Re: [PyMOL] Visualizing sp3-hybridized electron orbital
Hi Yury, if you have the electron cloud as map data, you can load it into PyMOL and use any map visualization (volume, isosurface, isomesh). Once the map is loaded into PyMOL, use the A (Action) button next to the object name in the object menu panel on the right. Supported map formats include: xplor, ccp4, phi, dx. Cheers, Thomas Yury Polikanov wrote, On 06/13/13 20:50: Dear PyMOL users, I need to visualize sp3-hybridized electron cloud with lone pair of electrons to make figure explaining the chemical mechanism of the reaction. Does anyone know if it is possible to accomplish with PyMOL??? Any comments or suggestions would be valuable! Thanks a lot in advance! Best regards, Yury -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-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] Isomesh plot in Pymol vs Coot
Hi Partha, load your structure and map into PyMOL like this: PyMOL load your.pdb PyMOL load your_2fofc.map, format=ccp4 or: PyMOL load your_2fofc.ccp4 Hope that helps. Cheers, Thomas Munshi, Parthapratim wrote, On 06/13/13 21:20: Hi I am having some issues with the isomesh plot in PyMol. The map at same sigma level in Coot and PyMol varies by a certain factor. From google search, I notice that I am not the only one had such problem and following was the relevant post some years ago. Now, how do I mimic coot in case I want to load my own pdb and maps but not fetch? I did try the following steps with my pdb and maps but while loading it doesn't like type=2fofc and async keywords. Any help on this would be highly appreciating. Thanks Partha In PyMOL: # mimic Coot set orthoscopic set line_width, 5 # get the data fetch 1cll, async=0 fetch 1cll, type=2fofc, async=0 # create the map; carve 2.5 Ang from the polymer isomesh 1cll_map,1cll_2fofc, 1.06, poly, carve=2.5 # find example residue orient i. 78 # color color magenta, e. N color tv_yellow, e. C In Coot: * Fetch 1CLL and its map from EDS * zoom to residue 78 * scroll to 1.06 sigma -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-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] Distorted secondary structure using 'alter' command
Hi Ritu, do I understand correctly that resi 3-9 are *not* in helix conformation, and you want to perform a modelling task? Altering the ss property is not sufficient, that's just an annotation and not a modelling constraint. PyMOL is primarily a visualization tool and less a modelling tool, although you have some options here. Have a look at this PyMOLWiki script: http://pymolwiki.org/index.php/Set_phipsi And this page: http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Hope that helps. Cheers, Thomas Rituparna Sengupta wrote, On 06/13/13 19:30: Hi All, I'm trying to change a stretch of a polypeptide chain (residues 3-9) into a helix. I use the alter command: alter 3-9/, ss='H' But when I try to see the updated structure in cartoon, the structure doesn't appear like a helix. It looks like a distorted helix. How do I correct it? Thanks, Ritu -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-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] PyMOL 1.6 pre-release announcement
Hello Thomas and David, Was there any resolution of this? I've just compiled the latest version from SVN and I have the same problem opening files created under version 1.5.0. This is on Debian testing (32-bit). Cheers, Rob On Fri, 2013-04-26 19:15 EDT, David Hall li...@cowsandmilk.net wrote: Hi Thomas, I'm running into issues with color compatibility between 1.6 and earlier versions when opening pses (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: Setting-Error: type read mismatch (color) 6 Setting-Error: type read mismatch (color) 663 Setting-Error: type read mismatch (color) 664 (b) background color disparity: saved in 1.5 with black background; opens in 1.6 with a white background saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red background These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, others who would like to beta test can use devel:languages:python repo in openSUSE: https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython -David -- 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 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-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
