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

[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

[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

[PyMOL] AMBER Style Hydrogen

of the 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] 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

is. 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] 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] 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