Re: [PyMOL] script error? SyntaxError: invalid syntax
Hi Petro, run expects a python script (.py), whereas you're trying to run a pymol script (.pml). For that you nead '@': @c:\pict.pml Cheers, Tsjerk On 7/6/06, Piter_ x.pi...@gmail.com wrote: Hi all I have some errors if I run script: PyMOLrun c:\pict.pml Traceback (most recent call last): File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py, line 273, in parse parsing.run_file (exp_path(args[nest][0]),pymol_names,pymol_names) File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py, line 407, in run_file execfile(file,global_ns,local_ns) File c:\pict.pml, line 1 show sticks,tups1 ^ SyntaxError: invalid syntax PyMOLshow sticks,tups1 (if i run it in command line it works) or the same: PyMOLrun c:\pict.pml Traceback (most recent call last): File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py, line 273, in parse parsing.run_file (exp_path(args[nest][0]),pymol_names,pymol_names) File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py, line 407, in run_file execfile(file,global_ns,local_ns) File c:\pict.pml, line 1 select cyt100,1HRC_Cys8_TUPS_W_1_MD_100 not resn ben+sul+thi+npr+wat+hem ^ SyntaxError: invalid syntax The script: show sticks, tups1 show surface, cyt100 png tups1.png hide sticks, all hide surface, all tups1 and cyt100 are named selections. Thanks for help. Petro Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
Re: [PyMOL] How do you show the coordinates of an atom?
On Thu, Jul 06, 2006 at 10:14:33AM -0500, Scott P Brown wrote: That's not a very helpful response, as it may not be clear how one maps an atom selection in Pymol to the corresponding line in a PDB file. Helfpulness is in the eye of the beholder. I certainly intended, and still expect, that what I posted might have been of some help to the original poster, and to the quality of the list in general. I thought of digging up and posting a link to the PDB specification--specifically to that of the ATOM record and to the coordinate fields of that record--and getting into the whole question as to how one works with text files on particular platforms, but it just didn't seem the right thing to do at the time. Someone who shows an explicit unfamiliarity with what a PDB file provides or does not provide is, in my opinion, best nudged in the direction of learning about this crucial file format itself--certainly about the ATOM record if nothing else. Such familiarity is more general and more useful over the long-term than knowledge about the peculiarities of the current syntax of a single command in just one of the many programs which work with PDB files. Of course, your mileage may vary. The primary question was how to get the coordinates of an atom, with the original poster using a selection as an example. My response addressed the primary question. Your response addresses the example. Even so, I found your response helpful, since I wasn't familiar with iterate_state before (though I see it has been mentioned in passing over the years in example code). My archive of this list has some holes, but for the most part it now stretches back over 4 years and over four thousand posts. Any post which in turn elicits a detailed answer on a feature of PyMOL, from someone who has not in that time (as best I can tell) ever before offered their expertise, counts as a helpful post indeed. I look forward to reading further helpful posts from you in the future, and hope that those posts needn't be in reaction to something I've sent that has been found wanting. Regards, -- Joe To print out the coordinates within Pymol, you need to use the command iterate_state, e.g.: iterate_state 1, selection_name, print x,y,z Where selection_name is the name of the object for the atom(s) you've selected, and x, y, z are the coordinates of the atom(s). D. Joe Anderson dee...@iastate.edu Sent by: pymol-users-boun...@lists.sourceforge.net 07/06/2006 09:10 AM To pymol-users@lists.sourceforge.net cc Subject Re: [PyMOL] How do you show the coordinates of an atom? On Wed, Jul 05, 2006 at 04:33:16PM -0400, John Anderson wrote: or are the coordinates in the pdb file? They are, yes. -- D. Joe Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- D. Joe Anderson, Asst. Sci.2252 Molecular Biology Bldg Biochem, Biophys, Mol Bio Iowa State Univ, Ames, IA 50010 How to help someone use a computer http://polaris.gseis.ucla.edu/pagre/how-to-help.html
Re: [PyMOL] Movie to Powerpoint
In my experience, animated gifs run beautifully in web browsers on all platforms and in openoffice under linux. They are usually awful in powerpoint on any platform. (And to be honest I don't really notice the lack of color depth.) Alternatively, MPEGs tend to run well in powerpoint, but are troublesome under linux. One can convert between MPEGs and gifanims using a complicated combination of imagemagic and mencoder/MPEG. Cheers, Charlie Noinaj wrote: My vote is against animated-GIFs. I have experienced problems with animated GIFs in the past where they seem to run fine on my computer, then not work properly (very slow) on a laptop during a presentation, etc. Could be that I am setting them up wrong, but for this reason, I avoid animated-GIFs unless for websites and such. Hope this helps. Best of Luck! cheers, nick - Original Message - From: Grégori Gerebtzoff gregori.gerebtz...@unibas.ch To: 'Karsten Seidel' k...@nmr.mpibpc.mpg.de; pymol-users@lists.sourceforge.net Sent: Friday, July 07, 2006 2:28 AM Subject: Re: [PyMOL] Movie to Powerpoint The problem with animated gif is the color limitation to 254 + one transparent colors, whereas PyMOL generated png's have millions of colors + alpha channel... -Original Message- From: Karsten Seidel [mailto:k...@nmr.mpibpc.mpg.de] Sent: jeudi, 6. juillet 2006 18:15 To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Movie to Powerpoint Hi there, first of all, let me say hello to all list subscribers, as I'm new here. I've been evaluating PyMOL for a couple of months now, coming from Molmol. Chiradip, one option next to creating an MPEG file is to make an animated GIF. Unfortunately, I don't know a free program under Windows to do this job, but you might want to look for it on the web, there must be some. I created a GIF from a set of PyMOL pictures using GraphicConverter on a Mac, a program that came free with OS X (as of 10.3 or 10.4, at least). The file runs fine in Powerpoint under Windows, and one doesn't have problems with missing codecs when presenting the slides on an old computer. Just make sure the file is not too large, it may not run as smooth as an .avi on an old box (which implies that this may not be the most elegant solution to the problem, consider it a quick workaround). Karsten. chiradip chatterjee wrote: Hi Friends I am a new Windows pymol user. I made a movie in Pymol and saved the 120 ray traced *.png frames. Now I want to convert the *.png files to MPEG files and then directly convert/run the movie in the Powerpoint presentation. can anyone please help me in this regard Thanks Chiradip ___ The all-new Yahoo! Mail goes wherever you go - free your email address from your Internet provider. http://uk.docs.yahoo.com/nowyoucan.html Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Karsten Seidel Max-Planck-Institute for biophysical Chemistry Department of NMR-based Structural Biology (NMR II) Am Fassberg 11 D-37077 Goettingen Phone/Fax: ++49-551-201-2213/2202 Email: k...@nmr.mpibpc.mpg.de http://www.mpibpc.gwdg.de/abteilungen/030/baldus/ Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Dr Charles S. BondUniversity of Dundee Tel: +44-1382-388325 Honorary Lecturer Dow St, Dundee Fax: +44-1382-345764 BBSRC David Phillips Fellow DD1 5EH, Scotland c.s.b...@dundee.ac.uk School of Life Sciences http://stein.bioch.dundee.ac.uk/~charlie
Re: [PyMOL] hydrogen bonds
On Fri, 2006-07-07 at 11:22 -0400, Nalam, Madhavi wrote: Hello, How do I draw a hydrogen bond between two atoms in PyMol? Please see: http://www.rubor.de/bioinf/tips_modeling.html http://www.rubor.de/bioinf/pml/hbond1.pml http://www.rubor.de/bioinf/pml/hbond2.pml http://www.rubor.de/bioinf/pml/hbond.py Credits to the original authors. Regards, Shantanu -- Shantanu Sharma, Graduate Student - Dokholyan Group, Dept of Biochemistry Biophysics, Univ of North Carolina at Chapel Hill 405 MEJ Bldg CB#7260 Chapel Hill, NC 27599-7260 Ph: (919) 966-3137
[PyMOL] (no subject)
Hello all, I am a new PyMOL user trying to prepare figures for publication. I'm confused about the difference between the isomesh level of the 'mesh' in PyMOL and the contour level of the electron density map that I read in from CCP4. For example, for one of my figures I created a 3sigma Fo-Fc omit map and read it in to PyMOL. In order to make the density lovely I used the 'map_double' command and created a second 'mesh'. I then adjusted each of these 'mesh' to a 'level' of 4. Does this mean that my omit map is actually now contoured to 4sigma, or are the two not related? Thanks for any help, Gabrielle
