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 <[email protected]> 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: > PyMOL>bond 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. ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
