Re: [PyMOL] PyMOL on the Mac
I second Tsjerk on this, maybe in the .pymolrc? And auto_show_sticks would be very useful to me! Cheers, Greg -Original Message- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Tuesday, March 16, 2010 6:17 AM To: Jason Vertrees Cc: pymol-users@lists.sourceforge.net; David Hall Subject: Re: [PyMOL] PyMOL on the Mac Hi Jason, Along those lines, would it be possible to have a 'default' which can be set to a list of settings related to appearance? That might be more concise than to have everything in a separate setting. set default,[cartoon, lines, nonbonded, cbaw] The default value as pymol starts up now would be [lines, nonbonded, cbag]. Just my 2 eurocents... Cheers, Tsjerk On Tue, Mar 16, 2010 at 12:53 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: David, You may remember writing: A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Well, reading through the source today, I found a couple settings that few know about--and I might add more similar settings: auto_show_lines == show a newly loaded object with lines representation? auto_show_spheres == show a newly loaded object with spheres representation? auto_show_nonbonded == show newly loaded non-bonded? If these are considered useful, I can add others like: auto_show_cartoon(s) # example set auto_show_spheres fetch 1cll This offers some more flexibility for the user to choose lines or other default representation. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] color by element
What I personally do is: cmd.color(grey50,all) util.cnc(all) So that my carbons have the color I wish (grey50), and other atoms are colored by element. Best, Greg -Original Message- From: David Hall [mailto:li...@cowsandmilk.net] Sent: Wednesday, February 10, 2010 1:45 AM To: Ariel Talavera Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] color by element First of all, there is: color atomic which will do all the colors and for whatever reason does green for carbons Additionally, there's a general class of util.cba? where question mark is replaced by one letter representing the color of carbon. I've been told by people that these are supposed to be internal commands and I shouldn't use them, but I do and they've been there as long as I've used pymol. Currently, these are: util.cbab for slate util.cbag for green util.cbam for magenta util.cbap for purple util.cbaw for white util.cbac for cyan util.cbak for pink util.cbao for orange util.cbas for salmon util.cbay for yellow You can see how these are implemented in http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/modules/pymol/util.py?view=markup if you want to make your own custom versions. -David Hall On Tue, Feb 9, 2010 at 5:46 PM, Ariel Talavera talav...@cim.sld.cu wrote: Hi Pymolers, How can I use the color by element (HNOS) function present in the GUI, in a script? Thanks in advanced, Best, Ariel -- * Ariel Talavera Pérez, PhD Center of Molecular Immunology calle 216 esq. A 15, Atabey, Playa Havana 11600, CUBA tel: (53-7) 271 7933, ext. 221 fax: (53-7) 272 0644 email: talav...@cim.sld.cu * -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] unexpected EOF while parsing
Jouko, Try to use the cmd.load(pdb) command instead of load pdb Apparently, the load statement takes a file name as argument, not a variable, whereas the api call (cmd.load) can handle variables. Best, Grégori -Original Message- From: jo...@uchicago.edu [mailto:jo...@uchicago.edu] Sent: Tuesday, July 07, 2009 3:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] unexpected EOF while parsing I am new to pymol and python. I have a number of cross sections of lysozyme. I want to display them one by one, color them using a script file that I have written earlier, and save the image. I have written a script file that I had hoped would do this. I have a couple problems with script file, but the one that is frustrating me the most is that immediately after the beginning of for loop pymol says that there in an unexpected EOF. The other problem is that when I try to use the variable pdb, pymol does not use the value of the variable, but the variable name itself. I have pasted my script file below and part of the log file. from pymol.cgo import * import colorsys,sys,re from pymol import cmd z=-8.153 inc=0.5 Sections=100 for j in range(0, Sections): pdb=c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2-4a/DensityCube_Lysozyme2-4a_ + str(z) + .pdb load pdb @c:/b_color8.plm png pdb delete pdb z=z+inc PyMOL@c:/Users/jouko/CrossSections.plm PyMOLfrom pymol.cgo import * PyMOLimport colorsys,sys,re PyMOLfrom pymol import cmd PyMOLz=-8.153 PyMOLinc=0.5 PyMOLSections=100 PyMOLfor j in range(o, Sections): Traceback (most recent call last): File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py, line 256, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1 for j in range(o, Sections): ^ SyntaxError: unexpected EOF while parsing PyMOLpdb=c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2-4a/DensityCube_Lysozyme2-4a_ + str(z) + .pdb PyMOLload pdb ExecutiveProcessPDBFile-Error: Unable to open file 'pdb'. Thanks in advance for your advice. Jouko -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/blackberry ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Electrostatic surface visualization
Marco, Maybe you could replace (alter) the B-factor of your protein with the electrostatic values, and color it accordingly; some googling should give you more hints about how you could solve this issue, like http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/data2bfactor.py and http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/color_b.py from Robert Campbell. A lot of useful scripts are posted on his website: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Cheers, Greg -Original Message- From: se...@uniroma2.it [mailto:se...@uniroma2.it] Sent: Saturday, March 03, 2007 11:40 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Electrostatic surface visualization Dear all, I'm new to this list and to the software. I used PyMOL and APBS to calculate an electrostatic surface for a small protein (I'm using the WindowsXP version) and everything seems fine. Now I would like to visualize this surface AND the secondary structure of the protein, in order to understand the positive and negative regions. How I can do? Some software show the surface in trasparency but it seems this is not possible in PyMOL. A related question: it is possible to color the secondary structure according to the electrostatic surface properties? I have an NMR titration of this protein with its partner: I would like to relate the shifts of the NH backbone with the electrostatic surface. I looked at the archive but I haven't found an answer. Thanks in advance, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, Tor Vergata via della Ricerca Scientifica, 00133, Rome, Italy e-mail:se...@uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328
