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
>>
>>
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