Hi Martin, > when visualising data out of a GOLD docking run, where the software > has added lone pairs to active site residues and ligands is it > possible to remove them post hoc in Pymol? The "atoms" look like: > > 62 **** 45.6415 30.9229 12.1185 LP 1 <1> > 0.0000
the atom_type field after the x/y/z coordinates says "LP", which will be loaded as the element symbol into PyMOL. So this should work: remove elem LP > in the output .mol2 files so the **** "atom" names are clearly not > going to be helpful in a command line situation. For a single ligand > pose it's not too bad doing it by hand but for multiple poses of > multiple ligands it gets pretty old pretty fast. Usually I just tell > people to rerun the docking with the GOLD software told to turn the > LPs off but am after a post hoc solution if possible as people can't > always get on to our licenses fast enough to repeat jobs. > > GOLD also puts the extra protein LPs into the output ligand file, > not into a modded protein file. those lines in the output ligand > files look like: > > 52.0949 25.2031 14.8408 LP 0 0 0 0 0 0 0 0 0 0 0 0 # > atno 4332 bound_to 4006 this is a SDF file, right? So you can remove by name: remove name LP Cheeres, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
