David, thank you for your reply. I like writing a python script to do this. And I just got the code what I want from http://www.rubor.de/bioinf/tips_python.html#chempy.
Model building becomes so easy when using chempy. But I can't get the manual about chempy. So pity! And Here is the partial code: 1 #!/usr/bin/python 2 import __main__ 3 __main__.pymol_argv = ['pymol','-qc'] 4 5 import sys 6 import pymol 7 from scipy import * 8 from chempy.models import Indexed 9 from chempy import Atom 10 from pymol import cmd 11 12 pymol.finish_launching() ............ 47 ATOM=L*array(ATOM) 48 model = Indexed() 49 for i in ATOM: 50 at=Atom() 51 at.name = "C" 52 at.coord = list(i) 53 at.symbol = "C" 54 model.atom.append(at) 55 cmd.load_model(model,"CNT") 56 cmd.label("CNT","name") 57 cmd.save("Test.pdb") On Wed, Mar 10, 2010 at 10:20 AM, David Hall <li...@cowsandmilk.net> wrote: > What are you using to create the xyz file (and why can that software > not write a pdb)? The command you have below is pretty simple. An > alternative is also the xyzpdb program that comes as part of tinker. > ( eg: xyzpdb graphite.xyz charmm22.prm gives you graphite.pdb ) > > -David > > On Tue, Mar 9, 2010 at 7:46 PM, Cun Zhang <apzc2...@gmail.com> wrote: >> Hi,pymolers: >> I want to create a pdb file for the structure of graphite. But my >> method is a bit complex. >> I create the xyz file,then call pymol to translate it into pdb format >> with the command: >> os.system('pymol -cd "load graphite.xyz;save graphite.pdb"') >> >> Is there any easy way to create pdb file with the information of >> atoms' coordinates in pymol? >> >> Thank you! >> >> >> Cun Zhang >> Ph.D.Candidate >> LNM, Institude of Mechanics >> Chinese Academy of Sciences >> Beijing 100190, China >> Tel:86-10-82544204 >> >> ------------------------------------------------------------------------------ >> 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 (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 >> > -- Blog: http://blog.4message.net ------------------------------------------------------------------------------ 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 (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