structures. This script was then improved by those in the PyMOL community. Please see

[PyMOL] Displaying PDB files that were determined via fiber diffraction

Hello, Does anyone know how to display PDB files that are determined by fiber diffraction? The default just shows a single peptide, when in fact it is supposed be a bunch of peptides interacting with one another to make a fiber. Thanks a lot. Chad *** Chad R. Simmons

Re: [PyMOL] Loading PDB Files does not work with Linux

From: greipel.joac...@mh-hannover.de [mailto:greipel.joac...@mh-hannover.de] Sent: Thursday, September 24, 2009 5:51 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Loading PDB Files does not work with Linux Hi all, I can't get the functions to load pdb-data

Re: [PyMOL] writing pdb files with headers

Conilleau [mailto:sconill...@chimie.u-strasbg.fr] Sent: Tuesday, January 20, 2009 7:56 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] writing pdb files with headers Hi, I noticed that pymol omits the headers (I mean the 5 first line) when you try to write a pdb file. At this point I do

[PyMOL] writing pdb files with headers

Hi, I noticed that pymol omits the headers (I mean the 5 first line) when you try to write a pdb file. At this point I do it using this command line in my script : cmd.save(newName+.pdb,tmp) Is there an implemeted way to avoid this behaviour or do I have to play around with files ? Thanks

[PyMOL] Keeping PDB ordering

Hi all, is there a simple way to prevent reordering of atoms and insertion of additional TER records by pymol? I have a protein embedded in a bilayer with tip4p water, where this occurs when I delete parts and export the rest of the System. Best wishes Martin

Re: [PyMOL] Keeping PDB ordering

...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Martin Höfling Sent: Thursday, April 24, 2008 11:13 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Keeping PDB ordering Hi all, is there a simple way to prevent reordering of atoms and insertion

[PyMOL] generating pdb coordinates

Hi all- I was wondering if it is possible to generate coordinates in a .pdb file from the docking I made using pymol. thank you, Juliana

Re: [PyMOL] generating pdb coordinates

Hi, You can save the structure as a pdb file: save name.pdb, selection-name that might do what you want. Type help save for more details. gilleain torrance On 3/15/07, Juliana R Cortines corti...@uab.edu wrote: Hi all- I was wondering if it is possible to generate coordinates in a .pdb

Re: [PyMOL] transforming PDB in Pairfit or align

Ravi, Do you use pairfitting or align command in PyMol? Align works well for me even for different (but homologous) proteins. Another popular alternative is to use Stamp (U. of Dundee) for the alignment of the PDBs (http://www.compbio.dundee.ac.uk/Software/Stamp/stamp.html) Hugo Ravi Bojja

[PyMOL] transforming PDB in Pairfit or align

Hi, I have an unique problem with pairfitting, My Protein is comprised of helices and loops, In active and inactive forms there are no changes in helical structures, but only loops orientation are changed after pairfitting, one the structure is shifted about 0.5 angstroms,

Re: [PyMOL] transforming PDB in Pairfit or align

Quoting Ravi Bojja bojja...@yahoo.com: Hi, I have an unique problem with pairfitting, My Protein is comprised of helices and loops, In active and inactive forms there are no changes in helical structures, but only loops orientation are changed after pairfitting, one the

Re: [PyMOL] transforming PDB in Pairfit or align

Hi Ravi, You could use the DALI-LITE (EMBL) server to align both pdbs, then open the new (aligned) pdbs generated by DALI into PYMOL - that should align the identical helices perfectly and show you the differences in the loops. Sivaram. On 3/12/07, Andy Purkiss a.purk...@mail.cryst.bbk.ac.uk

[PyMOL] Merge PDB files

I was wondering if there was a simple way to merge pdb files generated by Pymol's 'generate symmetry mates' command? I have a dimer in the available pdb file and want to make the full hexamer that is formed via a trimer of dimers. Any suggestions would be most appreciated. Josh

Re: [PyMOL] Merge PDB files

@lists.sourceforge.net Subject: [PyMOL] Merge PDB files I was wondering if there was a simple way to merge pdb files generated by Pymol's 'generate symmetry mates' command? I have a dimer in the available pdb file and want to make the full hexamer that is formed via a trimer of dimers. Any suggestions would

RE: [PyMOL] Saving PDB with CONECT information

, March 20, 2006 12:16 PM To: Warren DeLano Cc: Pymol Subject: Re: [PyMOL] Saving PDB with CONECT information Thanks a lot Warren. If you allow me, my script to build sequences of 3 peptides is almost done. I could even use sculpt to improve my molecules structures. For the moment I am

[PyMOL] Saving PDB with CONECT information

Hello List! Is PyMol able to save the built protein/molecule in a PDB file with CONECT information. If so, how to do it? Thanks in advance for any help. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road,

RE: [PyMOL] Saving PDB with CONECT information

Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Alan Sent: Monday, March 20, 2006 11:39 AM To: Pymol Subject: [PyMOL] Saving PDB with CONECT information Hello List! Is PyMol able to save the built protein/molecule

[PyMOL] load pdb files of non-standard format

Hi all. I am trying to find a way to load pdb files that do not follow the standard format. For example, I would like to have 2 characters for the chain identifier, larger residue serials, etc. Does anyone know if this is possible? I apologise if similar question has been asked before, but I

RE: [PyMOL] load pdb files of non-standard format

Ioannis, The PDB format and PyMOL both support the 4-character segment ID (segi) field as an alternative to the increasingly inadequate 1-character chain ID. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd

Re: [PyMOL] non-pdb coordinate help

On Mon, Oct 24, 2005 at 10:18:40AM -0500, Kristl Adams wrote: I have several txt files of coordinates (mostly heme type compounds) that I'd like to format correctly for pymol to be able to read. I've tried several things looking at PDBs with hemes, but can't figure it out. Will someone

[PyMOL] non-pdb coordinate help

I have several txt files of coordinates (mostly heme type compounds) that I'd like to format correctly for pymol to be able to read. I've tried several things looking at PDBs with hemes, but can't figure it out. Will someone with more experience please show me how this should be formatted

Re: [PyMOL] non-pdb coordinate help

Hi Kristl, The pdb-file is column formatted. You can find a specification of the file format at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html The easiest is to write a python script to do the conversion. Hope it helps, Tsjerk On 10/24/05, Kristl Adams

Re: [PyMOL] Creating PDB files from Primary Sequence

Hi folks, * Warren DeLano war...@delsci.com [2005-08-10 16:41] wrote: James, PyMol would allow one to enter a peptide sequence (generally short in length) to create a template structure that can then be used Just hold down ALT/OPTION and type in the peptide sequence. The numbering

Re: [PyMOL] Creating PDB files from Primary Sequence

Hi pymolers is it possible to generate a template nucleic acid structures from sequence in pymol? Blanton Tolbert PhD Candidate University of Rochester Biophysics and Structural Biology 575 Elmwood Ave Rochester, NY 14642 Blanton Tolbert PhD Candidate University of Rochester Biophysics

Re: [PyMOL] Creating PDB files from Primary Sequence

Hi, I just felt like making a correction to the language I used. It seems a few words went missing! * Robert Campbell r...@post.queensu.ca [2005-08-11 11:28] wrote: I had already written a script to do this, but making it easier to specify the exact phi/psi angles to use. I borrowed bits of

Re: [PyMOL] Creating PDB files from Primary Sequence

Hi Blanton, * Blanton Tolbert blanton_tolb...@urmc.rochester.edu [2005-08-11 11:53] wrote: Hi pymolers is it possible to generate a template nucleic acid structures from sequence in pymol? Not as far as I've found. There are other programs that can do this: B (aka Biomer)

[PyMOL] Creating PDB files from Primary Sequence

Hello, This may be slightly off-topic, but I was wondering whether PyMol would allow one to enter a peptide sequence (generally short in length) to create a template structure that can then be used for structural refinements (minimizations, etc.) elsewhere. If PyMol cannot do this, is

RE: [PyMOL] Creating PDB files from Primary Sequence

James, PyMol would allow one to enter a peptide sequence (generally short in length) to create a template structure that can then be used Just hold down ALT/OPTION and type in the peptide sequence. The numbering will be arbitrary, but at least you'll have something to work with.

Re: [PyMOL] Creating PDB files from Primary Sequence

Hi James, Sounds like you want a homology model type set up, ie generate coordinates based on a template. Modeller can do this and an easier way is via the swissmodel http://swissmodel.expasy.org//SWISS-MODEL.html If however you want a relatively random structure then pymol _can_ do this.

Re: [PyMOL] Creating PDB files from Primary Sequence

Thanks for the prompt responses, Warren and Joe! Works like a charm! Now, I just wish that my Kensington Expert Mouse could function as a true three button mouse...is there a keystroke that mimics the third mouse button? Thanks again, james

[PyMOL] changing pdb files during a movie

Hi, I am trying to show different pdb files successively in a movie, loading the first and displaying certain residue contacts, then dropping it and loading the second, etc... Is this possible? If so, how do I drop a file? Any advice would be greatly appreciated. Thanks. Nadine

RE: [PyMOL] changing pdb files during a movie

Nadine, The way you'd do this PyMOL is by either loading multiple PDB files into PyMOL as molecular states and then playing through them sequentially, or by loading multiple objects and turning them on and off sequentially. Cheers, Warren -- Warren L. DeLano, Ph.D

[PyMOL] Re: pdb-l: protein visualization/interaction tools?

Hi Marty, Sorry if this misses your point, but it is possible to translate molecules independantly in pymol: http://sourceforge.net/mailarchive/message.php?msg_id=11658301 However, that won¹t help if you want to show overlap. To do this, you would have to repeatedly call translate and

[PyMOL] RE: pdb loader service

is it possible to use the pdb loader in a *.pml style script? With the shipped plugin it may be hard. I wrote the original, but have since written a new/improved one that does not tough the filesystem and adds a remote command that will fetch and load pdbs as well. You can see the code for

[PyMOL] Re: PDB-Codes

Dear Christian, Summary: From within the same PyMOL instance, the command pdb 1n1m works, but the script from pymol import cmd time.sleep(1) list = ('1n1m') for strc in list:     pdb strc does not. (IMO, the import is not necessary here). Analysis: You use the code above as a PyMOL .pml

[PyMOL] Does (PDB) size really matter? (Jason Vertrees)

Hi Warren and Jason. I've playing around once with nice movies but memory has been a problem. Now I got a dual Athlon with 2Mb Ram, but didn't test it yet, I'm afraid (such server cannot stop :-). Warren, you really have a great software and I really want to do with it what I've done with

RE: [PyMOL] Does (PDB) size really matter?

... http://delsci.com/img/scene1_final.jpg Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jason Vertrees Sent: Saturday, April 24, 2004 11:03 PM To: PyMol Users List Subject: [PyMOL

[PyMOL] Does (PDB) size really matter?

Warren, Thanks! I was setting 'hash_max' higher and higher (but my memory monitor always showed at least 90 megs free at the least). I'll try the lower hash_max; I'll try lower this time. I think we have a really great movie in the works, and as I play with PyMol more and more, I can make much

[PyMOL] Does (PDB) size really matter? (Help!)

PyMolers, Our setup is a Dual Xeon 3.2 GHz 1GB RAM and Nvidia Quadro running PyMol 0.95. (Also available, Dual Opteron 240 64-Bit Linux w/0.95 w/1 GB RAM w/same problems.) We are trying to render a nifty movie but can't. PyMol keeps crashing during the render process. The scene had originally

RE: [PyMOL] Does (PDB) size really matter? (Help!)

: Tzintzuni Garcia I.; Roger B. Sutton Subject: [PyMOL] Does (PDB) size really matter? (Help!) PyMolers, Our setup is a Dual Xeon 3.2 GHz 1GB RAM and Nvidia Quadro running PyMol 0.95. (Also available, Dual Opteron 240 64-Bit Linux w/0.95 w/1 GB RAM w/same problems.) We are trying to render

[PyMOL] local PDB updates

Hello, There is a script which accesses a PDB server to get the weekly update lists of PDB structures. It downloads the new and modified structures and can be run as a cronjob under Linux. The script is freely accessible from http://www.rubor.de/bioinf/ Cheers, Kristian Rother