RE: [PyMOL] nmr ensemble alignment
Doug, As far as I know there isn't any resource online, so I'll try to answer your questions here: PyMOL does not automatically align structures. intra_fit is presumably the command you're looking for to do this, since you're placing models are in one object. intra_fit name ca, 1 would for example align all of the models to the first model using alpha-carbon coordinates. intra_fit resi 10-15, 1 would align all models to the coordinates of atoms in residues 10-15. As far as RMS statistics go, PyMOL may be the best tool for this yet, since it doesn't current have the ability to generate statistics for the ensemble. What statistics in particular would you like it to provide? Also note that if you have you ensemble in a multiple-model pdb file (with MODEL and ENDMDL records), you can just load it in one command load ens.pdb Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Douglas Kojetin Sent: Monday, January 26, 2004 11:22 AM To: pymol Subject: [PyMOL] nmr ensemble alignment Hi All- Will reading in a structural ensemble load pdb01.pdb, ens load pdb02.pdb, ens ... ... automagically align the structures? If not, do I need to run another command, such as ' intra_fit (name ca) ' ? Or should I use normal 'fit'? Also, what is the best method for determining the RMS of the ensemble? There are a few commands in the reference manual (rms, rms_cur, intra_rms, intra_rms_cur), and I'm confused as to which is best for structural ensembles. Or, to save typing, is there a current web resource for using PyMOL with NMR models (with hints, scripts, etc.)? One thing I /miss/ from MOLMOL is the 'sausage' display -- has anyone implemented this in PyMOL yet? Thanks, Doug --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] How to send pymol command to pymol by python interpreter
Takefumi, You only need to worry about this if you're using an external Python interpreter with a modular build of PyMOL. For example, after installing a late-model linux PyMOL RPM, you run python script.py Where script.py contains the following sequence: import pymol pymol.finish_launching() which is needed to insure that PyMOL's API in the parallel thread is defined ready to receive messages. The problem is that PyMOL can't launch until import pymol completes and returns and __main__.pymol is defined. However, that means that the next command in your script will need to be executed before PYMOL has had a chance to initialize itself. So the current approach is to launch the PyMOL thread, and then call a function which blocks until PyMOL is all ready to go... Cheers, Warren [PS If there's anyone out there with a more elegant alternative for launching the PyMOL thread from a standalone Python script, I'd sure like to hear it : )]. -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Takefumi Sora Sent: Wednesday, January 21, 2004 10:57 PM To: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] How to send pymol command to pymol by python interpreter Hi. I appreciate your answer, Warren. Thank you. Please let me ask one more question. You said I need two lines first: import pymol pymol.finish_launching() As long as I use,I can't the role of pymol.finish_launching() if I don't call this, what troubles will happen ? Takefumi SORA --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Ray Tracing Crash
Morri, The RH9 Patch is described and published on: https://rhn.redhat.com/errata/RHBA-2003-136.html I would not expect Debian to suffer from the same crash. If it does, then we may be dealing with a genuine bug in PyMOL (assuming that you're not simply running out of RAM). With respect to Debian, in order to debug the problem, you might want to send me a PyMOL session file which crashes on your system when the next command issued is ray. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: Morri Feldman [mailto:morrifeld...@yahoo.com] Sent: Tuesday, January 20, 2004 10:36 PM To: Warren L. DeLano; 'Matt Franklin'; 'Morri Feldman' Cc: 'pymol-users' Subject: RE: [PyMOL] Ray Tracing Crash Warren and Matt, Thanks so much for your help. I must be using the stock glibc because set max_threads, 1 allows me to ray trace without crashing. I will tell my system administrator to patch glibc. Do you know where I should look for the patch? My debian/testing system at home also has trouble ray tracing especially sticks. When it fails I get a segmentation fault. Is my problem at home also due to an unpatched glibc? The error message is: /usr/bin/pymol: line 7: 32460 Segmentation fault python /usr/lib/python2.3/site-packages/pymol/__init__.py $* Thanks for creating such a great program, Morri --- Warren L. DeLano war...@delanoscientific.com wrote: Morri, (First, thanks Matt for the great diagnostic advice!) This sounds to me like a potential threading deadlock, possible due to the broken threading in RedHat 9. Are you using the stock version or have you patched glibc? If you haven't patched your RedHat 9, then one way to be sure this is the problem is to set max_threads, 1 before issuing the ray command. If PyMOL doesn't hang, then you've found the culprit. If have already patched your RH9, then let's do some more work to determine what's going on... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Matt Franklin Sent: Tuesday, January 20, 2004 6:25 PM To: Morri Feldman Cc: pymol-users Subject: Re: [PyMOL] Ray Tracing Crash Morri Feldman wrote: I am running pymol .93. When I try to ray trace a scene, the gui shows a white status bar that moves halfway across the screen and then freezes. After this the GUI is frozen and must be killed. No error messages are shown. The computer is running RedHat 9 and has 4 processors. Has anyone else experienced this problem? Do you have any solutions? This message may double post because I accidentally tried to post it from my other email account. Sorry Thanks, Morri Morri Feldman Hi Morri - The progress bar for raytracing doesn't move linearly - the first half of the bar is covered fairly quickly, then more slowly, then very slowly, then the last fifth is usually covered in one jump. Are you sure you just aren't being impatient? Try raytracing a very simple scene, like a single amino acid in spheres mode, to see if it hangs then. Also try raytracing parts of your scene in case some funny bit of your molecule is causing this problem. Finally, try reducing the complexity of your surfaces and/or spheres: set surface_quality, -1 (0 is the default). Feel free to contact me directly - I'm local! (Although Warren will be more helpful...) - Matt -- Matthew FranklinPhone:(650)225-4596 Postdoctoral Researcher Fax:(650)225-3734 Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080 --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https
RE: [PyMOL] Ray Tracing Crash
Morri, (First, thanks Matt for the great diagnostic advice!) This sounds to me like a potential threading deadlock, possible due to the broken threading in RedHat 9. Are you using the stock version or have you patched glibc? If you haven't patched your RedHat 9, then one way to be sure this is the problem is to set max_threads, 1 before issuing the ray command. If PyMOL doesn't hang, then you've found the culprit. If have already patched your RH9, then let's do some more work to determine what's going on... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Matt Franklin Sent: Tuesday, January 20, 2004 6:25 PM To: Morri Feldman Cc: pymol-users Subject: Re: [PyMOL] Ray Tracing Crash Morri Feldman wrote: I am running pymol .93. When I try to ray trace a scene, the gui shows a white status bar that moves halfway across the screen and then freezes. After this the GUI is frozen and must be killed. No error messages are shown. The computer is running RedHat 9 and has 4 processors. Has anyone else experienced this problem? Do you have any solutions? This message may double post because I accidentally tried to post it from my other email account. Sorry Thanks, Morri Morri Feldman Hi Morri - The progress bar for raytracing doesn't move linearly - the first half of the bar is covered fairly quickly, then more slowly, then very slowly, then the last fifth is usually covered in one jump. Are you sure you just aren't being impatient? Try raytracing a very simple scene, like a single amino acid in spheres mode, to see if it hangs then. Also try raytracing parts of your scene in case some funny bit of your molecule is causing this problem. Finally, try reducing the complexity of your surfaces and/or spheres: set surface_quality, -1 (0 is the default). Feel free to contact me directly - I'm local! (Although Warren will be more helpful...) - Matt -- Matthew FranklinPhone:(650)225-4596 Postdoctoral Researcher Fax:(650)225-3734 Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080 --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] homologous alignments?
Camille, If I understand your question, you're looking for the setting which creates a discrete color transition at the edges of helices and strands, instead of blending. It is: set cartoon_discrete_colors, on For example color grey, name ca color yellow, ss s and name ca color red, ss h and name ca set cartoon_discrete_colors, on Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of cami...@mrc-lmb.cam.ac.uk Sent: Monday, January 19, 2004 7:37 AM To: Warren L. DeLano Cc: 'Michael Bovee'; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] homologous alignments? Hello, I am unable to read the archive at the moment so can anyone tell me the command that allows colouring of the edge of helices and strands (usually grey). I think this was posted recently but I don't have it in any of my saved scripts. Many thanks, Camille Dr Camille Shammas Medical Research Council Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK. Tel: +44 (0)1223 402407 Mobile: 07812035842 E-mail: cami...@mrc-lmb.cam.ac.uk --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] working directory
Lesley, If you always want PyMOL to start in a different directory, you can create a .pymolrc file in you home directory with a command like cd /users/lesley/scripts Which will be executed every time you start PyMOL. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Lesley Debono Sent: Sunday, January 18, 2004 11:56 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] working directory i have pymol installed on an OSX machine. When I begin pymol i am in the root (\) directory. My scripts are in a different directory. Is there a way I can begin in another directory when starting Pymol? cheers Lesley --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] mouse
Thierry, This behavior could be the symptom of either malfunctioning OpenGL, or a screen with two few colors to support color-encoded picking (which is what PyMOL uses behind the scenes). Please confirm that your display is running in 24 or 32 bit color. If that is the case and picking still fails, then please try saving a png file of what you see on the screen (png filename.png). If that PNG file exhibits any distortion or artifacts, then that's the cause of the problems. Otherwise, PyMOL may have a bug... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Thierry Granier Sent: Friday, January 16, 2004 12:52 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] mouse Good morning, I am trying to use pymol on a PC linux RedHat 9.0 using the software summit 2.2 of Xig, and I run into the following problem: after loading a molecule, when I try to click on an atom, for selection, using CTRL shif lb or CTRL shift lb, I get the message no atom found nearby I have tried all the mouse settings from the gui with no success. Any help will be appreciated, thank you Thierry Granier. --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Restrict surface transparency to limited region
Roger, This isnt possible right now. The only way to do it is to create two objects, surfacing different atoms in each object, and then enabling transparency in just one of the two objects. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Roger Dodd Sent: Wednesday, January 14, 2004 4:49 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Restrict surface transparency to limited region Dear PyMOL users/devs, I am trying to produce a figure with a molecular surface and would like to make this surface transparent only covering certain residues. I have tried creating a separate surface for these residues and the rest of the protein and setting transparency for the object covering only those residues, but this gives a very discontinuous looking surface representation. Is it possible to just enable transparency on a limited region of a surface? Thanks Roger -- Roger Dodd CIMR University of Cambridge Wellcome Trust / MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 2XY
RE: [PyMOL] build instructions
Steve, Although static building isn't supported by us, and although we make no guarantees that the static launch process won't change drastically without warning and at any time, you may wish to consult setup/Rules.linux-semistat-py22 for an example. The trick with static builds is that PyMOL needs to do a bunch of magic to get the environment right before the Python interpreter gets going and Tkinter starts up. Also note that you need to provide static builds of all of the external dependencies in order to generate a truly portable static build. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Steven F. Killen Sent: Tuesday, January 13, 2004 12:37 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] build instructions Greetings, I'm trying to build pymol statically (instead of as a Python module) and the documentation doesn't seem to have the options listed for the variables in the Makefile. Is there somewhere I may not be looking? -- Steve Killen skil...@umbc.edu --- This SF.net email is sponsored by: Perforce Software. Perforce is the Fast Software Configuration Management System offering advanced branching capabilities and atomic changes on 50+ platforms. Free Eval! http://www.perforce.com/perforce/loadprog.html ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] DeLano Scientific Closed Until Jan 7, 2004.
PyMOL Users, This is the final reminder that I am now off-line and away from DeLano Scientific (which will be closed) until January 7th. Everyone please have a wonderful holiday and a Happy New Year! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] Question
Avram, set cartoon_highlight_color, red Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of slo...@mail.med.upenn.edu Sent: Friday, December 19, 2003 11:38 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Question Hi, does anyone know how to color the inside of helices a different color than the outsides? thanks Avram -- Avram M. Slovic Biochemistry and Molecular Biophysics University of Pennsylvania 420 Curie Blvd. 1010 Stellar Chance Bldg. Philadelphia, PA 19104 L:215-898-3496 --- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278alloc_id=3371op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Display of electrostatic potential surfaces
Roger, The problem with computing electrostatic maps in PyMOL currently is that the Coulomb equation assumes a uniform dielectric and thus doesn't give you correct potentials for macromolecules. It is much better to use an external tool such as Grasp, MEAD, APBS, or Delphi, which can apply a different dielectric constant to the inside of the protein than to the surrounding solvent. Yes, PyMOL can compute a Coulombic map using the approach you've outlined if partial charges have been assigned - but there isn't a good way to do that in PyMOL just yet. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Roger Dodd Sent: Thursday, December 18, 2003 3:53 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Display of electrostatic potential surfaces Dear PyMOL users, I would like to generate a figure of my protein where the surface electrostatic potential is displayed. PyMOL now comes with a demo function for display of such a surface. However, when I apply the commands used in this demo, i.e. cmd.set(coulomb_dielectric,80.0) cmd.map_new(e_pot,coulomb,1.0,pept,5) cmd.ramp_new(e_lvl,e_pot,[-3.6,-1.6,0.4]) cmd.set(surface_color,e_lvl,pept) cmd.refresh() to the model from my pdb file, I get a uniformly blue surface. I believe this must be due to the lack of assignment of partial/formal charges to the atoms in the pdb file. So, my questions are: 1. Is it possible to automatically assign the correct charges to atoms within PyMOL 2. If not, is there a program that will do this and if so can the output from this program be understood by PyMOL in some way. Thanks for your help Roger -- Roger Dodd CIMR Addenbrooke's Hospital Cambridge
[PyMOL] RE: 3-button mice
Chris, I hereby nominate the Targus PAUM01U as the official 3-button mouse for PyMOL users on the go. http://www.targus.com/us/product_details.asp?sku=PAUM01U They might be too small for some, but they work great for me, at home and on the road! (plus, they color-coordinate with Ti PowerBooks) Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- Sent: Thursday, December 18, 2003 5:45 AM To: war...@delanoscientific.com Subject: pymol Hi, I plan to update the website (http://www.macinchem.fsnet.co.uk) over the Christmas Break and one question I'm often asked is which 3-button mouse should I use for PYMOL under MacOSX? Any suggestions? Thanks Chris
RE: [PyMOL] unsetting cartoon_colors
David, For settings such as cartoon_color, surface_color, mesh_color, the default value is -1. set cartoon_color, -1 or set cartoon_color, -1, object-name will restore the color. Thanks for pointing out that: set cartoon_color, default doesn't work! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A. Horita Sent: Thursday, December 18, 2003 10:50 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] unsetting cartoon_colors Hi all, I have a collection of molecules and want to color a particular helix (in cartoon mode) a specific color different from other helices. Unfortunately, I had previously set cartoon_color from default to another color, so now specifying a color for that helix (or even color red, ss h) has no impact. (it does change the color of the Calpha, but not the cartoon itself). So, the question is, how do I unset the cartoon_color variable (without wiping out my scene)? The variable setting comes with the .pse file, set cartoon_color, default gives an error about not knowing what color default is. Thanks, Dave Horita - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/
[PyMOL] RE: Stereo on G4 Laptop?
Doug, Yes, I just confirmed that PyMOL on a Mac 17 G4 PowerBook can drive stereo using the StereoGraphics SVGA display adapter with an external monitor. I would expect any G4 PowerBook to be able to do this. The command line way to launch in stereo mode is given below. /Applications/PyMOL.app/Contents/MacOS/PyMOL -BGS Alternative, you could simply click on the PyMOL Stereo icon in the Demos folder. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- Sent: Monday, December 15, 2003 11:16 AM To: war...@delanoscientific.com Subject: Stereo on G4 Laptop? Dear Warren, I am a crystallographer from the university of oregon. I am considering purchasing a G4 laptop and was wondering if you had used the crystal eyes from Stereographics on a vga monitor plugged into one of these laptops. Thanks, Doug
RE: [PyMOL] expand to molecule (by connectivity)
Michal, This capability is not in PyMOL yet as a selection operator, but if you issue edit on a single atom, then the resulting pkchain selection will contain that atom and all covalently attached atoms. edit 14/ca color red, pkchain unpick Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Michal Bozon Sent: Saturday, December 13, 2003 7:25 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] expand to molecule (by connectivity) Dear pymol experts, I wonder if there's a simple way how to select a molecule (or expand the selection to molecule) by connectivity. I mean the case there if there are more molecules in the object and I want to select one of them and create a new object from it in order to change it's properties. 'Byres' and similar seleciton operators do not work. thanks, Michal Bozon --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (not working yet)
Michael, Impressive! I think you're one of the few people to delve into PyMOL's source like this. Obviously I'd be the best person to look at your code, but I'm crunched right now getting ready for this upcoming trip. Also, if the code is GPL-contaminated, then it can't be useful in the main version, but perhaps we can rewrite this cleanly later on. I can probably help you in January. What you've written sounds right... One thing I'd suggest for debugging in the meantime is that you use the isomesh or isosurface routines to explore what data is ending up in the Map, before trying to use the color ramps. There may also be some code in the chempy brick stuff which could serve as an example for populating the list. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] assign secondary structure?
Michael, Unfortunately PYMOL/dss doesn't generate quite enough information to recreate PDB SHEET and HELIX records. PyMOL (like other programs) simplifies the secondary structure concept down to a per-residue property. There is no such thing as a sheet or helix in PYMOL, but merely sets of proximal residues with a secondary structure property (ss) of 'H' or 'S'. load object-name.pdb hide show cartoon dss object-name Should be sufficient to get you a secondary structure representation for any protein. States represent multiple conformations -- you shouldn't need to worry about them Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Michael Bovee Sent: Thursday, December 11, 2003 1:38 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] assign secondary structure? Hi, I have a 'raw' pdb file of atom coordinates only, and I'm hoping to use the dss command in pymol to get helix and strand designations that I can paste back into the header space of the pdb so that I can model fancy helices and strands and so forth to get a nice picture in pymol. Then I can superpose features with homologous proteins for which this header info is available. I just didnt want to modify or create this header info 'by hand' if I didn't have to... But, I can't get dss to work in pymol (even the refman warns that this algorithm has not been rigorously validated). The refman says USAGE is dss selection, state Does this mean I need to first make a selection that encompasses some part (or whole) of the molecule, or should this work on the entire pdb? I don't know what 'states' are so I just opted for '0' which is supposed to mean 'all states'. Thanks, --Michael Bovee --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] electron density settings
Robert, If you're using version 0.93 or greater, set mesh_width, value will adjust the mesh thickness in units of pixels. Something in the range of 1.5-2.5 usually works best. set mesh_width,2.0 ray If you're using an older version, you'll need to set mesh_radius instead, which is in angstrom units. To display the density around a ligand, create a mesh using the carve option. load map.ccp4 load protein.pdb load ligand.pdb isomesh m1, map, 1.0, ligand, carve=2.1 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Robert Sent: Wednesday, December 10, 2003 2:55 PM To: 'Warren L. DeLano' Cc: pymol-users@lists.sourceforge.net Subject: [PyMOL] electron density settings Hi there, 1. How can I reduce the density-map line thickness in the ray-traced image? 2. Is there a way to just display the density around a ligand many thanks robert Robert Schwarzenbacher, PhD The Joint Center for Structural Genomics phone: 858 822 3637 --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] DeLano Scientific Downtime (Dec. 22-Jan 7)
PyMOL Sponsors and Users, Please be advised that due to vacations, travel, and participation in the CCP4 study weekend, DeLano Scientific LLC will be officially closed from December 21st through January 7th. Sporadic email communication may be possible before Dec. 24th and after Jan. 3rd, but essentially all other business functions (phone, fax, quotes, invoices, receipts, etc.) will remain unavailable until after the 7th. During the break, please direct all PyMOL questions to the mailing list where your peers may be able to assist you. Also, please be sure to have yourself a wonderful holiday season and a happy new year! If there are any budgets out there with end of year money that simply must be spent, DeLano Scientific would be glad to process your PyMOL purchases and support subscription renewals prior to the 19th of December. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] Unable to read Gamess-US output
Jerome, Generally speaking, PyMOL doesnt read any GAMESS formats, although there is some code in the chempy modules which at one time could submit and retrieve output from a few simple GAMESS-US calculations. My advice would be to find another tool better suited for Quantum chemistry applications. But if you still want to use PyMOL, then you'll need to convert your files into something like .mol or .pdb... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Jerome Levesque Sent: Friday, December 05, 2003 8:37 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Unable to read Gamess-US output Hello, I am using GAMESS-US (not PC-GAMESS) on Linux to model very small molecules. When I try to load a GAMESS .dat file into PyMOL, it does not complain at all, but does not show anything either. There isn't even a new object appearing in the right part of the PyMOL visualization window. I find this behaviour somewhat strange, since it seems to be specific to my .dat files and do not even occur when I try to load silly files, such as jpegs for example. Even in such silly cases, a new object will appears in the list (but not for my GAMESS .dat files!) Thanks in advance for any help, Jérôme Levesque -- Jérôme Levesque, Ph.D. student Femtosecond Research Program National Research Council 100 Sussex drive, room 2044 Ottawa, ON K1A 0R6 Canada tel.: 613-998-9468 fax.: 613-991-3437 --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] More on A Few Good MacPyMOL OS X Beta Testers
and improve in synchronization with the cross-platform open-source version. The beta test remains open through January for those who meet the six qualifications. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] Object orientation matrices
Laurence, Sort of. Right now PyMOL doesn't fully support translations of individual objects by independent matrices, but you can translate their representations by a matrix for animation purposes using translate and rotate with the object argument. However, you can cleanly transform the atoms in an object. See print cmd.transform_selection.__doc__ for details on the matrix used for that. The object matrix system is just about due for an overhaul -- we need more flexibility than is currently provided... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Laurence Pearl Sent: Tuesday, December 02, 2003 5:47 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Object orientation matrices Is there any way of accessing the matrices that define the orientation and position of an individual object relative to the world in PyMol in the same way that get_view and set_view do for the overall view matrix ? -- Laurence H. Pearl Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Phone +44-207-970 6045 : Secretary +44-207-970 6046 FAX +44-207-970 6051 : E-Mail laurence.pe...@icr.ac.uk -- Live Simply and do Serious Things .. - Dorothy Crowfoot Hodgkin -- --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] cannot 'fit' a particular pdb file
Michael, Try align... Fit only works when all of the atom identifiers match. Align matches atoms through a 1D alignment and then performs some optimization: align TtHisRSca, EcHRSadeca align SaHRSca, EcHRSadeca Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Michael Bovee Sent: Tuesday, December 02, 2003 11:17 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] cannot 'fit' a particular pdb file Hi, I have loaded 3 pdb files of homologous forms of an enzyme. The 'fit' command works for superimposing/aligning two of them, but the third file always gives a No Atoms Selected error. Is there something in the pdb file I can fix? As a general rule now, I Hide Everything at first and then Show Lines as I begin with a new PyMOL session. I can see all three molecules, just can't align the third one (EcHRSade) with the first two (TtHisRS and SaHRS). PyMOLfit TtHisRS, SaHRS Executive: RMS =4.222 (718 to 718 atoms) PyMOLfit TtHisRS, EcHRSade ExecutiveRMS-Error: No atoms selected. PyMOLfit EcHRSade, TtHisRS ExecutiveRMS-Error: No atoms selected. PyMOLfit EcHRSade, SaHRS ExecutiveRMS-Error: No atoms selected. Thanks, --Michael --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Clarification on A Few Good MacPyMOL OS X Beta Testers
with the cross-platform open-source version. The beta test remains open through January for those who meet the six qualifications. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] Viewing homotetramers with PyMol
Rene, The problem is that each biological unit copy in the PDB is handled as a separate molecular state (i.e. a movie), which then become distinct states in PyMOL. Hit play to see what I mean. To solve this, the most recent versions of PyMOL can split multi-state objects into multiple single-state objects automatically: load 1f41_tetra.pdb split_states 1f41_tetra dele 1f41_tetra With older versions, you'll need to create the new objects manually load 1f41_tetra.pdb create 1f41_tetra_1, 1f41_tetra, source_state=1, target_state=1 create 1f41_tetra_2, 1f41_tetra, source_state=2, target_state=1 dele 1f41_tetra Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of René Wuttke Sent: Tuesday, December 02, 2003 1:08 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Viewing homotetramers with PyMol Hi everyone, I am quite new to PyMol and structural biology as well, since I am still a student. I installed PyMol via Fink on my iBook running Panther 10.3.1. I want to view the homotetramer of the TTR-protein. I got it from the PDB (PDB-id: 1f41). The asymmetric unit is a dimer. But the assumed biological molecule is the tetramer. One can download the coordinates of this molecule. But when I try to load it in Pymol, only the dimer shows up. I am quite sure that this file should contain the right coordinates, because the origin of rotation differs between the tetramer file and the dimer file. How can display the other dimer? This is necessary in particular, because i am supposed to examine the loops which mediates the dimer-dimer-interaction. Do you want me to send the coordinates file to the list? Thanks in advance and please apologize my bad english, René Wuttke --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] residues deviate from protein secondary catoon representation
(becoming an FAQ) For starters, set cartoon_smooth_loops, off set cartoon_flat_sheets, off If that doesn't meet your needs, then you'll need to split your object into separate objects to get the desired effect of mixing smoothed and non-smoothed cartoons. Thankfully, the next version will provide an easier workaround for this... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Yunfeng Hu Sent: Tuesday, December 02, 2003 1:57 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] residues deviate from protein secondary catoon representation Dear pymol users, I am trying to show some residues in sticks while the whole protein is in cartton representation. However I find that some residues do not attach to the cartoon at all. I understand that the secondary cartoon is an approximation along the backbone. Is there a way that I can show at least those residues are anchored in the cartoon? Thanks. Yunfeng --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] detecting the existence of a selection
Tina, Use the Python in operator selection-name in cmd.get_names(selections) PyMOLprint foo in cmd.get_names(selections) False PyMOLselect foo, all Selector: selection foo defined with 1631 atoms. PyMOLprint foo in cmd.get_names(selections) True Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Tina Li Sent: Monday, December 01, 2003 11:50 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] detecting the existence of a selection Hello, I wonder if there is a quick and simple way of detecting whether a selection exists without triggering any errors. e.g. to check if there are currently any atoms picked (and collect the residue IDs if there is any), I do: cmd.iterate((lb),stored.list.append((resi))) if no atoms were picked, I would see the alarming error messages: Selector-Error: Unknown keyword or selection. Selector-Error: Malformed selection. ( ( lb-- Is it possible to suppress them and still get the result? Thanks in advance! Tina --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] A Few Good Mac PyMOL OS X Beta Testers
Mac Users: I have something new in the works for OS X/Aqua and need some beta testers for the next couple of months. Specifically, I am looking for users who: 1) have experience with full PyMOL (under Fink, X11, or Windows). 2) are current PyMOL sponsors/subscribers. 3) are running OS X 10.2.8 or 10.3. 4) have QuickTime 6.4 installed. 5) would value a Mac-enhanced PyMOL derivative. 6) don't mind closed-source software. If you meet all of these qualifications, please email me. If you don't, then please sit tight for now -- more information will be forthcoming in January. Thanks, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] electron density settings
Igor is right. However, there is a new command in recent versions map_double map-name that will cut the map spacing in half by interpolating a new map via trilinear interpolation. This will generate a map with 2^3 = 8-fold more grid points (and require 8X more RAM!) load map1.ccp4 map_double map1 isomesh mesh1, map1, 1.0 will generate a mesh with half the spacing of the original map. Note that map_double can usually only be used once on a given map before averaging artifacts appear. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Igor Pechersky Sent: Tuesday, November 25, 2003 7:23 AM To: mwilke Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] electron density settings mwilke mwi...@interchange.ubc.ca: Does anyone know how to alter the isomesh settings? I'm trying to prepare a figure with pretty electron density and would like to be able to decrease the gap size of the mesh. I found the variables that seem to make sense like mesh_quality and min_mesh_spacing, but changing these variables doesn't seem to do anything. mesh_width and mesh_radius only control the thickness of the mesh lines. Mark, you are correct, saying that mesh_quality and min_mesh_spacing have nothing with isomesh. They are used only for surface maps (RepMesh). For map-based mesh, PyMOL uses dimension from the density map itself, without smoothing interpolations. So, to increase visual toughness of your isomesh, you should just load more fine-grained density map... As a visualization trick, one might try to play with the set of isomeshes, based on the same density map and slightly differentiated by level, like this: isomesh mesh1, map1, 1.0 isomesh mesh2, map1, 1.25 isomesh mesh3, map1, 1.50 isomesh mesh4, map1, 1.75 isomesh mesh5, map1, 2.0 and then color them differently. BTW, even with RepMesh you can't decrease gap size (via min_mesh_spacing) less than some hard lower threshold - roughly, it is equivalent to 80 lines per maximal dimension of the surrounding box for the underlying object. mesh_quality deals rather with the level of icosahedron approximations for spheres... --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] dss ribbon representation
There is one other convenient format: .pkl, that works like PDB, but is a Pickled copy of the PyMOL Model Class. The main advantage this has over .pdb is that it saves and restores extra properties such as secondary structure code, atom types, van der waals radii, formal and partial charges, etc. load myprot.pdb dss show cartoon alter 100-110/, ss='H' alter 65-67,ss='L' save myprot.pkl ... quit program, complete your PhD, take a vacation, and come back... load myprot.pkl show cartoon will work. .pkl has the additional advantage of being a simple molecular object useful in straight Python, outside of PyMOL. All you need to do is have a copy of PyMOL's chempy module available in your PYTHONPATH from chempy import io model = io.pkl.fromFile(myprot.pkl) for atom in model.atom: print atom.name Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Igor Pechersky Sent: Friday, November 14, 2003 3:07 AM To: andr...@biochem.utah.edu; Andreas Foerster Cc: pymol Subject: Re: [PyMOL] dss ribbon representation Andreas Foerster andr...@biochem.utah.edu: - The dss algorithm is great, a very quick way to assign secondary structure. Is there a way of conserving the information when saving the pdb? There are at least 3 ways to store SS assignments from PyMOL. Depends on your needs: 1. Save PyMOL session (*.pse). Atom properties, including ss, will be restorable by PyMOL. 2. Print SS in PHD-like format. So, assuming that unfamous 1tii.pdb is loaded PyMOLimport pymol PyMOLstored.ss = [] PyMOLiterate 1tii//a//ca, stored.ss.append(string.ljust(ss,1)) PyMOLprint string.join(stored.ss,) will print single string like LSSLLLHHHLHHLLLSLL LLL LSSSHLLHHHLLHHHLSSSLLL LLLHHHLLLLL HLLHHHLL 3. Wait for Warren to vivify cSetting_save_pdb_ss :) Sometimes it's nice to edit the assignment. I haven't understood your question. You might edit dss assignment just by PyMOLalter pk1, ss='S' Is it sufficient? -igor --- This SF.Net email sponsored by: ApacheCon 2003, 16-19 November in Las Vegas. Learn firsthand the latest developments in Apache, PHP, Perl, XML, Java, MySQL, WebDAV, and more! http://www.apachecon.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] RE: Stereo parameters, again
I still do not understand your stereo parameters: the stereo_angle should define the rotation (around the y-axis) between the pictures for the left and right eye, whereas the stereo_shift should define whether the origin or midpoint of the picture is within the plane of the screen or in front of or behind it. However, changing the settings of these parameters lead to completely unexpected results: setting the stereo_shift to 0 and the stereo_angle to 3.0 results in a mono picture with no separation at all, whereas setting the stereo_shift to 3.0 and the stereo_angle to 0 leads also to a mono picture shifted to the back. So, could you please check this and maybe explain it again to me? After looking back at the code, I realize that these parameters are perhaps misnamed. These are not the rotations of the objective, but rather parameters input into the stereo equations. stereo_shift is the separation between the two cameras observing the image, expressed as a % of the distance from the objective. stereo_angle is a scaling factor applied to the natural angular difference which would occur between two eyes at that distance, both looking at the objective. Generally speaking stereo_shift is the main depth control parameter, and stereo_angle should remain close to 2 in order to generate correct stereo geometry. However, adjusting stereo_angle can reduce ghosting and change the apparent Z location of the objective. Detting stereo_shift to zero makes you a Cyclops (you're basically telling PyMOL that your eyes are superimposed). The defaults are: PyMOLget stereo_shift, get: stereo_shift = 2.0 PyMOLget stereo_angle, get: stereo_angle = 2.1 which are tuned to minimize CrystalEyes ghosting in the foreground. The actual translation(+/-) and rotation(+/-) of the camera at distance are: translation = distance * (stereo_shift/100) rotation = (stereo_angle/2) * (arctan(stereo_shift/100)) (default = +/- 1.2 deg) If you want a stronger stereo effect, set stereo_shift to 3, 4, or 5 (resulting in rotations of 1.8, 2.4, and 3.0 degrees, respectively). Cheers, Warren
RE: [PyMOL] Reference
http://pymol.sourceforge.net/faq.html#CITE -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Chris Sent: Tuesday, November 11, 2003 1:29 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Reference Hi Warren Could you tell me how I should reference Pymol in papers etc? I've tried finding it one the web and i've not seen it Ta Chris
RE: [PyMOL] surface area calculation
Joel, Yes, PyMOL does have this capability, but it is immature and not routinely validated. The basic concepts are: 1) get_area selection command will return the effective surface area of the dots that you would see from show dots, selection. This is a discrete approximation -- not an exact calculation. 2) you can use the dot_solvent setting to control whether you get solvent surface area or a molecular surface area. 1=solvent, 0=molecular 3) the accuracy of the measurement depends on the density of dots, which is controlled by the dot_density setting (1-4). 4) the solvent radius is controlled by the solvent_radius setting (default 1.4). For example: PyMOL load $TUT/1hpv.pdb PyMOL show dots, resn arg PyMOL get_area resn arg cmd.get_area: 1147.956 Angstroms^2. PyMOLset dot_solvent, on PyMOLget_area resn arg cmd.get_area: 673.084 Angstroms^2. PyMOLset dot_density, 3 PyMOLget_area resn arg cmd.get_area: 674.157 Angstroms^2. PyMOLset dot_density, 4 PyMOLget_area resn arg cmd.get_area: 672.056 Angstroms^2. PyMOLget_area all cmd.get_area: 13837.804 Angstroms^2. This code has not been recently validated (though I did check it a couple years back), so I would suggest that people perform some kind of independent check on their system before trusting the results. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Harp, Joel M Sent: Wednesday, November 12, 2003 2:10 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface area calculation Is it possible to get pymol to calculate surface area for a defined object? For instance, can it calculate surface area occupied by arginines. Thanks, Joel Joel M. Harp Vanderbilt University
RE: [PyMOL] surface area calculation
Close, but it depends on whether you want the surface area of the residues alone, or in the context of the molecule. load protein.pdb get_area resn arg will be less than create arg_object, resn arg get_area arg_object This is because the first example will give you only the exposed area of the arginines in the presence of the other atoms, whereas the second gives the area of the arginines in isolation. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Kaushik Raha Sent: Wednesday, November 12, 2003 2:50 PM To: Harp, Joel M Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] surface area calculation To calculate surface area for a defined object from the PyMOL command line type: print cmd.get_area(obj) where obj is the name of your object. for arginines: create ARG, resn ARG print cmd.get_area(ARG) Kaushik. On Wednesday, November 12, 2003, at 05:10 PM, Harp, Joel M wrote: Is it possible to get pymol to calculate surface area for a defined object? For instance, can it calculate surface area occupied by arginines. Thanks, Joel Joel M. Harp Vanderbilt University
RE: [PyMOL] DSSP
Ben, Great response! Indeed, the PDB's limited capacity for secondary structure does indeed represent this as one single helix, not two. +/- 15 degrees is pretty difficult to see - so I think that DSSPs +assignment in this case, while liberal, is certainly acceptable. I hardly think it acceptable that one residue with 3-10 PHI/PSI constitutes a helix when you have so many other telltale characteristics of a Type II' beta turn, including a Glycine in position i+1 and all deviations within 22 deg. of ideal turn, as well as four planer CA atoms (actually five, C-alphas 98-102 are all nearly planer). Some turns do look like helices, but not this one -- not even close. Great example of where DSSP fails, but perhaps a bit contrived. I don't think this example is contrived. One of the many tests I put PYMOL through regularly is to render the entire PDB over several hours, so I literally see thousands of structures on a routine basis. Such objective but bogus assignments are far more common than one would like to think. It is a real problem. The reason that consistency is of paramount importance in assigning secondary structure is so that different scientists can talk about the same protein in context. If everyone uses the same definition of secondary structure - helix 1 is always helix 1. Good point, but I disagree. In acknowledging the subjective and relative nature of assignments, I think it is more reasonable to ask scientists to define their terms rather than to perpetuate broken conventions. Given how evolution, crystallization, and protein processing work, even with DSSP, Helix 3 can easily be Helix 2 or 4 in another structure of the identical or a related protein, so the savings in confusion is slight. Also, keep in mind that all numbering is relative and increasingly problematic as more and more homologous structures are solved, and explicit conceptual labels are far more general than numeric ones. But finally, do understand that I would provide DSSP as an option if it were possible to do so, but frankly, it's not. The paper does not enable an exact reimplementation, and the owners of DSSP, instead of making DSSP source code usable and redistributable as an open standard, have decided to use the software for revenue generation (presumed modest at best). It is exatly this kind of short-sighted restrictiveness that PyMOL was created to combat. We must end this dismal pattern of scientists developing research software that is so drastically and artificially limited by licensing terms that it has little or no ability to enable future scientific advances. Computer-dependent scientific fields like structural biology and computational chemistry will be handicapped until we can all effectively access and improve upon existing software systems. That will not happen until research scientists and academic institutions stop viewing such software programs as potentially lucrative intellectual properties and start viewing them as the critical building blocks that will enable future breakthroughs if and when they become widely shared. Imagine... What would happen if all scientists stopped publishing their discoveries and kept all information within one lab or institution? Scientific progress would come to a halt. That's basically what has occurred with so much scientific software over the last 20 years. Don't get me wrong -- some great code has been written -- and some of that code has been shared without cost to some or for a low fee to others. However, most of that code has almost never been shared in such a way as to enable extension, modification, and redistribution. As a result, we are not making much cumulative progress. Software programs resemble ideas: they must be shared, questioned, altered, and refined in order for lasting progress to occur. Otherwise they stagnate just like old ways of thinking. DSSP (circa 1983) is a great example of how many computer-dependent sciences remain trapped in the 1980s. Whether it works better than PyMOL or not is almost beside the point. It is simply not an appropriate standard for us to be using today in this age of open standards, open source, and composite systems. We can and should do better than this. My hope is that if PyMOL and enough similar projects are successful, that governments, companies, and funding agencies will begin to back these kinds of efforts wholeheartedly with money and policies, and thus drive rapid progress and widespread benefits throughout the sciences. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: Ben Hitz [mailto:bh...@exelixis.com] Sent: Monday, November 03, 2003 11:01 AM To: Warren L. DeLano; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] DSSP Warren
RE: [PyMOL] secondary structure assignment and surface potential calc/mapping
1) Is the secondary structure assignment function in 0.92 more reliable? Or does the WARNING: it will make mistakes, so don't publish anything based on this algorithm! statement still apply? Good question! I added that warning message to util.ss back when I believed that there was such as thing as correct secondary structure assignment and because util.ss had a very primitive H-bonding definition -- distance only. dss is something completely new. In creating the new dss, I took some time to go through the 1983 DSSP paper (Kabsch Sander) and discovered much to my surprise that the H-bond criterion used by DSSP has very little to do with what crystallographers today think about hydrogen bonds. Did you know that DSSP H-bonds can be as long as 5.2 Angstroms between heavy atoms (Fig 1)? Plus, there is no simple analytic form of their criterion provided which could be implemented by something like PyMOL. Furthermor, and more disturbing, I discovered that DSSP doesn't take backbone torsion geometry into account at all, which finally explained to me why so many DSSP-assigned PDB structures have obviously non-helical regions assigned as HELIX. It's just a naive algorithm, and as far as I'm concerned, H-bonds just aren't the whole story when it comes to secondary structure. Thus, I had to admit that DSSP itself wasn't correct with repect to my personal interpretation of secondary structure. In looking at RasMOL's code it suffers from some of the same problems, and I don't think it actually implements DSSP -- just an approximation to it. So I decided to create my own best-attempt at a secondary structure assignment algorithm based on the spirit of DSSP, but which also takes into account backbone geometry as well as hydrogen-bonding . Like DSSP, PyMOL's hydrogen-bonding criteria is angle-dependent, but the default range is more contemporary (within 3.2 A at 63 deg, 3.6 A at 0 deg). After validating the algorithm manually on ten structures, I sat down and visually compared PDB (DSSP) assignments to PyMOL's dss over several hundreds proteins. In general, both programs find the same set of helices and large sheets. However, they differ on the exact start and stop points of these elements. On small sheets or helices, one program may miss something that the other finds. However, divergent regions seemed to involve borderline cases for the most part. dss and DSSP seem to do equally well on cut-and-dry idealized systems. So dss is reasonably validated, in my view, but I am looking for feedback and specific problem cases when they're found. But speaking as an artist rather than as a scientist, I think dss has better aesthetics than DSSP when it comes to cartoon diagrams -- there are simply fewer goofy-looking assignments. Whether it is more scientifically correct or not is an open question. Cartoons themselves are pretty misleading...one might add. By the way, there are a some new settings in PyMOL 0.92 which cover h-bond detection and secondary structure assignment. Here are the most important ones: h_bond_max_angle, 63.0 h_bond_cutoff_center, 3.6 h_bond_cutoff_edge, 3.2 ss_helix_psi_target, -48.0 ss_helix_phi_target, -57.0 ss_strand_psi_target, 124.0 ss_strand_phi_target, -129.0 Basically, if helix or sheet hydrogen bonds are present, and backbone geometries are close to the target values, PyMOL will assign residues as helix or sheet. Otherwise, they're considered loops. The allowable Phi/Psi inclusion/exclusion boxes are adjustable with settings too. For the curious, my algorithm is about 1,000 lines of code and consists of the SelectorAssignSS function found in layer3/Selector.c around line 500. 2) Is there a 0.92 function to calculate and map surface potential? This would be useful beyond compare. I wish. Your choices for this are Grasp, MEAD, Delphi, or Zap. Only MEAD is freely available. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Neiditch, Matthew Sent: Friday, October 31, 2003 12:46 PM To: 'pymol-users@lists.sourceforge.net' Subject: [PyMOL] secondary structure assignment and surface potential calc/mapping Dear List, Regards, Matthew Neiditch Postdoc Hughson Lab Princeton University neidi...@molbio.princeton.edu --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/p ymol-users
RE: [PyMOL] labeling atoms in GUI
Richard,
It's not GUI, but you could simply bind a function key such as F1 to
that command:
cmd.set_key('F1',lambda :cmd.label((lb),'%s %s
%s%(name,resn,resi)'))
You might then want to bind 'F2' to something which hides all labels.
cmd.set_key('F2',cmd.label)
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
rbax...@uchicago.edu
Sent: Wednesday, October 29, 2003 5:14 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] labeling atoms in GUI
Dear All,
I want to look at my structure in PyMOL and, having centered
on something defined by my selection script, pick atoms
nearby and see what residues they belong to. That is, I want
to pick select an atom with the mouse and have its name,
residue name and residue number appear on screen, like it does in O.
I figured out that [Ctrl] + Left-Mouse-Button selects the
atom as lb, and that the command 'label (lb),%s %s %s %
(name,resn,resi)' gives me the label I want. Now how could I
get something like that to appear as a menu function in the
GUI so I don't have type it in all the time? Can it be a
command executed as part of my startup script?
Maybe some function like this already exists, otherwise I
think it is a very useful thing.
regards,
Richard Baxter
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RE: [PyMOL] How to load O/BRIX map
Huiying, PyMOL will recognize the following extensions for O maps: .o .omap .brix The following will render the entire brick at 1 sigma: load map.o isomesh m1, map, 1 Or if you have a pdb load model.pdb isomesh m1, map, 1, 100/, 8 will give you an 8 A brick around residue 100, etc. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Huiying Li Sent: Wednesday, October 29, 2003 3:52 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to load O/BRIX map I am wondering how to load the O/BRIX maps into Pymol using version 0.92. Is there a default file extension, say *.dsn6, for O map, or need to define the map format with a keyword? Thanks for any help. -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@bragg.bio.uci.edu -- --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/p ymol-users
[PyMOL] RE: Writing info to files
Currently, i work on a complexe proteinic which includes two proteins. I calculate distances (in a cut-off of 10 Angström in order to obtain atoms which are within the interface of both molecules) between these proteins. Now, i would like to know what atoms belong to my selection and write them in a file. Could you help me please ? iterate selection, python-code For example: load $PYMOL_DATA/demo/pept.pdb output= open(output.txt,'w') iterate (name ca), output.write(%s %s %s %s\n%(resn,chain,resi,name)) output.close() Would create output.txt containing: ASP E 1 CA CYS E 2 CA ALA E 3 CA TRP E 4 CA HIS E 5 CA LEU E 6 CA GLY E 7 CA GLU E 8 CA LEU E 9 CA VAL E 10 CA TRP E 11 CA CYS E 12 CA THR E 13 CA Notice how you can freely intersperse Python and PyMOL commands in PyMOL command scripts in order to accomplish tasks such as this. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] Save session on Mac OSX latest version?
Douglas, Simply: save filename.pse ie save today.pse Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Douglas Freymann Sent: Sunday, October 26, 2003 2:26 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Save session on Mac OSX latest version? I'm having a hard time finding how to save my session running on a G4 Powerbook, using PyMOL v0.91. The command, File::Save, is grayed out, and there's no command File::Save Session as described in the Users Manual. Is there a trick, or a command line statement? By the way, is there a way to set a default working directory when PyMOL starts? Sorry if these are FAQ's but I didn't find the answers anywhere. Thanks, Doug -- Douglas M. Freymann freym...@northwestern.edu Molecular Pharmacology Biological Chemistry Ward 7-247, Northwestern University 303 E. Chicago Ave., Chicago, IL 60611 (312) 503-1877fax: (312) 503-5349 --- This SF.net email is sponsored by: The SF.net Donation Program. Do you like what SourceForge.net is doing for the Open Source Community? Make a contribution, and help us add new features and functionality. Click here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/p ymol-users
RE: [PyMOL] solvent accesible surface
Marcelo, PyMOL doesn't currently do a very good job with a solid solvent accessible surfaced because they aren't smooth like the Connolly surface. But here's what you can do: show spheres set sphere_solvent,1 or hide spheres show mesh set solvent_mesh,1 now add in show surface for a nice combination of the solvent and molecular surfaces. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Marcelo Castilho Sent: Sunday, October 26, 2003 4:04 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] solvent accesible surface Dear all, I am new to pymol and appologyze if his is an easy question, anyway here it goes; Is it possible to change the surface radius in pymol so that I can represent the solvente accesible surface ? By the way, I am running pymol 0.90 under windows XP Thanks, Marcelo Castilho = Marcelo Santos Castilho tel 016 273 98 68 R; Américo J. Canhoto 223 Apto 23 Bl 2 São Carlos CEP 13564-350 e-mail alternativo: casti...@if.sc.usp.br __ Do you Yahoo!? Exclusive Video Premiere - Britney Spears http://launch.yahoo.com/promos/britneyspears/ --- This SF.net email is sponsored by: The SF.net Donation Program. Do you like what SourceForge.net is doing for the Open Source Community? Make a contribution, and help us add new features and functionality. Click here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/p ymol-users
RE: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window
Florian, The main trick is to use an X11/Fink build of PyMOL. Under 10.3, I'm hoping OpenGL performance under X11 will be more that of the native version -- any early returns on this yet? For proficient developers with X11 installed, there another trick you can try: Link source-built PyMOL against native GLUT/OpenGL frameworks while simultaneously linking against X11-based Python/Tkinter/Tcl/Tk. This is what I call the hybrid build, which gives native-like OpenGL performance and X11-like user interface compatibility. Stability was a problem with this config though, which is why I've never tried to distribute such a build. Finally, there is a native Tcl/Tk Aqua port which doesn't require X11, and which in theory at least would enable a native-like GUI without having to write Aqua code directly. However I've heard that there are stability problems with this Tcl/Tk, and I'm not sure Python's Tkinter can even work with it. Does anyone out there have experience using Tkinter on OSX without X11? Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Florian Nachon Sent: Thursday, October 23, 2003 5:53 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window On Oct 22, 2003, at 8:42 PM, pymol-users-requ...@lists.sourceforge.net wrote: Tkinter is a separate Python module that's an interface to the Tcl Tk library. It's probably just not installed on your system, but it is included in the RH 9 distribution (tkinter-2.2.2-26.i386.rpm) so it should be easy to find and install. By the way, isn't there a trick to get the Tk menu in the native MacOS X version of Pymol? --- This SF.net email is sponsored by: The SF.net Donation Program. Do you like what SourceForge.net is doing for the Open Source Community? Make a contribution, and help us add new features and functionality. Click here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Release in progress...
(in a whisper) I'm still in the process of building binaries, but pioneers are welcome to start downloading 0.92, if your platform is represented. It has been a long time since our last release, so proceed with caution! http://sourceforge.net/project/showfiles.php?group_id=4546 Please bring any problems to my attention ASAP, before the Monday deluge. Warren
RE: [PyMOL] Using PyMol as a library - no GUI
Truls, That looks to me like a crash where the PyMOL API was somehow called before PyMOL was initialized...how and why this could happen is a mystery to me though -- that's what pymol.finish_launching() is supposed to prevent -- but there may be some flaw in the logic. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: Debian Chooser [mailto:ker...@herocamp.org] On Behalf Of Truls A. Tangstad Sent: Friday, October 17, 2003 3:18 PM To: Warren L. DeLano Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Using PyMol as a library - no GUI On Fri, Oct 17, 2003 at 09:41:24AM -0700, Warren L. DeLano wrote: Truls A. Tangstad wrote: I'm very interested in using alot of the functionality that PyMol offers programmatically from Python, i.e. without using a GUI at all. The chempy package seems to cover alot of my needs, loading different file formats etc. even though it doesn't seem to be documented. Is it also possible to use the rest of the functionality in PyMol from other Python scripts? Right now, just importing the pymol package seems to force the GUI to open. If you've got PyMOL configured to open on import pymol pymol.finish_launching() You can suppress the GUI feature and suppress startup output by providing command line arguments as follows. Before importing PyMOL, set a pymol_argv list in the __main__ namespace. PyMOL will interpret this as a sys.argv styled list of command line arguments. import __main__ __main__.pymol_argv['pymol','-qc'] import pymol pymol.finish_launching() Thanks, seems to work like a charm in scripts after adding the assignment operator: __main__.pymol_argv = ['pymol', '-qc'] # adding miss Somehow it segfaults when trying the same thing in an interactive python interpreter though, right after importing pymol. This might be due to a shoddy install on my part, but I'm including a gdb backtrace: #0 0x41d7b21a in SettingGetGlobal_f () from /usr/lib/python2.3/site- packages/pymol/_cmd.so #1 0x41d7c683 in SettingGet () from /usr/lib/python2.3/site- packages/pymol/_cmd.so #2 0x41d6296d in OrthoAddOutput () from /usr/lib/python2.3/site- packages/pymol/_cmd.so #3 0x41d679a5 in PCatchInit () from /usr/lib/python2.3/site- packages/pymol/_cmd.so #4 0x4006d74d in PyCFunction_Call () from /usr/lib/libpython2.3.so.1.0 #5 0x40045e37 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #6 0x400a2a4a in PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.3.so.1.0 #7 0x4000 in PyFile_WriteObject () from /usr/lib/libpython2.3.so.1.0 #8 0x400556e6 in PyFile_WriteString () from /usr/lib/libpython2.3.so.1.0 #9 0x400d56b6 in PySys_WriteStderr () from /usr/lib/libpython2.3.so.1.0 #10 0x400d4b2c in PySys_WriteStderr () from /usr/lib/libpython2.3.so.1.0 #11 0x400d2c74 in Py_AtExit () from /usr/lib/libpython2.3.so.1.0 #12 0x40101043 in _PyUnicode_TypeRecords () from /usr/lib/libpython2.3.so.1.0 Any idea why it shouldn't work interactively? I'm using PyMol 0.90 and Python 2.3.2 on Debian unstable. -- Truls - kerfue+pymol-us...@herocamp.org
RE: [PyMOL] Off screen drawing bug on a nForce 2 computer
Paulo, As far as I know, what you're reporting is a platform-dependent OpenGL bug (or feature). Many graphics cards don't support rendering to display context that is not visible. Ray-tracing doesn't have this limitation of course, but in theory we could teach PyMOL how to use auxillary buffers to enable off-screen OpenGL rendering as well. Unfortunately there isn't any way to color bonds independent of atoms in PyMOL. The closest thing you can do is create a new object consisting of just those to bonds and to color that object separately. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Paulo Lai Sent: Tuesday, October 21, 2003 7:55 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Off screen drawing bug on a nForce 2 computer Hi, I have added a very limited SOAP interface to PyMol and I've found that when the viewer window is covered there are errors in the png files it generates. For example if I load a structure and rotate it, it will save the image of the structure in its new orientation overlaid on top of its original position. It works fine on my laptop which uses the ATI Mobility Radeon 7500, and I can get it to work on my nForce 2 desktop, if I use the minimal level of hardware acceleration (when using the latest version of the NVIDIA drivers). The other issue I've had is PyMol freezes if I have it open normally, and then I use remote desktop to connect to that computer, neither of these are critical. If anyone is interested, the SOAP libraries for Python (SOAPpy and ZSI) are still quite rough with many relatively simple things not functioning correctly, I've resorted to passing lists around. Final thing, is there a way to colour a single bonds in sticks view without affecting the colour of the other bonds the atom is connected to? Cheers, Paulo --- This SF.net email is sponsored by OSDN developer relations Here's your chance to show off your extensive product knowledge We want to know what you know. Tell us and you have a chance to win $100 http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] atom sphere radius
Robert, alter selection, vdw=number for example: alter elem fe, vdw=1.0 rebuild Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: Robert Schwarzenbacher [mailto:robe...@sdsc.edu] Sent: Wednesday, October 22, 2003 1:43 PM To: Warren L. DeLano Cc: pymol-users@lists.sourceforge.net Subject: [PyMOL] atom sphere radius Hi there, I would like to show an active site metal but the sphere radius is too big. Is there a way to change the sphere radius for an atom or display it otherwise with a radius of say 1A. thanks, robert --- Robert Schwarzenbacher, PhD The Joint Center for Structural Genomics phone: 858 822 3637
RE: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window
Fred, The tkinter dependency is missing. RPM is supposed to check that, but I forget to add it to the list. Look for the tkinter RPM on your RH9.0 CDROM (or on the net). Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of fr...@mit.edu Sent: Wednesday, October 22, 2003 3:33 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window Hi PyMOLers, Can someone tell me why I don't get the Tk window with all of the menus when I start PyMOL under redhat 9.0? I installed the RPM file pymol-0.90-1.rh90.py22.i386.rpm and got no errors during installation. Here's the content of the shell window after starting PyMOL: Xlib: extension XFree86-DRI missing on display :0.0. PyMOL(TM) Molecular Graphics System, Version 0.90. Copyright (C) 1998-2003 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 most 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 campaign to create open and affordable software for molecular research. Updates and other information can be found at http://www.pymol.org;. Please cite PyMOL in publications and presentations: Warren L. DeLano The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, USA. 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 based graphics front end: GL_VENDOR: Mesa project: www.mesa3d.org GL_RENDERER: Mesa GLX Indirect GL_VERSION: 1.3 Mesa 4.0.4 Traceback (most recent call last): File modules/pymol/__init__.py, line 177, in exec_str exec s in globals(),globals() File string, line 1, in ? File modules/pymol/__init__.py, line 292, in launch_gui __import__(invocation.options.gui) File modules/pmg_tk/__init__.py, line 22, in ? # as /usr/lib/python2.1/site-packages File modules/pmg_tk/PMGApp.py, line 15, in ? ImportError: No module named Tkinter Thanks everyone. --- This SF.net email is sponsored by OSDN developer relations Here's your chance to show off your extensive product knowledge We want to know what you know. Tell us and you have a chance to win $100 http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] new error
Tom, Yes you're right: MGL's stuff messes with PYTHONPATH and possibly PYTHONHOME. These need to be undefined for PyMOL to work correctly. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Tom Thompson Sent: Friday, October 17, 2003 11:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] new error I just started to get this error mac-osx 10.2.6. Could it be correlated with a recent installation of the python-based molecular visualization programs from the MGL at Scripps. I have reinstalled the program and I get the same error. Traceback (most recent call last): File /Applications/PyMOL/Darwin/modules/pymol/__init__.py, line 58, in ? import threading File /Applications/PyMOL/Darwin/ext/lib/python2.2/threading.py, line 4, in ? import time ImportError: No module named time Thanks, -Tom -- __ Tom Thompson, Ph.D.PH 847-467-4049 Northwestern University 2205 Tech Drive Evanston IL 60208-0001
[PyMOL] 2004 PyMOL Budget Reminder
PyMOL Users, For all of you fortunate enough to have recurring annual software budgets, this is a gentle reminder and request for you to consider leaving room in your 2004 budget plans for a PyMOL support subscription ( license for new sponsors). We have been functioning as an independent open-source software company for a little over six months, and I am thrilled to be able to now state with confidence that as long as present trends continue, DeLano Scientific LLC will endure to support PyMOL and pursue its development indefinitely. We have reached a minimal break even point where our current (albeit low) costs are met by current revenue. PyMOL is now officially a sustainable long-term project with a bright future! However, we are not yet running as efficiently as possible because current sponsorship can just barely support one full-time equivalent, meaning that my time is split between support, development, system administration, management of contractors, and (unavoidable) paperwork. This achievement of minimal sustainability is an important milestone, but we are not yet able to tap into the significant gains in productivity that can be had through effective divisions of labor. Of course, I will multi-task for as long as is needed to insure the project's vitality -- that goes almost without saying. However, the greatest benefits to you, our users, will accrue when we can afford separate dedicated people, each focusing on one area: support (training, documentation, site-visits, etc.), development (new features, bug-fixes, customization), or general administration (including preparation of SBIR grant applications to cover aggressive new development projects). My hope is that with gradually increasing sponsorship, we will reach that level within the next year or so. However, control over our growth rate and the rate of PyMOL improvement ultimately lies in your hands. What would you like to see happen with the project? Do you share our vision for accessible and ubiquitous molecular graphics software? Are you willing and able to help bring it about sooner or later? If you have a budget, then please make room for a PyMOL subscription in it. Alternatively, if you are preparing a new grant, then please consider adding a line item for PyMOL along with any new hardware or software purchases. We can provide quotes to help with this kind of advanced planning upon request ( http://www.pymol.org/funding.html ). Thanks to all of you who have already sponsored the effort -- you are making this all possible. Thank you especially for your trust, your patience, and your continued belief in the value of our mission ( http://www.delanoscientific.com/about.html ). Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] Using PyMol as a library - no GUI
If you've got PyMOL configured to open on import pymol pymol.finish_launching() You can suppress the GUI feature and suppress startup output by providing command line arguments as follows. Before importing PyMOL, set a pymol_argv list in the __main__ namespace. PyMOL will interpret this as a sys.argv styled list of command line arguments. import __main__ __main__.pymol_argv['pymol','-qc'] import pymol pymol.finish_launching() Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Truls A. Tangstad Sent: Friday, October 17, 2003 4:48 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Using PyMol as a library - no GUI I'm very interested in using alot of the functionality that PyMol offers programmatically from Python, i.e. without using a GUI at all. The chempy package seems to cover alot of my needs, loading different file formats etc. even though it doesn't seem to be documented. Is it also possible to use the rest of the functionality in PyMol from other Python scripts? Right now, just importing the pymol package seems to force the GUI to open. -- Truls - kerfue+pymol-us...@herocamp.org --- This SF.net email is sponsored by: SF.net Giveback Program. SourceForge.net hosts over 70,000 Open Source Projects. See the people who have HELPED US provide better services: Click here: http://sourceforge.net/supporters.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Command line equivalent available?
Nick, There are a few commands that I've been using for which I can't seem to find a command line equivalent: This actions can be performed using selections with standard atom identifiers: show/hide mainchain atoms show lines, object-nameca+c+n+o+h hide lines, object-nameca+c+n+o+h where object-name is the name of your object show/hide sidechain atoms show lines, object-name and ((not name c+n+o+h) or pro/n) hide lines, object-name and ((not name c+n+o+h) or pro/n) Of course, you can substitute sticks, sphere, etc. for lines in the above. select atoms for 'dist' command (H-bond creation) dist dist-name, selection1, selection2 i.e. dist d1, prot//N/23/CA, lig//X/1/O dist d2, prot//O/24/CA, lig//X/2/N Cheers, Warren
RE: [PyMOL] Underside of surface color
Jason, Not really -- it's either blackish or lit, just like the front. To see the backside of surfaces: set two_sided_lighting,1 set backface_cull,1 Also, sometimes it is helpful to get rid of shadows when doing this: set ray_shadows, 0 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Jason Thomas Maynes Sent: Friday, October 10, 2003 3:11 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Underside of surface color Hello: Is there any way to change the color of the underside of a surface. Right now it is a very dark version of the top color. I would like to be able to look at the surface contour from underneath. Thanks in advance. Cheers, JTM We can be sure that if a detailed understanding of the molecular basis of chemo-therapeutic activity were to be obtained, the advance of medicine would be greatly accelerated. Linus Pauling, Nobel Laureate 1954 ...everything that living things do can be understood in terms of the jigglings and wigglings of atoms. Richard Feynman * Jason Thomas Maynes PhD/MD Program Department of Biochemistry Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca * --- This SF.net email is sponsored by: SF.net Giveback Program. SourceForge.net hosts over 70,000 Open Source Projects. See the people who have HELPED US provide better services: Click here: http://sourceforge.net/supporters.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Accessing PyMol's commands from outside (or without viewer)
Shu-hsien Sure, instead of cmd.select, use cmd.do(select ligand, resn XYZ) cmd.do(select protein, ! ligand ) etc. ./pymol -qc select_box.py Is the command line mode of PyMOL. pymol -qc can be used like python in most cases. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Shu-Hsien Sheu Sent: Saturday, November 08, 2003 10:58 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Accessing PyMol's commands from outside (or without viewer) Hi, This should be a trial question though I cannot find a way of doing it. I have a simple script that looks like this: (the original commands, rather than cmd.select..) select ligand, resn XYZ select protein, ! ligand select box, protein within 8 of ligand select box, box or byres box save box as box.pdb I don't need the viewer at all and would be even more efficient if I can call the PyMol API from the shell. Or, in a python script. For example, I would like to have something like: ./pymol select_box.py thanks! --- This SF.net email is sponsored by: SF.net Giveback Program. SourceForge.net hosts over 70,000 Open Source Projects. See the people who have HELPED US provide better services: Click here: http://sourceforge.net/supporters.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Pymol script screenplay
Nat, PyMOL's ray-tracer is pretty simple -- it just divides 3D space up into equally sized boxes, so that ray-intersection and identification calculation can be performed rapidly. The smaller the boxes, the fewer the number of partial geometries will be present in the box. Hash_max is a hint to the ray tracer about the maximum number of subdivisions it should allow on each axis. In principle, the amount of RAM used is a 3rd-order function of this value. However, the ray-tracer will often use less RAM than that for a variety of reasons. PyMOL usually ships with hash_max set to 100, since that is reasonable for a machine with 256 MB of RAM. 300 is about the highest I've tried, and you could easily require over a Gig of RAM for a situation like that. However, there is definitely a point of diminishing returns, which depends on scene complexity, total number of pixels, etc. Typically each ray-tracing scene will have a different optimum, but usually 140-180 gives the shortest overall rendering times. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Nat Echols Sent: Sunday, October 05, 2003 2:28 PM To: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Pymol script screenplay By the way, you can also use extra RAM to speed up ray-tracing by 2-3 fold if you set hash_max to 150-200. Wait, I'm curious - what does this command do, and what are the limits? For a machine with 2GB of memory, what can I get away with? Will I have problems if I run multiple invocations of PyMOL at once? -Nat --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] why is PyMOL renaming my residues?
Also note that by some conventions, 2OA2 in a PDB file really means atom OA22. I didn't know that. What conventions are those? Well, PDB atom names are supposed to have the atomic symbol right justified in the first two columns followed by a remoteness indicator and then a branching number. However, that isn't a sufficient number of fields for all situations, such as when significant symmetry is present in a system, and so a third field is required. This numeric field occupies the first column when the atom symbol itself is only one character. With hydrogens, this first numeric field has the additional defined purpose of enumerating (NMR?) equivalent hydrogens, so you will see atoms like 2HD and 3HD in ARG for instance. However, in the Amber world, the atomic symbol always comes first. Thus a PDB hydrogen 2HH2 becomes HH22 in Amber. Going from PDB to Amber is easy, but the reverse is not trivial, since Amber CD1 remains PDB CD1, but Amber HE2 becomes 2HE and HH22 becomes 2HH2. Ambiguity occurs when there is a four-letter atom name which is not a hydrogen. OA22 in Amber would thus need to become 2OA2 in order to comply with the PDB convention of having the Atomic symbol right justified in the first two columns of the file. However, that convention is only explicitly enforced for amino acids, so in theory OA22 would be legal for a non-amino acid, whereas 2OA2 is required if the residue is an amino acid. What a mess! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 Also note that by some conventions, 2OA2 in a PDB file really means atom OA22. I didn't know that. What conventions are those? Furthermore, in your example, they [ATOM IDs] are not unique (a mistake?). yup, a mistake. However, I am trying to bend PyMOL around to meet your needs a bit better. Towards this end, I've created a new setting pdb_retain_ids which preserves the original PDB serial numbers in the output file. In future PyMOL versions, so long as set retain_order, 1 set pdb_retain_ids, 1 set pdb_no_end_record, 1 That's absolutely fantastic. Right now, I have to use PyMOL, MOE and AMBER (sander and carnal are the real problems) on the same systems, and anything that makes this less painful is great! I'll probably set retain_order and pdb_retain_ids in my .pymolrc.py and upgrade to the CVS version within the next couple of days. Thanks! -michael -- michael lerner --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Pymol script screenplay
Alan, VMD is more memory efficient that PyMOL. Probably the main reason for this is that PyMOL pre-calculates and stores all of the geometries it is going to show down to the last vertex. You can reduce the amount of memory PyMOL needs for cartoons by setting: set cartoon_sampling, 3 But the real way to solve your problem is to get more RAM. If you're using PyMOL to visualize MD trajectories, I recommend buying as much RAM as you can afford (and your system can take). 1 GB is a reasonable minimum. 1.5-2 GB is definitely better. I don't know what prices are like in Brazil, but a GB of RAM can be purchased here in the states for $150-400. By the way, you can also use extra RAM to speed up ray-tracing by 2-3 fold if you set hash_max to 150-200. To answer to your second question: import os os.system(mencoder \*.png -mf on:fps=30 -o mvc1ec2.avi -ovc lavc -lavcopts vcodec=mpeg4:vbitrate=6000:vhq:keyint=30) Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Alan Wilter Sousa da Silva Sent: Thursday, October 02, 2003 5:32 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol script screenplay Hi List! I finally got a Pymol script which does what I want, but I still have problems. I follows my actual script: - del all mclear set cache_frames=0 set cartoon_fancy_helices, 1 load c1/forcedin.pdb,c1 frame 1 hide all run Pymol/stride_ss.py stride2pymol c1 stride2pymol c2 show sticks, (resi 199) show cartoon, all color red, c1 color blue, c2 set orthoscopic=1 viewport 640,480 run Pymol/eixos.py translate [18,18,20],object=axes run Pymol/cgotext.py translate [18,55.5,40],object=txt reset zoom all,-55 clip near,2 mset 1 x10 1 x72 -28 28 x72 28 x10 util.mroll(11,82,1) util.mroll(111,182,1) set antialias=1.0 set ray_trace_frames=1 mpng png2/mvc1e2 --- It works for a 28 frames of MD. But a test. Extending it for a real MD (~500 frames) I found out that Pymol crashes when command 'show cartoon, all' is running (after done the half of frames, I believe). Problably memory problems, right? However a similar operation works fine in VMD (sorry for comparison). I use a P4 1.6 GHz with 256 Mb Ram. BTW, how could I insert in Pymol script (python language) such command bellow: mencoder \*.png -mf on:fps=30 -o mvc1ec2.avi -ovc lavc -lavcopts vcodec=mpeg4:vbitrate=6000:vhq:keyint=30 Thanks in advance for any help. Cheers, -- -- Alan Wilter Sousa da Silva -- B.Sc. - Dep. Física - UFPA M.Sc. - Dep. Física - PUC/RJ D.Sc. - IBCCF/UFRJ Bolsista Pesquisador LAC-INPE São José dos Campos (SP), Brasil www.lac.inpe.br/~alan --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] why is PyMOL renaming my residues?
Michael, PyMOL's PDB handling is an attempt to navigate a minefield of incompatible standards which exist in the conventions of various software packages. Amber in particular poses significant challenges, as its PDB files are unusual. Since version 0.90, PyMOL's behavior has changed. Nowadays, your input data: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1314 XYZ NAP 164 30.554 66.174 18.2751.05 O HETATM 1314 LMN NAP 164 32.554 68.174 20.275 41.05 O Would be returned as: HETATM1 OA22 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM2 OA23 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM3 ABCD NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O HETATM5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O END ...which does preserve atom names, but not the order. Note that white-space in the atom names is not preserved (an inherent limitation in PyMOL -- significant white-space within identifier is hell on users and parsers). Conventionally, atom names of length 3 or less are placed in the second column, not the first -- so your LMN atom may cause trouble. Also note that by some conventions, 2OA2 in a PDB file really means atom OA22. PyMOL used to work this way (up to 0.90). Nowadays (v0.91+), 2OA2 is treated as 20A2 unless pdb_literal_names is on, in which case the old behavior returns. Note that in PyMOL, the PDB ATOM IDs are treated more as a property of the PDB file than of the atoms themselves since TER records also have unique IDs in that sequence and repeated MODELs sometimes do as well. Furthermore, in your example, they are not unique (a mistake?). However, I am trying to bend PyMOL around to meet your needs a bit better. Towards this end, I've created a new setting pdb_retain_ids which preserves the original PDB serial numbers in the output file. In future PyMOL versions, so long as set retain_order, 1 set pdb_retain_ids, 1 set pdb_no_end_record, 1 The following behavior will be obtainable: Assuming input of: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1315 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1316 XYZ NAP 164 30.554 66.174 18.2751.05 O HETATM 1317 LMN NAP 164 32.554 68.174 20.275 41.05 O You'll get an output of: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM 1315 ABCD NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM 1316 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O HETATM 1317 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O Which is as close as I think PyMOL is going to get... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of michael lerner Sent: Friday, September 26, 2003 8:44 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] why is PyMOL renaming my residues? Hi, If I load up a PDB file that looks like this: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1314 XYZ NAP 164 30.554 66.174 18.275 1.05 O HETATM 1314 LMN NAP 164 32.554 68.174 20.275 41.05 O and then save it from PyMOL, the resulting PDB file looks like this: HETATM1 2OA2 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM2 3OA2 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM3 DABC NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O HETATM5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O END You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed to 3OA2 and ABCD has been renamed to DABC. It looks to me like residue with a four-letter name is getting renamed. No .. wait .. it's a little stranger than that .. if I open up the second file (the one with DABC) and save *it*, I get this: HETATM1 2OA2 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM2 3OA2 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM3 CDAB NAP 164 28.554 64.174 16.275
RE: [PyMOL] two_sided_lighting
Meitian, Sorry, this is not possible. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of M Wang Sent: Monday, September 22, 2003 9:49 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] two_sided_lighting Hello everybody, For two_sided_lighting, is there a way to change the relative brightness of the two lights? Thanks, Meitian Wang --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] RE:
One quick question... how do I tell PyMOL to draw a cylinder (or bond) of a given radius between two positions X,Y,Z and X', Y',Z'? (From Python...) from pymol.cgo import * from pymol import cmd obj = [] obj.extend( [ CUSTOM_CYLINDER, 1.0, 2.0, 3.0, # XYZ 1 4.0, 5.0, 6.0, # XYZ 2 2.0,# Radius 1.0, 1.0, 1.0, # RGB Color 1 1.0, 1.0, 1.0, # RGB Color 2 1, 1, # End caps (0=none, 1=flat, 2=round) ] ) cmd.load_cgo(obj,'my_cgo') Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] getting color of a residue + selecting non-natural residues
Tina, I have two operations that I want to perform, and am not aware of a simple way (if possible) of doing them. So here it goes: 1. how (if possible) to retrieve the color for a residue as identified in an expression, e.g. resi 9? Note that it's not a range so no multiple answers is possible. I guess the question could extend to other attributes like representation, etc. The reason I need that is to be able to switch back to a residue's original color after highlighting it in another. The iterate command can do this... iterate all, print color import pymol pymol.color_list = [] iterate all, color_list.append(color) print pymol.color_list 2. how to select all non-natural residues (anything that's not in the list of 20 standard AAs)? I'm going the brute-force way, i.e. naturals1='asp+glu+lys+arg+phe+tyr+cys+met+ser+thr' naturals2='asn+gln+leu+val+ile+gly+ala+his+trp+pro' select naturals1, resn naturals1 select naturals2, resn naturals2 select nonnaturals, !naturals1 !naturals2 Does the above work? I wouldn't expect variables to function in PyMOL statements, but perhaps you're actually using cmd.select(...), which can access variables. However, you don't need to brake it up quite so much: select naturals, resn asp+glu+lys+arg+phe+tyr+cys+met+ser+thr \ or resn asn+gln+leu+val+ile+gly+ala+his+trp+pro select nonnaturals, !naturals Cheers, Warren
RE: [PyMOL] bug in rpm?
Nat, Are you running stock RedHat 9.0? The threading library in RH90 is broke. You may need to apply the glibc patches released by RedHat in order to get a stable system. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Nat Echols Sent: Friday, September 19, 2003 12:47 AM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] bug in rpm? I just got a shiny new Gateway laptop - essentially a ripoff of the 15 Apple (but cheaper), with NVidia chipset. I installed RedHat 9.0, NVidia drivers, and the PyMOL rpm for rh9, but I get segfaults when I try to run 'pymol'. The tar.gz file works perfectly, so it's not a problem for me, but I figured I should check and see if this was a known issue or if I'm doing something dumb. -Nat --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] modifying atom coordinates
Edmund, No, this kind of technical information isn't documented... If I recall correctly, when PyMOL hooks fragments together, it replaces hydrogen with a bond along the existing vectors. In other words, one fragment is translated so as to fit onto another. Peptides are a special case because the phi-psi vectors are fairly well defined. Nevertheless, I wouldn't trust peptide geometries generated by PyMOL until they've passed through some external force-field, such as MMFF or Amber/OPLS. PyMOL is a reasonable builder for defining the covalent scaffold of peptides and arbitrary small molecules, but it knows nothing about forces and energies. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Edmund Kump Sent: Thursday, September 18, 2003 8:59 PM To: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] modifying atom coordinates Yes, but what happens when, for example, I take a lysine residue, and connect a glutamine residue? Shouldn't all the atoms have different coordinates from when they are stand alone, based on the forces from nearby atoms? Does pymol account for this as residues are added, or is there a command or wizard which accounts for nearby atomic forces that I would execute after I build my chain? To give some background to what I'm trying to do, the end goal of my project is to modify the forces involved in protien folding. I'm sorry if I'm asking questions that are documented, but I haven't seen anything that answers my question yet. Much Thanks, Edmund On Wed, 17 Sep 2003, Warren L. DeLano wrote: Hi Edmund, Actually, PyMOL uses a set of stored coordinates for fragments and residues. They can be found in $PYMOL_PATH/data/chempy/fragments. The files have .pkl extensions, which stands for pickled chempy model. These files can be viewed directly in PyMOL, or can be introspected by unpickling them in a Python interpreter. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Edmund Kump Sent: Wednesday, September 17, 2003 3:49 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] modifying atom coordinates Greetings, I am interested in modifying how pymol generates the coordinates of atoms in a peptide chain as you add residues to it. I am an undergraduate math student, so my knowledge in this area is in the range of nothing. I would assume that this would be in the bonding or editor modules, but so far I haven't found what I'm looking for. In what Chempy or Pymol module(s) can I find the code that determines these coordinates? Thanks, Edmund Kump ek...@mathlab.sunysb.edu Applied Mathematics and Statistics SUNY Stony Brook --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] negative images
Jules, I think there's a problem with the alpha channel with certain PyMOL images, which means that portions end up being transparent when they shouldn't be. A quick workaround is to put a black rectangle behind the PyMOL image, but I'd like to get a little more information about when the problem occurs so that we can generate a permanent bug-fix. 1) Does it happen with ray-traced images, OpenGL images, or both? 2) Does is only happen with transparent surfaces? 3) Does it only happen on selected platforms? And if possible, can you send me directly (not to the mailing list), a copy of the problematic PNG file. Thanks, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Jules Jacobsen Sent: Thursday, September 18, 2003 12:37 AM To: Pymol users list Subject: [PyMOL] negative images Hello Pymol types, I have a quick question- has anyone had any trouble printing out images in word using version 0.9 in word XP? The images look fine when viewed on the screen yet when it comes to printing them out they appear as negatives, including the white background which becomes black. I though this might be a ray_trace_fog problem as my newer images were using this set to 1 but either on or off, the same problem arises. I have other images rendered using 0.86 and there is no problem with them. Has anyone else had this problem and found a fix for it? thanks in advance Jules --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] A couple of movie questions
First up: Is there any way to tell PyMol *not* to change its view when loading a PDB file set auto_zoom,0 Secondly: Below is an example of a small hack I have written when making one particular movie. This one overlays two molecules related by a 2-fold axis by doing a simple rotation. def overlay_chains(write_frames=0, ray=0): # Now interpolate each point in the matrix i = 1 n = 45 while i = n: # This is the only code I would imagine I should need: # cmd.mdo( %d % (i), rotate y,2,chain_a; rotate y,-2,chain_b ) # In the end I used the following cludge: cmd.do( rotate y,2,chain_a ) cmd.do( rotate y,-2,chain_b ) if ( ray ): cmd.do( ray ) if ( write_frames ): cmd.do( png overlay_frames/overlay_%03d.png % (i) ) i = i+1 cmd.extend( overlay_chains, overlay_chains ) What is wrong with the cmd.mdo line above? The functionality I would expect would be that in each frame of the movie both chains are rotated 2 deg (in the relevant directions). What I get is that the change only occurs once per loop of the movie. That is to say that if I set up a movie using 'mset 1 -45' the positions only get updated once per 45 frames, not once per frame (which is what I would have expected). Do you have 45 states, or just one? If you have just one, did you use the mset 1 x45 statement to create 45 frames consisting of that one state? And finally, are you using mpng to write the movie? Thridly: Is there any command to tell PyMol to play a movie ONLY ONCE. This would be *really* useful if it has not yet been implemented. I just added a movie_loop setting for you. Look for it in the next version. Fourth (and last): Is there a difference b/w the ray-tracing used by the standard 'ray' command and the 'mpng' command? I have noticed that if I take a still of a molecule, and then render the molecule rotating (for example) all within the one script I observe real differences b/w what should be identical frames. The clipping planes and the z camera distance move considerable. I can post code if that would help. Ray simply passes the current scene to the ray tracer. Mpng runs through the movie from the beginning and applies any mmatrix, mdo, or mappend operations you may have defined for the movie before handing each scene off to ray. (Note that movie.rock and movie.roll use mdo) What you describe sounds more like the difference between having a perspective view in OpenGL and orthoscopic in the rendered scene, but that difference should occur with both ray and mpng. Cheers, Warren
RE: [PyMOL] alternative method for loading coordinates
Rob, There isn't a public API function which does this at present but the private _cmd.get_pdb call does exactly that. To see an example of how it is used, look at the save function in modules/pymol/exporting.py. I'll add a cmd.get_pdbstr() function to the next version of PyMOL, since _cmd isn't meant to be called by anyone except PyMOL. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Robert Campbell Sent: Thursday, September 11, 2003 7:07 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] alternative method for loading coordinates Warren, * Warren L. DeLano war...@delanoscientific.com [2003-09-09 17:42] wrote: If you're willing to switch into Python, there is an undocumented read_pdbstr function which can take a PDB file as a string variable. See modules/pymol/importing.py for the code. Temporary files are unnecessary. This could be very handy, but is there a way to write a pdb string from within PyMOL? I've found export_coords, but that creates a PyCObject and I'm not sure how that can be used. I suppose it needn't be PDB format, but something that could be used (or converted for use) by other programs or user-written routines. Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
RE: [PyMOL] modifying atom coordinates
Hi Edmund, Actually, PyMOL uses a set of stored coordinates for fragments and residues. They can be found in $PYMOL_PATH/data/chempy/fragments. The files have .pkl extensions, which stands for pickled chempy model. These files can be viewed directly in PyMOL, or can be introspected by unpickling them in a Python interpreter. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Edmund Kump Sent: Wednesday, September 17, 2003 3:49 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] modifying atom coordinates Greetings, I am interested in modifying how pymol generates the coordinates of atoms in a peptide chain as you add residues to it. I am an undergraduate math student, so my knowledge in this area is in the range of nothing. I would assume that this would be in the bonding or editor modules, but so far I haven't found what I'm looking for. In what Chempy or Pymol module(s) can I find the code that determines these coordinates? Thanks, Edmund Kump ek...@mathlab.sunysb.edu Applied Mathematics and Statistics SUNY Stony Brook --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Transparent cartoons?
Christian, Transparent cartoons have been implemented, but not yet released excepted in the latest G4/G5 Mac demo version. If you have a Mac, you can set cartoon_transparency, 0.5 using that version. Note that cartoon transparency is really only useful when ray-tracing, because visual artifacts will occur with standard OpenGL rendering. If you're on a PC, then you'll need to wait for the next big release, which will probably happen next week. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Christian Siebold Sent: Monday, September 15, 2003 10:11 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Transparent cartoons? Dear Pymol users How can I create transparent cartoon? I tried to use the transparency option from the setting panel, but this only worked for surfaces and not for cartoons. Thanks a lot, Christian -- Dr. Christian Siebold Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Tel: (+44)-1865-287550 Fax: (+44)-1865-287547 Email: christ...@strubi.ox.ac.uk Website: http://www.strubi.ox.ac.uk --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] pymol raytracing crash
Thomas, I tried running your script on the current development version and on a version 0.90 binary, and wasn't able to get PyMOL to crash. How is PyMOL installed on your system? Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Thomas Siegmund Sent: Wednesday, September 10, 2003 6:16 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol raytracing crash Hi everybody, I am new to pymol. So maybe I'm doing something wrong, but pymol almost everytime crashes when I try to raytrace a picture. I had some success with small protein structures in cartoon representation. The same molecule in lines or sticks representation crashes the pymol raytracer. Here some console output: siegm...@siegmund:~ /usr/local/bin/python /usr/local/lib/python2.3/site-packages/pymol/__init__.py -x /tmp/pymol/7LYZ.pdb PyMOL(TM) Molecular Graphics System, Version 0.90. Copyright (C) 1998-2003 by DeLano Scientific LLC. // I cut some lines here OpenGL based graphics front end: GL_VENDOR: NVIDIA Corporation GL_RENDERER: RIVA TNT2/AGP/SSE2 GL_VERSION: 1.4.0 NVIDIA 44.96 PDBStrToCoordSet: Attempting to read symmetry information Crystal: Unit Cell 27.400 31.900 34.400 Crystal: Alpha Beta Gamma88.000 108.000 112.000 Crystal: RealToFrac Matrix Crystal:0.03650.01470.0133 Crystal:0.0.03380.0031 Crystal:0.0.0.0307 Crystal: FracToReal Matrix Crystal: 27.4000 -11.9500 -10.6302 Crystal:0. 29.5772 -3. Crystal:0.0. 32.5785 Crystal: Unit Cell Volume26402. Symmetry: 1.0 0.0 0.0 0.0 Symmetry: 0.0 1.0 0.0 0.0 Symmetry: 0.0 0.0 1.0 0.0 Symmetry: 0.0 0.0 0.0 1.0 Executive: object 7LYZ created. PyMOLutil.ss util.ss: WARNING: This is not a correct secondary structure // I cut some lines here util.ss: assignment complete. PyMOLhide lines PyMOLshow cartoon PyMOLray Ray: total time: 1.14 sec. = 3145.7 frames/hour. (1.15 sec. accum.) PyMOLhide cartoon PyMOLshow sticks PyMOLray Speicherzugriffsfehler (segmentation fault) Pymol is version 0.9, installed from source package on SuSE linux 8.2. To make sure that it is not a problem of the python installation (standard SuSE 8.2 rpm, python-2.2.2) I installed python 2.3 from source. Same result. In the mailing list archive I found comments about memory usage for raytracing. This machine has 500 MB RAM. Top shows about 150-200 MB free RAM and 1GB untouched swap just before the raytracing. I tried the command set hash_max, 60 as recommended, but this also did not help. Any hints? Tanks for your help Thomas -- Thomas Siegmund, Ph.D. DeveloGen AG Bioinformatics and Data Management Phone: +49(551) 505 58 651 --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] individual surfaces?
Dirk, The trick for displaying contact surfaces in PyMOL is to create separate objects for each surface: create res431, resi 431 create res440, resi 440 show surface, res431 or res440 For CPK, you don't need to do this show spheres, resi 431+440 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Dirk Kostrewa Sent: Monday, September 08, 2003 11:15 PM To: PyMOLBB Subject: [PyMOL] individual surfaces? Dear PyMol users, I'm currently trying to display individual surfaces around different selections of a molecule to show how they contact each other. However, either I get only the last surface displayed or a joined surface using the command examples below: this one gives only the surface of residue 440 show surface, ( resid 431 ) flag ignore, ( not resid 431 ) show surface, ( resid 440 ) flag ignore, ( not resid 440 ) rebuild whereas this one gives the joint surface of residues 431 and 440 show surface, ( resid 431 or resid 440 ) flag ignore, ( not ( resid 431 or resid 440 ) ) rebuild How can I display the individual surfaces separately? Alternatively, is there a command to display atoms in a CPK representation? Best regards, Dirk. -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OSRA/007 CH-5232 Villigen PSI, Switzerland E-mail: dirk.kostr...@psi.ch Phone: +41-56-310-4722 Fax: +41-56-310-4556 WWW: http://www.sb.psi.ch --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] incorporation of unusual amino acids
Uwe, We plan a research project where we want to stepwise incorporate D-amino acids into a peptide. To determine the exchanges it would be very useful if PyMol could assist. If I might dream I would like to have D-amino acids (and maybe other un- usual amino acids) available in the mutation-tool; You can flip residue 5 from L to D with the following two commands edit 5/ca invert 5/n, 5/c some simple energy minimization / bond relaxation; storing the resulting molecule in PDB- format. Sculpting can relax VDW/bond/angle strain, but it is not energy minimization by any means. Can I hope ? Is this something others find useful as well ? We'd all like to see a real forcefield in PyMOL, but no one has written the code yet. Cheers, Warren
[PyMOL] PyMOL for Mac G5, with Demos
sponsor of the PyMOL project, but they have taken steps to promote PyMOL on Macintosh by providing early access to hardware, exposure, and limited developer assistance. DISCLIAMER to the DISCLAIMER: So what? We're not afraid to criticize Apple. Apart from the iPod, the dual 2 Ghz G5 PowerMac is the ONLY system we recommend you purchase from the company at this time. Their laptops, cluster nodes, single-processor G5s, and mid-range G4 systems are arguably still behind the competition, even after taking OS X's advantages into account. I'm no Mac-addict, but I do like to recognize and celebrate a good product when I see one. The dual 2 Ghz G5 running Mac OS X is a killer desktop computer for research -- Apple's first in a long time, and hopefully more will come if we appropriately reward this one with our business. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC
RE: [PyMOL] adding a new external GUI
Tina,
You don't want to create a new thread -- Tcl/tk can only support
a single thread. Instead, you either need to wholly replace the
external GUI with your GUI, or you simply need to make your gui work
with the standard external GUI. The latter is generally done by adding
your own menu, which then creates it's own window in response to user
requests.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
ad...@lists.sourceforge.net] On Behalf Of Tina Li
Sent: Friday, September 05, 2003 11:49 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] adding a new external GUI
Hello,
I'm trying to add another external GUI to be positioned at the bottom
of
the
structure window for displaying sequence alignments, with not much
luck.
Here
is what I want and what I've done:
Goal: when opening a sequence alignment file in the existing GUI,
launch a
new
GUI at the bottom displaying the alignments. So:
- in \modules\pmg_tk, add a new class alignApp that inherits from
AbstractApp
(very similar to PMGApp for the exsting GUI), which adds widgets to
the
new
GUI and will parse files, etc..
- in \modules\pmg_tk\startup, add startNewGUI.py, whose __init__()
adds an
additional file open option (all files in this directory are
__init__'d
upon
startup of the existing GUI) to the existing GUI's File menu:
---
from pmg_tk.alignApp import *
def run_alignApp():
if not hasattr(sys,argv):
sys.argv=[pymol]
alignApp(balloon_state='both').run()
def alignment_open(self):
ofile = askopenfilename(initialdir = self.initialdir,
filetypes=[(XML File,*.xml),
(All Files,*.*),
(All Files,*),])
if len(ofile):
self.initialdir = re.sub(r[^\/\\]*$,,ofile)
t_alignApp = threading.Thread(target=run_alignApp,args=())
t_alignApp.setDaemon(1)
t_alignApp.start()
def __init__(self):
self.menuBar.addmenuitem('File', 'command', 'Open alignment
file.',
label=self.pad+'Open alignments',
command=lambda s=self:alignment_open(s))
---
The result: the new GUI appears as a one-piece small square frame
(1/6
the
width of the existing). No menu, output area or other widgets is
shown.
After
clicking in either GUI, the cursor turns busy, and both GUIs turn
non-responding.
I'm not sure if it's a Python thread problem on my part. Has anyone
done
something similar before? Let me know if it's more appropriate to ask
in a
Python newsgroup.
Thanks much!
Tina
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RE: [PyMOL] Filled view for deoxyribose rings, bases in DNA ???
Raji, Sorry, PyMOL can't do that yet. However, since you are probably the 10th person to ask for this, so it has become high priority for a future version... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of raji Sent: Saturday, September 06, 2003 7:34 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Filled view for deoxyribose rings, bases in DNA ??? Hi Everyone, How can I show the deoxyribose sugar and the bases in the DNA in the stick mode but as filled representations ? Thanks, Raji Raji Edayathumangalam Dept. of Biochemistry Molecular Biology Colorado State University Fort Collins, CO 80523 USA Tel:(970)491-4614 Fax:(970)491-0494 --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Re: cannot find _cmd module
Tina, Did you do a full installation? After running: python setup.py build install python setup2.py (in that order) pymol.bat should just work. There shouldn't be any need to copy anything over, nor should you set PYMOL_PATH -- that is all taken care of automatically with this approach. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Tina Li Sent: Wednesday, August 27, 2003 8:34 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Re: cannot find _cmd module Hello, So I figured that in my $PYMOL_PATH\build\lib.win32-2.2\pymol, there is a _cmd.pyd that's missing in $PYMOL_PATH\modules\pymol. I copied it over, and PyMOL started up, but said that it failed to import the xray module, which however exists in $PYMOL_PATH\modules\pymol, so I don't understand why it doesn't import that. Anyways, it seems to be up. I guess every time I build PyMOL, I'll have to copy the _cmd.pyd file over. Tina - Original Message - | From: Tina Li t...@bioinformaticssolutions.com | To: pymol-users@lists.sourceforge.net | Date: Mon, 25 Aug 2003 11:57:27 -0400 | Subject: [PyMOL] cannot find _cmd module | | Hello, | | Eh, I think this is a rather basic question. So I built PyMOL on Win32, tried | to run pymol.bat, which calls python $PYMOL_PATH/modules/pymol/__init__.py, | which complained: | | Traceback (most recent call last): | File D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py, line 92, in ? | import pymol | File D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py, line 300, in | ? | import _cmd | ImportError: No module named _cmd | | I have PYTHONPATH set to $PYMOL_PATH/modules. Is it something obvious I'm | missing? | | Thanks much! | | Tina --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Python commands and variables
Yes, but you need to write in Python directly. For example: from pymol import cmd cmd.select(mysel,none) for i in range(10,20): cmd.select(mysel,mysel or resi %d%i) Would work in a .py file. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Shu-Hsien Sheu Sent: Wednesday, August 27, 2003 1:10 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Python commands and variables Hi, I am new to Pymol with some experiences with Python. I have a basic question which maybe a little stupid. Does Pymal take Python commands in selecting atoms? For instance: i = range(1, 299) select resi i or, further: for i in range(1, 299) select resi i I understand the above can be easily done with: select resi 1-288 However, I am wondering if variables can work in Pymol in general. Thanks! --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] linker errors on win32?
Tina, layer0/MemoryCache.c is missing from the list of sources in the setup.py file. If you add that in right after the layer0/MemoryDebug.c, it should build. Sorry about that! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Tina Li Sent: Friday, August 22, 2003 10:31 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] linker errors on win32? Hello, I was following instructions in setup/INSTALL.win32 (as in pymol-0_90- src.tgz) to build PyMOL. I have all the external components (glut, zlib, libpng) in place. When I tried python setup.py build It generated linker errors: C:\Program Files\Microsoft Visual Studio\VC98\BIN\link.exe /DLL /nologo /INCREME NTAL:NO /LIBPATH:win32/lib /LIBPATH:C:\Python22\libs opengl32.lib glu32.lib glut 32.lib libpng.lib zlib.lib /EXPORT:init_cmd build\temp.win32-2.2\Release\Block.o [...more .obj here...] ... Creating library build\temp.win32-2.2\Release\_cmd.lib and object build\temp.win32-2.2\Release\_cmd.exp Map.obj : error LNK2001: unresolved external symbol _MemoryCacheFree MemoryDebug.obj : error LNK2001: unresolved external symbol _MemoryCacheFree Basis.obj : error LNK2001: unresolved external symbol _MemoryCacheFree Ray.obj : error LNK2001: unresolved external symbol _MemoryCacheFree Map.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc MemoryDebug.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc Basis.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc Ray.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc Map.obj : error LNK2001: unresolved external symbol _MemoryCacheCalloc MemoryDebug.obj : error LNK2001: unresolved external symbol _MemoryCacheRealloc main.obj : error LNK2001: unresolved external symbol _MemoryCacheDone main.obj : error LNK2001: unresolved external symbol _MemoryCacheInit build\lib.win32-2.2\pymol\_cmd.pyd : fatal error LNK1120: 6 unresolved externals error: command 'C:\Program Files\Microsoft Visual Studio\VC98\BIN\link.exe' failed with exit status 1120 I wonder if I'm missing a particular library. Thanks much, Tina --- This SF.net email is sponsored by: VM Ware With VMware you can run multiple operating systems on a single machine. WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the same time. Free trial click here:http://www.vmware.com/wl/offer/358/0 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] RE: E-mail worm is going around
Jan, Thanks for that -- copy hereby sent to the PyMOL list. This is a relief. I was wondering why strange bounced email was coming back and had become concerned that infection had occurred here despite every precaution. SMTP-based email is indeed a hopeless cause. I vote for a return to smoke signals and semaphores. - Warren Summary: The current viruses add a bogus From field, so don't get upset at the person who seemed to have sent that infected email to you since it wasn't really them. They are not infected -- someone else is. -Original Message- From: Computational Chemistry List [mailto:chemistry-requ...@ccl.net] On Behalf Of Dr. Jan K Labanowski Sent: Thursday, August 21, 2003 9:50 AM To: chemis...@ccl.net Cc: Dr. Jan K Labanowski Subject: CCL:E-mail worm is going around Dear CCL, Since I got few a questions, I will post an answer to the whole list to cool you down... There is a malicious Internet worm going on, which infects the (guess what...) Windows machines. It is an e-mail message which carries a virus with it (so it is about 100kB large to be able to pack the virus executable). It grabs addresses from the victim address book, and resends itself to these addresses, and to make things worse, it also changes its From: (i.e., the address from which the message is supposedly coming from) to some address from the victim's address book. Of course, according to the old saying: The worse, the better Microsoft will sell us upgraders, and improved products, and scoop millions of dollars in consulting hours from people who use their maintainance program. Hopefully events like this will revive economy and create new job opportunities. Obviously, the chemis...@ccl.net is in many people address books, as well as, my personal address. Many of you got the mail which is supposedly coming from, say, chemis...@ccl.net, but it really did not come from this address. If you want to know more about this malice, read on... The e-mail message consist of header and body. The header should contain the information about intended recipients, message origin, path which message traveled (gateways) before it got to you and the information about the type and methods of encoding used for the body of the message. The message body is the actual pay-load of the e-mail message). But make no mistake... Header is not the envelope of your mail. It is not used by mail software (mail transfer agent - MTA) to deliver your mail. Header has only an informational (or lately often dis-informational) value. The problem is that you can put anything you want in the header (beside maybe the top Received: header line, which is usually added by your own computer or mail gateway). The top Received: line (depending on the way your mail is configured) contains the information about the IP address of the machine which had sent you the the message, and the destination of the message (i.e., in most cases it lists your own machine and sometimes your user id, or mail alias). However, beside the first Received: line (or maybe more, if the mail was traveling to you via some trusted gateways as each legitimate MTA should add its Received: line to the header -- SHOULD, but DOES NOT HAVE TO!!!), all other header lines can be set by the mail originators to anything they want. Most importantly: the To:, From:, Cc: do not have to be real, and THESE FIELDS ARE NOT USED IN DELIVERING THE MESSAGE !!!. To be more precise, if you use a legitimate mail composing program, the destination of your mail message will be taken from the To: and/or Cc: lines, and the From: line will point to you, when your message is passed to your own mail transfer agent. BUT THE BAD GUYS DO NOT USE STANDARD AND LEGITIMATE MAIL COMPOSERS AND TRANSFER AGENTS!!! Note that the mail is delivered to your mail server by a special protocol (SMTP), where the recipient's and originator's address is given to your local mail server as a part of delivery process, and THEY DO NOT HAVE TO BE EVEN CLOSE to what is being given on the To: and From: lines of your message. At the same time, what is displayed in your e-mail browsing tool as message origin, is the From: line from header. CURRENTLY, THERE IS NO WAY TO ESTABLISH THE IDENTITY OF THE PERSON WHO HAD SENT MAIL TO YOU!!! The only thing which can be (in most cases!!!, not always!!!) established is the IP address of the machine which forwarded you the message (this can be guessed from inspecting the top Received: line of the header). In most cases the IP address of the originating machine is a TOTALLY USELESS information, since it gives you the pointer to the machine which was: 1) either hacked by spammers, 2) or infected by the virus (i.e., a victim like you), 3) or represents an open relay machine (made an open relay either intentionally or not) We badly need a new electronic
RE: [PyMOL] Pymol 3D printing
Thanks for your code! P.S. I wish this mailing list had archives ... But it does! http://sourceforge.net/mailarchive/forum.php?forum_id=60 You can search by keyword. Look for the text box upper-left. Cheers, Warren
RE: [PyMOL] Different symmetry positions
Alex, Symexp creates object with names of the form: prefixSSXXYYZZ After the prefix, the first two digits SS are the symmetry operation. The next six digits correspond to the relative integral unit cell translation XXYYZZ *after* an initial unit cell translation intended to bring the translated atoms back into closest adjacency. In other words, the exact XXYYZZ will depend on the atoms in the object, since that will determine the initial origin 00 translation. Nevertheless, the actual symmetry mates displayed should be equivalent, even if their names differ slightly. Are you finding otherwise? Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Alexander Zuev Sent: Tuesday, August 19, 2003 2:43 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Different symmetry positions Dear All, I have two pdb files: 1) protein trp and 2) the same protein with crystallographic water - tr. After creating symmetry related objects with symexp sp=trp,(trp),3.2 and symexp s=tr,(tr),3.2 the corresponding objects have different symmetry operations, for example, sp0201 corresponds s0200. Could you explain please, what this does mean? Thanks in advance, Alexander Zuev --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click- url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Delete Bonds
Jose, Select the bond using Ctrl-right-click, then either unbond pk1,pk2 or hit Ctrl-D. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Jose Avalos Sent: Monday, August 18, 2003 6:45 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Delete Bonds Hi I would like to know how can I break bonds that are wrongly drawn in pymol. I am only using a coordinate file with no connectivities. I know how to select the bond, but then I don't know how to delete the bond without deleting other correct bonds that involve one of the atoms in the incorrect bond. Thank you in advance Jose --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click- url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] strand representation + free label
Tina, That would be very difficult to do at present...I'll take this as a suggestion for a future version. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Tina Li Sent: Thursday, August 14, 2003 8:19 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] strand representation + free label Hello, I'm wondering if it's possible to simulate RasMol-styled strand representation (a number of smooth curves that run parallel to one another along the peptide plane of each residue). I would like something like that to repersent gaps in a structural alignment (i.e. a segment that doesn't exist in an approximated structure). Currently I'm using the dash lines as for bonds. However, is there a way to change the distance label into something I can specify, like 7 AA to indicate the gap length? Thanks, Tina --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click- url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] cartoons through nonstandard residues
David, You found a bug -- it turns out PyMOL was getting confused by the presence of a P atom in P-tyr. It thought the residue contained both protein and DNA, and so the cartoon had an extra gap. The following workaround should get you a complete cartoon with 1fmk. Future versions of PyMOL should not suffer from this problem. alter all.type='ATOM' alter name P,name='P1' sort Thanks for your help in quashing that bug! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: David A. Horita [mailto:dhor...@wfubmc.edu] Sent: Wednesday, August 06, 2003 5:27 AM To: Warren L. DeLano Subject: RE: [PyMOL] cartoons through nonstandard residues Warren, Thanks for the reply, but I still don't get the cartoon running through the phosphotyrosine. I've tried it on Src (1fmk.pdb), and still get a break between residues Gln526, Ptr 527 and Gln 528. Regards, David Horita -Original Message- From: Warren L. DeLano [mailto:war...@delanoscientific.com] Sent: Tuesday, August 05, 2003 7:17 PM To: David A. Horita; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] cartoons through nonstandard residues David, The problem: PyMOL sorts PDB hetatms apart from molecules. The solution: alter all, type='ATOM' sort rebuild I'm thinking about disabling this behavior before the next release... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A. Horita Sent: Tuesday, August 05, 2003 1:53 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] cartoons through nonstandard residues Hi, When I try to draw a cartoon through the backbone of a nonstandard residue (in this case, phosphotyrosine), the cartoon strand stops prior to the PTR and starts after. How do I get a continuous strand through the phosphotyrosine backbone (or other residues, in the general case)? Ribbons seem to go through the PTR without problem, and selenomets don't seem to cause trouble, either. Thanks, David Horita - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/
RE: [PyMOL] electrostatic potential ramp
If I understand the question correctly, the answer is disable ramp-name Cheers, Warren Hello: Is there anyway to remove the colour ramp from an electrostatic potential figure via a script (help hide doesn't list anything reasonable for this and there is nothing that I can see in the settings). Cheers, JTM
RE: [PyMOL] cartoons through nonstandard residues
David, The problem: PyMOL sorts PDB hetatms apart from molecules. The solution: alter all, type='ATOM' sort rebuild I'm thinking about disabling this behavior before the next release. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A. Horita Sent: Tuesday, August 05, 2003 1:53 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] cartoons through nonstandard residues Hi, When I try to draw a cartoon through the backbone of a nonstandard residue (in this case, phosphotyrosine), the cartoon strand stops prior to the PTR and starts after. How do I get a continuous strand through the phosphotyrosine backbone (or other residues, in the general case)? Ribbons seem to go through the PTR without problem, and selenomets don't seem to cause trouble, either. Thanks, David Horita - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/
RE: [PyMOL] cartoons through nonstandard residues
David, The problem: PyMOL sorts PDB hetatms apart from molecules. The solution: alter all, type=ATOM sort rebuild Im thinking about disabling this behavior before the next release Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A. Horita Sent: Tuesday, August 05, 2003 1:53 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] cartoons through nonstandard residues Hi, When I try to draw a cartoon through the backbone of a nonstandard residue (in this case, phosphotyrosine), the cartoon strand stops prior to the PTR and starts after. How do I get a continuous strand through the phosphotyrosine backbone (or other residues, in the general case)? Ribbons seem to go through the PTR without problem, and selenomets don't seem to cause trouble, either. Thanks, David Horita - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/
[PyMOL] Upcoming Rendering Changes. Comments?
PyMOLer's I've made some changes in the development version which I am considering for the next release. However, they will affect existing scripts, so I am warning people now, and asking for objections (if there are any). *** Subject 1: Ray tracing of lines, dots, mesh, dash, isomesh, ribbon, and nonbonded representations. Currently, when you ray, you have to manually adjust the radius of these objects for optimum quality. I propose that in version 0.92, that PyMOL will do this automatically to match the OpenGL image, unless you explicitly specify otherwise THIS WILL CHANGE THE OUTPUT OF EXISTING SCRIPTS, but it will be much easier for users going forward. PyMOL raytracing will be more WYSIWYG -- what you see in OpenGL will be closer to what you get when you ray trace. Prior behavior can be restored by setting the radii explicitly to their original values. *** Subject 2: Antialiased rendering The next version of PyMOL will default to a different antialiasing algorithm. In the past, we're used blanket 2X over-sampling of the complete image. The next version will focus that extra rendering energy where it counts: on the edges of objects. This turn out to be so much faster that I plan to make it the default (antialias=1). In most cases, image quality will improve and rendering times will improve by about 1 to 4-fold for antialiased images!. Blanket 2X, 3X, and 4X oversampling will still be possible using antialias=2, 3, or 4. Prior behavior can be restored by changing two settings (ray_oversample_cutoff-0 and antialias-0 or 2). If you have strong objections to these changes, please speak up. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] comprehensive rules for selection-expressions
Hi Tina, Welcome to PyMOL! We plan to use PyMOL as the alignment/structure viewer in a protein threading package we developed. Mostly there will be some new features/enhancements on the existing viewer. e.g. Great. That is one of the ways I hope people will make use of PyMOL. Do realize however that we're still in early days, and so don't expect it to be easy. PyMOL may be inexpensive from a cost standpoint, but you still need to invest substantial resources in order to get the most out of it. - highlight/color by mappings of amino acid porperties (cysteines, charge and hydrophobicity, size, secondary structure) - a sequence alignment pane in sync with the structure window; selecting residues in one selects them in the other - show multiple alignments simultaneously - permit structural superposition of templates (i.e. structures) There are all things PYMOL should be capable of doing in tandem with an external application. I'm personally new to PyMOL, and am poking around to explore the features (BTW, excellent graphics!). Right now I'm having difficulty with the syntax of selection-expressions. I don't see a comprehensive documentation of what counts as selections. Can cysteines already be highlighted? Is any of the mappings already available? On another note, I'm aware of the following way to color by secondary structures: The most comprehensive selection docs can be found at: http://pymol.sourceforge.net/newman/user/S0220commands.html#7 Getting started with commands in another must read http://pymol.sourceforge.net/newman/user/S0210start_cmds.html#6 color red, ss h color yellow, ss s color green, ss l+ which however seems a bit cumbersome. I'd prefer having a Color by... with options like secondary structure, charge, size, etc. under the menu item Display. But then, I figure many prefer command lines. The idea with PyMOL (from a developer/integrators standpoint) is that you can create the menus which suit the needs of your specific application. These are just some initial random thoughts. BTW, could someone explain what the different elems CHNOS* represent? I'd really appreciate more comprehensive documentation. That's just the coloring for Carbon, Hydrogen, Nitrogen, Oxygen, Sulfur, in the color pop-up menu. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] H-bond display
Gareth, CGO is currently the way to go... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Gareth Stockwell Sent: Friday, July 18, 2003 2:46 AM To: pymol-users Subject: [PyMOL] H-bond display I am using distance objects at the moment, to display h-bonding contacts. My question is ... is there any easy way to display the direction of an h-bond using distances (i.e. putting a little arrow on the dashed line)? I am prepared to bash out some functions which do this using CGOs, but of course I won't if it's already implemented! Gareth -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute --- This SF.net email is sponsored by: VM Ware With VMware you can run multiple operating systems on a single machine. WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the same time. Free trial click here: http://www.vmware.com/wl/offer/345/0 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] 0.90 Two Minor Bug Advisories
Two bugs to watch out for in version 0.90: (1) When ray tracing on a light background with antialiasing enabled, a one pixel wide border may appear. To workaround this, either crop your image after saving using something like Photoshop, or simply don't antialias (just ray with dimensions 2X as large). Thanks to David Chimento for finding this one! (2) Sessions containing isosurface-generated surfaces may not be saveable due to a Python exception. There is no workaround for this in the current version. Both bugs have been fixed in the development version under CVS. Cheers, Warren PS. Today I also added support for InsightII's ascii/formatted grid file (just in case anyone has some old Biosym GRD files lying around...). -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] Interaction surfaces
Joe, Currently with PyMOL, you are selecting are atoms, not points on the surface. Thus, you may need to increase the distance by 1-2 A or so to get what you want. It's also possible that something else is going on. I would not expect to see whole at the points of contact, but between them, where the contacts aren't so close. If the above advice doesn't help, then perhaps you could send me an example PNG file which illustrates the problem as an attachment? Cheers, Warren (PS. Selection of individual surface points will likely come in a future version...) -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Becker, Joseph W Sent: Friday, July 11, 2003 10:45 AM To: PyMOL (E-mail) Subject: [PyMOL] Interaction surfaces I have a problem representing the contact surface between, e.g., a protein and its ligand. The surface is displayed, but it is full of holes, apparently at the points of contact. The script: load protein.pdb, protein load ligand.pdb, ligand hide everything show surface, (protein and (ligand around 4)) gives something like one wants, but full of holes. With that object displayed, if one says show surface, protein one gets the full surface, without the holes. Any ideas on how to get the *partial* surface *without* the holes? Joe Becker Merck Research Labs P.S. load protein.pdb, protein load ligand.pdb, ligand hide everything create junk, (protein and (ligand around 4)) show surface, junk gives a similar (holey) result -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (Whitehouse Station, New Jersey, USA) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it. -- --- This SF.Net email sponsored by: Parasoft Error proof Web apps, automate testing more. Download eval WebKing and get a free book. www.parasoft.com/bulletproofapps1 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] New Map Formats Coming...
PyMOLers, In response to user requests, I have added support for BRIX (O maps) and FLD (AVS Field) map formats in the current development version. Are there any other map formats which people would use heavily if PyMOL were able to support them? Thanks, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] pymol on OSX
John, The native OSX port is incomplete with respect to the user interface. You can get the complete package if you use the Fink version under X11. PyMOL doesn't export 3D data well at present. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of John Holt Sent: Tuesday, July 08, 2003 7:02 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol on OSX I've just started experimenting with Pymol on OS X. The close, save, save as items are greyed out in the file menu. Could someone explain this to me? Also, is Pymol capable of saving as vrml files or some other 3D format? John Holt John Holt Studio 25 Drydock Ave. Boston, MA 02210 617.426.4658 617.426.1425 fax visiond...@johnholtstudio.com www.johnholtstudio.com --- This SF.Net email sponsored by: Parasoft Error proof Web apps, automate testing more. Download eval WebKing and get a free book. www.parasoft.com/bulletproofapps ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Electrostatic potential maps in PyMOL
Yes, you have identified the problem: PyMOL 0.90 currently only reads PHI files in one of the two endian formats (not sure if it is big or little). The problem is, how it PyMOL to determine which format the incoming map is in? The file format is so darn implicit, I haven't yet come up with any effective way of doing it without risking a floating exception on finicky hardware. Any ideas? If we can just determine the enddian-ness of the incoming file, then the rest is a snap. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] ca trace
Jason, In version 0.90, there is a ribbon_trace setting which allows you to do this for the ribbon representation. In versions 0.91+, I've added the same thing for cartoons cartoon_trace. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Jason Thomas Maynes Sent: Wednesday, July 09, 2003 10:30 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] ca trace Hello: I think this was asked before but the list archives are down: If I have a pdb of Ca's only, is there a way to trace through them without iteratively bonding them all (change allowed bond distance??) Can the tube cartoon recognize this? If I bond all the Ca together iteratively, the cartoon tube doesn't recognize that and go through the bonds, is there another way? Cheers, JTM We can be sure that if a detailed understanding of the molecular basis of chemo-therapeutic activity were to be obtained, the advance of medicine would be greatly accelerated. Linus Pauling, Nobel Laureate 1954 ...everything that living things do can be understood in terms of the jigglings and wigglings of atoms. Richard Feynman * Jason Thomas Maynes PhD/MD Program Department of Biochemistry Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca * --- This SF.Net email sponsored by: Parasoft Error proof Web apps, automate testing more. Download eval WebKing and get a free book. www.parasoft.com/bulletproofapps ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] RE: (no subject)
I just download PYMOL into my Linux and it's working very nicely but I want to check whether it is possible to move a pdb file within a 3D density map independently to get a best fitting. Yes, you can move the molecule, but not the map. First, get into editing mode: edit_mode (or select 3 Button Editing Mode from the Mouse menu, if you have one) Then, to move the whole molecule: shift-middle-click-and-drag on the molecule to translate shift-left-click-and-drag on the molecule to rotate ctrl-shift-middle-click on an atom to reset origin of rotation To rotate bonds, Ctrl-right-click-and-drag. Always click on the mobile side of the bond, otherwise, you'll end up moving the wrong portion of the molecule. To write out the new coordinates... save file.pdb, object-name NOTE: some of the above is specific to version 0.90, so make sure that's the version you have. Cheers, Warren
RE: [PyMOL] Further functionality
1- calculation of surface potentials- will this be coming soon? Creation of a Possion-Boltzman solver is a bit of work, so this will not happen very soon -- probably not until we accumulate enough sponsorship to contract with someone to perform the task. But perhaps someone might volunteer to write an open-source Python PB module in the meantime? [sounds like a good summer project for a graduate student in computational chemistry : )] In the meantime, I recommend using Grasp to calculate the potential, saving the potential as a .phi file, and then loading the potential into PyMOL for visualization. Delphi should work too in theory, but we're currently working to resolve a few problems with the approach... 2- Are you thinking of including any kind of sequence viewer and sequence alignment tools to tie in with the fitting - as seen with swissPDB? This would be verh high on my wishlist. It is high on my list as well. 3- Will you be including any more NMR biased features like a quick fitting and RMSD calculation for ensembles of structures? This is currently possible using intra_fit if the ensemble is loaded as a single object. Between objects, you can do pair-wise fits using fit or align, but that gets tedious with a lot of structures. The sequence viewer will hopefully make multi-object fitting easier. 4- Is there any chance you will be able to include non-continuous selections ie select (resi 10-20,30-40) rather than just 10-20 and ignore residues 30-40? This is already possible using the selection macros: 10-20,30-40/ which is equivalent to resi 10-20 or resi 30-40 Please see the new Command Syntax and Atom Selections chapter in the User's Manual for more information on selections. http://pymol.sourceforge.net/newman/user/S0220commands.html#7 Cheers, Warren
RE: [PyMOL] can't initialize module sglite
Yu Chen, There are two likely causes of this problem: (1) An old pymol.com file This may be caused by use of an outdated pymol.com startup script. The launch requirements for PyMOL changed slightly in this new version, so it may be necessary to create a fresh pymol.com from one of the templates in the setup directory. (2) Linking against Python 1.52 Make sure that Python is linking against version 2.x if possible. If you must use 1.52, you will need to compile the older versions of ExtensionClass.c and ExtensionClass.h located in the contrib/modules directory. I hope this helps. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Yu Chen Sent: Monday, July 07, 2003 12:34 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] can't initialize module sglite Hello, pymolers I installed pymol-0.90 from tar file on Redhat Linux 7.2 the same way as I installed pymol-0.88, the compiling all went well. But when running pymol, it gives out: Fatal error: can't initialize module sglite Not sure what happened, any help would be appreciated! Thanks in advance! Yu === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 122 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone:(410)455-6347 (410)455-2718 fax: (410)455-1174 email:c...@hhmi.umbc.edu === --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click-url.com/go/psa0016ave/direct;at.asp_061203_01/01 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] stereo parameters?
Dirk, stereo_angle is the amount of toe-in stereo_shift is the horizontal displacement of the camera Initially, stereo_angle=2.1 and stereo_shift=2.0 Generally, you don't need to adjust stereo_angle very much. Stereo_shift is what you want to focus on. Try increasing it by 1 or 2. For hardware or cross-eye, set stereo_shift, 4 For walleye, set stereo_angle, 1.95 set stereo_shift, 4 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Dirk Kostrewa Sent: Thursday, July 03, 2003 4:06 AM To: PyMOLBB Subject: [PyMOL] stereo parameters? Dear PyMol users, my subjective stereo impression with pymol in window stereo mode is too flat, both on SGI and on Linux, at least when I compare it with my ~10 years or so experience using other applications. I started to fiddle around with the stereo parameters stereo_angle and stereo_shift, but the results were not as expected from the presumed meaning for these parameters. Could anyone (maybe Warren?) please explain to me what the exact meaning of these two parameters IN PYMOL is? If I will find a subjectively better set of parameters I will post them as a suggestion on this board, then. Best regards, Dirk. -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OSRA/007 CH-5232 Villigen PSI, Switzerland E-mail: dirk.kostr...@psi.ch Phone: +41-56-310-4722 Fax: +41-56-310-4556 WWW: http://www.sb.psi.ch --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click-url.com/go/psa0016ave/direct;at.asp_061203_01/01 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] PyMOL v0.90 Released
PyMOL version 0.90 has been released for Windows, Linux, IRIX, and MacOS X*! http://sf.net/project/showfiles.php?group_id=4546 This is primarily a bug-fix and performance-enhanced release over version 0.88, which included many new features but suffered from unexpected problems. Version 0.90 has been more extensively tested then 0.88. The performance improvements include: * Faster ray-tracing (up to 2X improved). * Much faster calculation of partial surfaces. * Multiprocessing when ray-tracing. * Faster OpenGL using display lists (on some systems). If you have a dual-processor machine, then ray-tracing may now be up to four times faster. If you have a quad system, ray-tracing may now be up to eight times faster! (Please let me know if you run PyMOL on a system with more than four processors -- I'd like to see the results and know that it works.). Multiple CPUs should be auto-detected on Linux, Mac, and IRIX systems. Under Windows, set max_threads,2 if you have two CPUs, etc. To enable display lists, set use_display_lists,1. This helps all software renders, but it also helps the Mac hardware with dots, lines, and meshes. PCs with hardware accelerators generally see no benefit from using display lists. Cheers, Warren PS. If you like this release, then please do help out by purchasing a license and maintenance subscription. We're still a long ways from breaking even! * MacOS X users may prefer to wait for the 0.90 Fink update in order to get menus... -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
