[PyMOL] ccp4 question
Dear Pymolers, I tried to run ncont on a pdb structure and got a .ncont file as output, but the only thing the file contains is an error message (see below). I tried copying default.def into the working directory, but couldn't get the darn thing to work. If someone can help I'd appreciate it. -- CCP4 library signal ccp4_general:Cannot open default.def (Error) raised in ccp4fyp ### ### ### ### CCP4 6.4: NCONTversion 6.4 : ## ### User: unknown Run date: 3/ 2/2014 Run time: 16:00:09 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. -- * ERROR #40 READ: Logical file name not found. -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk ___ 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] ccp4 question
Dear Stefan, On Tue, 2014-02-04 14:44 EST, Stefan Ivanov stefan.iva...@postgrad.manchester.ac.uk wrote: Dear Pymolers, I tried to run ncont on a pdb structure and got a .ncont file as output, but the only thing the file contains is an error message (see below). I tried copying default.def into the working directory, but couldn't get the darn thing to work. If someone can help I'd appreciate it. You might have better luck asking on the ccp4bb, but I'll try to answer... -- CCP4 library signal ccp4_general:Cannot open default.def (Error) raised in ccp4fyp ### ### ### ### CCP4 6.4: NCONTversion 6.4 : ## ### User: unknown Run date: 3/ 2/2014 Run time: 16:00:09 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. -- * ERROR #40 READ: Logical file name not found. You haven't told us how you tried to run it, but the error tells you that it is not finding your .pdb file. Did you run it on the command line? If so, did you type something like: ncont xyzin file.pdb The standard command line format for CCP4 programs is such that coordinate files are indicated by the xyzin (and xyzout) logical names. It can also be run from the ccp4i interface. Did you try that? Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk ___ 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
[PyMOL] arbitrary distance label for atom pair
Hi, Is there an easy way to change the label on a distance object to some arbitrary string? I would like a line connecting two atoms with an arbitrary label at the midpoint between the two atoms. for example: #make atom pair selection distance d, (id 3651, id 3691) # actual distance = 2.00 #replace 2.00 with 100% # or any other string label d, 100% Thanks. -- --- Regards Richard Smith Research Associate Department of Zoology Smith Research Group University of Cambridge Downing Street Cambridge CB2 3EJ Tel.: +44 (0)1223 330933 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk ___ 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] arbitrary distance label for atom pair
Richard, The PyMOL team was just discussing this a few days back. Sadly, there is no way to do this using standard labels. If you have Incentive PyMOL v1.7 you can use the new callout command (http://pymol.org/dsc/dokuwiki/doku.php?id=command:callout). Otherwise you can use the pseudoatom (http://www.pymolwiki.org/index.php/Pseudoatom) as a label: # create a single ala frag ala # create a labeled distance dist 2/N, 2/O # hide the labels hide labels # create a new label at the center of the selection pseudoatom new_label, (2/N or 2/O), label=Some arbitrary label here: \316\261 orient Cheers, -- Jason On Tue, Feb 4, 2014 at 10:07 AM, Richard Smith re...@cam.ac.uk wrote: Hi, Is there an easy way to change the label on a distance object to some arbitrary string? I would like a line connecting two atoms with an arbitrary label at the midpoint between the two atoms. for example: #make atom pair selection distance d, (id 3651, id 3691) # actual distance = 2.00 #replace 2.00 with 100% # or any other string label d, 100% Thanks. -- --- Regards Richard Smith Research Associate Department of Zoology Smith Research Group University of Cambridge Downing Street Cambridge CB2 3EJ Tel.: +44 (0)1223 330933 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk ___ 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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk ___ 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
[PyMOL] PyMOL on Coursera
Greetings, I am happy to report that PyMOL will be used in a structural biolnformatics lab of an upcoming Coursera course, Bioinformatic Methods 2, taught by Nicholas Provart of the University of Toronto. The enrollment for these courses can typically be in the tens of thousands or more. If you would like to learn more about this free online course visit https://www.coursera.org/course/bioinfomethods2. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk ___ 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
[PyMOL] script with arguments.
Hello, I am making a script that loads in two molecules as arguments in the command line. I want to then align these molecules and make a pretty picture of the molecules that were input as arguments in the comand line but I am not sure how to name them as objects. I don't know how to select the new objects because they will have different names depending on the inputed arguments. My attempt is below. -Yarrow -- from sys import argv my_argv = argv[1:] print my_argv[0], my_argv[1] from pymol import cmd, stored def align_heme(arg1, arg2 ): cmd.load(arg1) cmd.load(arg2) cmd.create(obj1, arg1) #I know this line won't work. I need to use the#object name. but it depends on the input. -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk___ 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] script with arguments.
Oh, I see what your saying. This is a python question. from sys import argv c_arg1 = argv[1] c_arg2 = argv[2] from pymol import cmd, stored def align_heme(arg1, arg2 ): cmd.load(arg1) cmd.load(arg2) cmd align(arg1,arg2) #cmd.create(obj1, arg1) #There is no need to create an object here. align_heme(c_arg1,c_arg2) On Feb 4, 2014, at 6:57 PM, Yarrow Madrona amadr...@uci.edu wrote: Hello, I am making a script that loads in two molecules as arguments in the command line. I want to then align these molecules and make a pretty picture of the molecules that were input as arguments in the comand line but I am not sure how to name them as objects. I don't know how to select the new objects because they will have different names depending on the inputed arguments. My attempt is below. -Yarrow -- from sys import argv my_argv = argv[1:] print my_argv[0], my_argv[1] from pymol import cmd, stored def align_heme(arg1, arg2 ): cmd.load(arg1) cmd.load(arg2) cmd.create(obj1, arg1) #I know this line won't work. I need to use the#object name. but it depends on the input. -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk___ 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 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk___ 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
