Re: [PyMOL] dimer interface

Alex, * Alex Dajkovic [2005-04-15 10:30] wrote: > Dear all, > > I have a structure of a dimer and would like to see the surface at the > interface of the two proteins. Is there a way to do this in PyMol? Say the object has chains A and B: create chainA, object & c. a create chainB, objec

[PyMOL] dimer interface

Hi Alex, this should get you started. There may be other ways to do this, but this works: create two objects from your dimer create Ach, /yourPDB//A create Bch, /yourPDB//B show surface, Ach color grey, Ach color red, Ach within 5 name Bch This will color red all those objects within 5 Angst

Re: [PyMOL] Creating one object from two

Hi Jacob, * Jacob Corn [2005-04-15 09:28] wrote: > Hi Robert, > You're exactly right. It's a chainid issue. If I load 2 PDBs with > different chainids, they "merge" without a problem. If they have a the > same chainid, lines display OK, but the sequence viewer and > ribbons/cartoon view makes

Re: [PyMOL] Creating one object from two

Hi Robert, You're exactly right. It's a chainid issue. If I load 2 PDBs with different chainids, they "merge" without a problem. If they have a the same chainid, lines display OK, but the sequence viewer and ribbons/cartoon view makes the problem clear. As background, what we were trying to d

Re: [PyMOL] Creating one object from two

Jacob, * Jacob Corn [2005-04-13 16:40] wrote: > I am trying to create one composite object from two separate objects. > When I issue the command > > create objectx, object1 or object2 > > objectx is created and contains most of the two objects, but is missing > around 1/5-1/10 of the atoms (s

[PyMOL] dimer interface

Dear all, I have a structure of a dimer and would like to see the surface at the interface of the two proteins. Is there a way to do this in PyMol? Alex

Re: [PyMOL] SEPs in pymol generated pqr

Hi Jack, If you have AMBER you can define new residues pretty easily especially since you already have charges you like. Once you have a topology and coordinate file, "ambpdb -pqr -wrap -p FILE.top < FILE.crd > FILE.pqr" will generate a MEAD style pqr file. Richard --

RE: [PyMOL] SEPs in pymol generated pqr

Jack, Editing the output PQR sounds like a sensible approach. As far as obtaining charges goes: in order to be quantitatively correct, the ligand would need to be parameterized using the same approach as the protein force field...(for Amber99, I think that means performing an ab initio quantum