Cun, To answer your last outstanding question, I don't think PyMOL saves anything beside the basic atom info for PDB files. PSE files--PyMOL session files--save everything. If you're using linux or a Mac, you can always just paste the header back on. An unideal solution, but it will work. For those familiar with Warren, he used to joke that PyMOL could read nearly everything, but didn't export much. :-)
Good work on that script. As an exercise, I created a similar script that given any selection, it will select atoms of a certain type within it. So, you can do something like: selInside someSelection, solvent selInside someSelection, * which will create a new selection of all those solvent atoms inside the bounding box (which can be any selection, box or object) you declare. You could also create two pseudoatoms anywhere you in your pdb and use those to define the bounding box. For example, load $TUT/1hpv.pdb pseudoatom b1, pos=[0,0,0] pseudoatom b2, pos=[10,10,10] selInside b1 or b2 and the new selection called (insideBoundingObj) has those atoms within b1 and b2 selected. You can access the script at http://pymolwiki.org/index.php/SelInside Hope this helps, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Thu, Nov 26, 2009 at 6:00 PM, Cun Zhang <apzc2...@gmail.com> wrote: > hi, Jason. > Thank you for your advice. I attach the pdb file at the end. > > Cun Zhang > > > The script which is to delete the water molecules inside CNT (with Radii > 6.26 A ) is : > > #!/usr/bin/python > import __main__ > __main__.pymol_argv = ['pymol','-qc']#Quiet and no GUI > > import sys,os,re,pexpect > import pymol > from pymol import cmd > > pymol.finish_launching() > > def selHOH(R): > cmd.delete("CNT") > cmd.delete("water") > cmd.select("CNT","resn UNK") > cmd.center("CNT") > CENTER=cmd.get_position()[0:2] > cmd.delete("CNT") > cmd.select("water","resn SOL") > atoms=cmd.get_model("water") > cmd.select("Water",None) > for at in atoms.atom: > if (at.coord[0]-CENTER[0])**2+(at.coord[1]-CENTER[1])**2<R**2: > cmd.select("Water","Water or byres index %d"%at.index) > cmd.remove("Water") > cmd.deselect() > > The command I use in pymol is: > >>load b4em.pdb >>run selSOL.py >>selHOH(6.2) >>save b4em.pdb > > b4em.pdb > > > > 27/11/09 04:48:54, Jason Vertrees <jason.vertr...@gmail.com>: > > Can you send me a copy of the PDB file? I'd like to try it on my computer. > > Jason Vertrees, PhD > > PyMOLWiki -- http://www.pymolwiki.org > > > > On Wed, Nov 25, 2009 at 9:28 PM, Cun Zhang <apzc2...@gmail.com> wrote: >> Hi, pymol users. >> I'm a pymol newbie .I have serval question. >> I have a pdb file which include the information about box size, like >> TITLE God Rules Over Mankind, Animals, Cosmos and Such >> REMARK THIS IS A SIMULATION BOX >> CRYST1 39.000 39.000 56.140 90.00 90.00 90.00 P 1 1 >> MODEL 1 >> HETATM 1 C UNK 1 25.851 19.500 0.710 1.00 0.00 >> >> I run pymol, and load it, then delete some molecules and save it. Now the >> information about box size is losing. >> >> 2. Is there any way to get the information about bonds, angles and >> dihedrals ? >> I found the following command can display the bonds information, but >> can't be assigned to a variable. >> >cmd.select('all') >> >atoms=cmd.get_model('sele') >> >print atoms.list() >> 3. Is there any way to learn these python api commands of pymol ? >> >> Thank you! >> >> >> Blog: http://blog.4message.net >> >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> 30-Day >> trial. Simplify your report design, integration and deployment - and focus >> on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> 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 >> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ 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