Hi Mohan,
You should just try to see what happen when you edit the pdb file. Of course you can make changes there. Just make sure to adhere to the format; it's rather strict. In pymol you can change coordinates e.g. using alter_state (help alter_state). The command Jason gave for retrieving the coordinates was for the C-alpha atom of residue 30 of chain A (A/30/CA). So it doesn't consider all atoms. I think you should make yourself morecomfortable about trying these things, playing with it. Learning by trying isone of the best ways. Cheers, Tsjerk On Thu, Mar 25, 2010 at 5:35 AM, mohan raj <[email protected]> wrote: > hi Jason: > > thank you so much.... your > print cmd.get_atom_coords("A/30/CA"); > > command is working fine!!! > > i wish to know how to edit the coordinates and change the position of the > atom..... > > when i open the pdb file in the word document i could see all the > coordinates.. is it possible that i can change the coordinates their > itself????? further the command line you have stated give the coords for > the entire amino acid.... is it considering all the atom in the aminoacid > and giving the coords for the central value???? > > -mohan > > jason wrote: > > In newer PyMOLs this is as simple as: > print cmd.get_atom_coords(oneAtom) > where 'oneAtom' is an object or selection of one atom in PyMOL. > For example, > load $TUT/1hpv.pdb > print cmd.get_atom_coords("A/30/CA"); > -- Jason > - Show quoted text - > On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar <[email protected]> wrote: >> Hi Mohan, >> >> You can use iterate_state, which would be the pymol approach: >> >> coords = {} >> iterate_state 1,n. ca,coords[i]=(x,y,z) >> >> Or you can take a lower level approach; the python one: >> >> for i in cmd.get_model('n. ca').atom: >> print i.coord >> >> cmd.get_model builds you a ChemPy model from a given selection. The >> .atom property is the list of atoms. If you want to know what else is >> possible you might want to have a look at the >> properties/attributes/methods defined: >> >> for i in dir(cmd.get_model('n. ca').atom[0]): print i >> >> Hope it helps, >> >> Tsjerk >> >> Of course neither way would restrict you to plotting... >> >> >> >> On Mon, Mar 22, 2010 at 1:38 PM, mohan raj <[email protected]> >> wrote: >>> hi all: >>> >>> could any one tell me how to get the coordinates for a specific atom >>> in >>> a particular amino acid using pymol commands.... >>> >>> is their a commant with can list the coordinates for each aminoacid >>> in >>> a protein molecule?? \ >>> >>> kindly clarify, thanking you in advance. >>> >>> >>> - mohan >>> >>> ------------------------------------------------------------------------------ >>> Download Intel® Parallel Studio Eval >>> Try the new software tools for yourself. Speed compiling, find bugs >>> proactively, and fine-tune applications for parallel performance. >>> See why Intel Parallel Studio got high marks during beta. >>> http://p.sf.net/sfu/intel-sw-dev >>> _______________________________________________ >>> PyMOL-users mailing list ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >>> >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> Groningen Institute for Biomolecular Research and Biotechnology >> University of Groningen >> The Netherlands >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> PyMOL-users mailing list ([email protected]) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/[email protected] >> > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > PyMOL-users mailing list ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
