RE: [PyMOL] electrostatic surface
Todd Geders said: Hello all, Here is a simple script that automates the electrostatic potential surface generation using Gromacs, MEAD, and Pymol for visualization. It's exclusively based off of the post by Esben Peter Friis: It requires you to massage your pdb file a bit, but it gets the job done. Please glance at the comments in the script to see what I mean. Thanks Todd for the script. I installed Gromacs 3.2 beta, MEAD 2.2.3 on Mac OS 10.3. The only change is that the $PDB.mdp file has to contain: cpp = /usr/bin/cpp to specify the cpp location in OS X. Run the script, seems to work. Now the question is how do I go about validating the results? I tried to compare one image I get with the one published for 1ALK.pdb but there were some differences :-(. Would anyone in the list be willing to send me the files for one of their proteins, so I can re-run the calculations and compare what I get? Thanks Michele Fuortes -- -- Michele Fuortes, M.D., Ph.D. Assistant Professor Departments of Surgery and of Cell and Developmental Biology Cornell University - Weill Medical College E-mail: mfuor...@med.cornell.edu
[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
RE: [PyMOL] Question
Hi Avram This is possible in cartoon mode in the newer versions of PyMOL (i don't remember exactly from which). You have to select highlight color in the cartoon menu. The default color is grey, but can be changed by set cartoon_highlight_color, color_name, object_name Cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net To: pymol-users@lists.sourceforge.net Sent: 19-12-03 20:37 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] 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
[PyMOL] Fwd: Re: PyMOL-users digest, Vol 1 #491 - 3 msgs
Hi, I would like to know how to insert a movie into PowerPoint (for Mac OS X). Should I firt convert it into an animated .gif in another program like flash? 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 -- Avram M. Slovic Biochemistry and Molecular Biophysics University of Pennsylvania 420 Curie Blvd. 1010 Stellar Chance Bldg. Philadelphia, PA 19104 L:215-898-3496
[PyMOL] Another question
Hi all, another question. Does anyone know how to make spheres smaller. I would like to make the ball and stick looking residues like those in Molscript thank you 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
RE: [PyMOL] Another question
Avram, You use the sphere_scale setting: i.e. set sphere_scale, 0.2 Best, Ken -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 12:40 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Another question Hi all, another question. Does anyone know how to make spheres smaller. I would like to make the ball and stick looking residues like those in Molscript thank you 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
