Re: [PyMOL] electrostatic potential as cartoon?

Erratum: Of course I meant "solvent accessible", not "excluded". On 05 Jan 2017, at 09:52, Thomas Holder wrote: > Hi Vincent, > > Coloring the cartoon with a color ramp is not possible unfortunately. > Incentive PyMOL since version 1.8 can color ribbon by ramp,

Re: [PyMOL] electrostatic potential as cartoon?

Hi Vincent, Coloring the cartoon with a color ramp is not possible unfortunately. Incentive PyMOL since version 1.8 can color ribbon by ramp, if that helps. However, electrostatic potential locally probed along the backbone will not be very meaningful. Typically you would look at

Re: [PyMOL] electrostatic potential as cartoon?

Vincent, You could use data2bfactor.py and then "spectrum b" to color residues in cartoon settings. https://pymolwiki.org/index.php/Color (data2bfactor from Robert Campbell's script repository: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Jed On 1/4/2017 11:05 AM, vincent Chaptal

Re: [PyMOL] Electrostatic potential surface

The problem with pdb2pqr have been solved :) Another question which I have is the calculation of the potential maps from the ensemble of the conformers (for example I want to compare potential distribution from the ensemble of the x-ray structures of one protein which were solved in different

Re: [PyMOL] Electrostatic potential surface

I have a similar requirement, taking density and potential dstriutbutions from  jdftx which are written as plain binarry doubles. I use a script and some code to create an xplor file which seems to work but I have to adjust the position and scale to let it overlay the ion positions that I read

Re: [PyMOL] Electrostatic potential surface

As I understood the APBs plugin which already exist in PyMol is the very efficient device for electrostatic potential calculations. 2 questions have been arisen: 1- How I could change cut-off distances for the electrostatic? E.g I'd like to consider only interactions within 5 A between any

Re: [PyMOL] Electrostatic potential surface

by the way have someone had problems with the pdb2pqr usage with APBS in pymol? I've tried to install pdb2pqr from source as well as via packages then I've add usr/bin/pdb2pqr to the APBs plugin window and when I've started APBS I obtained error like Error: 5 type

Re: [PyMOL] Electrostatic calculations with ligand bound

Hi Andrew, The main limitation for problems like this is that you need to have parameters for the ligand. Making sure that you have good parameters is often an expert-level topic, and you're probably best served by the APBS or PDB2PQR listservs as well as the literature ... but, you can get a

Re: [PyMOL] Electrostatic calculations with ligand bound

Hi Andrew. I experienced something similar for the autodock_plugin. http://www.pymolwiki.org/index.php/Autodock_plugin During my trials, I notified two things for autodock. It did not like funny atom names or Alternative configuration Could this be a case for your protein / ligand? I don't know

Re: [PyMOL] Electrostatic surface visualization

Subject: Re: [PyMOL] Electrostatic surface visualization To: se...@uniroma2.it, pymol-users@lists.sourceforge.net Message-ID: a4dfb50223089d468de79aac4018791139d...@rkamsem3.emea.roche.com Content-Type: text/plain; charset=US-ASCII Marco, Maybe you could replace (alter) the B-factor

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

Re: [PyMOL] Electrostatic surface visualization

On 3/3/07, se...@uniroma2.it 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

RE: [PyMOL] electrostatic

Are you using the same platform for both Grasp and Pymol? I don't think that big-endian maps (written by an SGI computer) can be read by a little-endian platform, such as a x86 based PC. - Esben The problem is getting the phi map in grasp. Can somebody explain me how to do it? This is

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

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:

RE: [PyMOL] Electrostatic potential maps in PyMOL

To: EPF (Esben Peter Friis) Sent: 14-09-03 20:28 Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL Dear Esben, no matter how hard I try, I cannot make pymol read a phi map converted from avs with your utility. The .fld file was generated with the potential program in the latest MEAD

RE: [PyMOL] electrostatic potential ramp

If I understand the question correctly, the answer is disable ramp-name Cheers, Warren Hello: Is there anyway to remove the colour ramp from an electrostatic potential figure via a script (help hide doesn't list anything reasonable for this and there is nothing that I can see in the

RE: [PyMOL] Electrostatic potential maps in PyMOL

] On Behalf Of Warren L. DeLano Sent: Wednesday, July 09, 2003 2:20 PM To: 'EPF (Esben Peter Friis)'; 'Kaushik Raha '; 'Yu Chen ' Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Electrostatic potential maps in PyMOL Yes, you have identified the problem: PyMOL 0.90 currently only

Re: [PyMOL] Electrostatic potential maps in PyMOL

] On Behalf Of Warren L. DeLano Sent: Wednesday, July 09, 2003 2:20 PM To: 'EPF (Esben Peter Friis)'; 'Kaushik Raha '; 'Yu Chen ' Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Electrostatic potential maps in PyMOL Yes, you have identified the problem: PyMOL 0.90 currently only reads

Re: [PyMOL] Electrostatic potential maps in PyMOL

Hi Esben, I tried to follow your instructions to create and display an electrostatic surface potential. I used 1UBQ.pdb as input. In Mead, I encountered the following error when running potential -epsin 2 -CoarseFieldOut 1UBQ 1UBQ Starting potential for molecule named 1UBQ with interior

Re: [PyMOL] Electrostatic potential maps in PyMOL

There has been some talk on the list regarding failure of PyMOL in reading Delphi generated potential maps that I missed. I have generated phimap using a modified version of Delphi in the GRASP format that PyMOL reads and displays without any problem. So I am not sure what the problem is.

Re: [PyMOL] Electrostatic potential maps in PyMOL

Hello, Kaushik Yeah, we do had problems with DelPhi to PyMoL. I don't know what your mean by modified version of Delphi... We bought the latest Delphi from their website, and used the data from all the example folders comes with Delphi. The calculation all went well. When we tried to read the

RE: [PyMOL] Electrostatic potential maps in PyMOL

Yes, you have identified the problem: PyMOL 0.90 currently only reads PHI files in one of the two endian formats (not sure if it is big or little). The problem is, how it PyMOL to determine which format the incoming map is in? The file format is so darn implicit, I haven't yet come up with