Hi Vincent,
can you load the 400 copies of your ligand into the same object? For example by
creating a multi-model PDB file, or using a trajectory format. In that case,
the 400 conformations will share the topology (the atoms and bonds) and you
only have to form the bond once.
Also, the residue name operator is resn, not resi. I think this should have
worked:
PyMOL bond resi 977 resn LIG name B1, resi 977 resn LIG name B2
or:
PyMOL bond LIG`977/B1, LIG`977/B2
Cheers,
Thomas
On 25 Feb 2015, at 11:37, vincent Chaptal vincent.chap...@ibcp.fr wrote:
Dear everyone,
I have a MD simulation of coarse grain molecules, therefore not defined as
typically for normal protein/ligands, but as beads.
I want to represent it using Pymol, and need to define bonds between the
beads.
The problem is that I have 400 copies of my ligand, and all with the same
name. I want to link bead1 with bead2, all having the name LIG.
How can I do it?
The CONECT record works only to define connections on a one-on-one basis, so
it would be horrible for the whole file.
I tried the bond command in pymol with the following argument, but it doesn't
work:
PyMOLbond resi LIG and name B1, resi LIG and name B2
Editor-Warning: bonds cannot be created between objects, only within.
I guess this command line will create also bonds between B1 to all the 399
other LIG B2...
(If resi would take into account the residue number, it would work?)
here is what the pdb file looks like:
ATOM 6129 B1 LIG 977 40.880 105.970 99.090 1.00 0.00
ATOM 6130 B2 LIG 977 41.700 105.200 97.180 1.00 0.00
ATOM 6131 B3 LIG 977 41.880 104.860 94.750 1.00 0.00
...
ATOM 6138 B1 LIG 978 116.680 127.990 105.990 1.00 0.00
ATOM 6139 B2 LIG 978 117.300 129.230 107.720 1.00 0.00
ATOM 6140 B3 LIG 978 119.340 130.290 108.590 1.00 0.00
...
thank you for your help.
best
Vincent
--
Vincent Chaptal, PhD
Institut de Biologie et Chimie des Protéines
Drug-resistance modulation and mechanism Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 07
http://www.ibcp.fr
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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