Re: [PyMOL] A faster way of unbonding things?

If you have a PDB file of the ligands and know the number of atoms in each ligand, then you could introduce a TER card after the each ligand. That way PyMOL will not draw bonds between the ligands. If you want to visualize it one after the other then MODEL and ENDMDL cards before and after each

[PyMOL] More on Plugins

yet) are platform independent. I just checked out the sequence viewer in 0.96 and its great. Kaushik -- Kaushik Raha Merz Research Group Penn State University On Wednesday, July 14, 2004, at 03:56 PM, Warren DeLano wrote: Charles, Simply awesome! It works great on Windows and Mac too

[PyMOL] Coloring atoms by charge

Hi, Is there a way to color atoms by charge in PyMOL? Can PyMOL read the charges in a PDB file use those charges to color the atoms? Thanks, Kaushik.

[PyMOL] Using Numeric from PyMOL

Hi Warren, I am trying to use the Numeric module from within my PyMOL "pluggin" but I can not get it to work. It complains while importing Numeric. The message is: ImportError: /usr/lib/python2.2/site-packages/Numeric/multiarray.so: undefined sybmol: _Py_NoneStruct I had to change the PYTH

[PyMOL] N-Terminal hydrogens with Chempy

Hi Warren, I found out that it is possible to write out AMBER style atom name formats with hydrogens added using the Chempy which is pretty neat. However it seems like this does not recognize the N-terminal residue for adding hydrogens. Is that still the case? I am still using PyMOL 088 (I w

Re: [PyMOL] surface area calculation

To calculate surface area for a defined object from the PyMOL command line type: print cmd.get_area("obj") where obj is the name of your object. for arginines: create ARG, resn ARG print cmd.get_area("ARG") Kaushik. On Wednesday, November 12, 2003, at 05:10 PM, Harp, Joel M wrote: Is it

[PyMOL] AMBER Style Hydrogen

hydrogens similar to the AMBER hydrogens. I notice that the Chempy has AMBER libraries so is it possible to use that library to protonate proteins? Thanks, Kaushik Raha.

Re: [PyMOL] New Map Formats Coming...

Hi, Is it possible to calculate and display a difference phi map between two electrostatic potential maps using PyMOL? Both the maps are created by Delphi and can be displayed in PyMOL. Kaushik. On Saturday, July 12, 2003, at 09:20 PM, Brian Chapados wrote: Warren, While you're adding suppo

Re: [PyMOL] Electrostatic potential maps in PyMOL

: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] 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] Ele

Re: [PyMOL] Electrostatic potential maps in PyMOL

altimore County 1000 Hilltop Circle Baltimore, MD 21250 email: c...@hhmi.umbc.edu ======= On Wed, 9 Jul 2003, Kaushik Raha wrote: There has been some talk on the list regarding failure of PyMOL in reading Delphi generated potential maps that I missed. I have

Re: [PyMOL] Electrostatic potential maps in PyMOL

. Can anybody please let me know what was the problem with PyMOL reading Delphi generated GRASP potential maps? Was wondering if PyMOL is doing the right thing?? Thanks, Kaushik Raha Penn State University On Wednesday, July 9, 2003, at 10:48 AM, EPF (Esben Peter Friis) wrote: Hi PyMOL users

[PyMOL] color schemes

Hi, I have been playing around with PyMOL 088 and I think the new features are absolutely great. However I notice that whenever I load a molecule in this version, it randomly (??) assigns it a coloring scheme for the representation. I see the same thing in the roving detail feature (which I

[PyMOL] 1-4 Lists

Hi, The sculpting feature of PyMOL indicates that it creates 1-4 neighbor list. Does it create all (1-2, 1-3 and 1-4)? Is it possible to access it? Kaushik Raha. Penn State

Re: [PyMOL] protein surface

two consecutive atoms. Is there anyway to get around this? Or can I read any surface file ouput by other programs in pymol? Thanks Jianghai On Tuesday 25 February 2003 09:56 am, Kaushik Raha wrote: Hi Jianghai, Some of these questions have been answered by Warren: PyMOL doesn't show the so

Re: [PyMOL] protein surface

Hi Jianghai, Some of these questions have been answered by Warren: PyMOL doesn't show the solvent accessible surface, rather it shows the solvent/protein contact surface. The solvent accessible surface area is usually defined as the surface traced out by the center of a water sphere, having

[PyMOL] Surface and SASA

as non-exposed. Another question I have is does PyMOL read AMBER topology (prmtop) files? And how do I load it and read it along with a crd file? Thanks in advance. Kaushik Raha Penn State University.

Re: [PyMOL] Disulfide Bonds

these...does it need to? Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. -Original Message- From: Kaushik Raha [mailto:kxr...@psu.edu] Sent: Friday, September 20, 2002 1:36 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Disulfide Bonds A similar question: Does P

Re: [PyMOL] Disulfide Bonds

A similar question: Does PyMOL have a PDB file parser that can read disulphide linkages from the file and connect the atoms or one has to explicitly issue bond commands. Also, can PyMOL display hydrogen bonds without the user having to write out a list? thanks, Kaushik Raha. Penn State