Re: [PyMOL] Electrostatic surface visualization
Marco, If you haven't found a workable solution, you may try this little trick of stuffing values into the B Factor column (as someone previously mentioned). I just posted something about this on the wiki not too long ago. The script should make things clear if you're still unsure how to continue. http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring Regards, -- Jason On Tuesday 06 March 2007 09:03, pymol-users-requ...@lists.sourceforge.net wrote: > Message: 2 > Date: Tue, 6 Mar 2007 11:19:44 +0100 > From: "Gerebtzoff, Gregori" > Subject: Re: [PyMOL] Electrostatic surface visualization > To: , > Message-ID: > > Content-Type: text/plain; charset="US-ASCII" > > 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 -- Jason Vertrees (javer...@utmb.edu) Doctoral Student Biophysical, Structural & Computational Biology Program University of Texas Medical Branch Galveston, Texas http://www.best.utmb.edu/ http://www.pymolwiki.org/
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
Re: [PyMOL] Electrostatic surface visualization
On 3/3/07, se...@uniroma2.it wrote: 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. You can do this with commands like set transparency, 0.5, myproteinname or set transparency, 0.2, iso_pos 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. Not sure about that one. -Michael 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 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
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
RE: [PyMOL] electrostatic surface
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: http://sourceforge.net/mailarchive/forum.php?forum_id=60&max_rows=25&style=flat&viewmonth=200307&viewday=9 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. Script: http://expert.ics.purdue.edu/~geders/utilities/pymol_electrostatic_surface.sh Screenshot: http://expert.ics.purdue.edu/~geders/utilities/pymol_electrostatic_surface.png ~Todd On Tue, 2003-12-16 at 16:04, Warren L. DeLano wrote: > Ruslan, > > PyMOL can't yet calculate the electrostatic surface, but it > can > display the potential as output by Grasp, Delphi, MEAD, or Zap. > > 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 Sanishvili, Ruslan > > Sent: Tuesday, December 16, 2003 8:29 AM > > To: Warren L. DeLano; pymol-users@lists.sourceforge.net > > Subject: [PyMOL] electrostatic surface > > > > Hi all, > > Inexplicably, I haven't been following the PyMol news lately. Does > it > > now calculate and display the electrostatic fields/surfaces of > proteins > > (a la GRASP, or similar)? If it does, starting from which version? > > Thanks, > > Nukri > > > > > > Ruslan Sanishvili (Nukri), Ph.D. > > > > GM/CA-CAT, Bld. 436, D007 > > Biosciences Division, ANL > > 9700 S. Cass Ave. > > Argonne, IL 60439 > > > > Tel: (630)252-0665 > > Fax: (630)252-0667 > > rsanishv...@anl.gov > > > > > > > > > > --- > > 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_id78&alloc_id371&op=ick > > ___ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > --- > 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_id78&alloc_id371&op=ick > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
RE: [PyMOL] electrostatic surface
Ruslan, PyMOL can't yet calculate the electrostatic surface, but it can display the potential as output by Grasp, Delphi, MEAD, or Zap. 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 Sanishvili, Ruslan > Sent: Tuesday, December 16, 2003 8:29 AM > To: Warren L. DeLano; pymol-users@lists.sourceforge.net > Subject: [PyMOL] electrostatic surface > > Hi all, > Inexplicably, I haven't been following the PyMol news lately. Does it > now calculate and display the electrostatic fields/surfaces of proteins > (a la GRASP, or similar)? If it does, starting from which version? > Thanks, > Nukri > > > Ruslan Sanishvili (Nukri), Ph.D. > > GM/CA-CAT, Bld. 436, D007 > Biosciences Division, ANL > 9700 S. Cass Ave. > Argonne, IL 60439 > > Tel: (630)252-0665 > Fax: (630)252-0667 > rsanishv...@anl.gov > > > > > --- > 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_id78&alloc_id371&op=ick > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
