pymol-users

[PyMOL] Atom Ordering when Saving

[Robert H. <rh...@sp...>]

I was curious how I might prevent Pymol from re-ordering the atoms when 
saving to a pdb file.
I am using a .pml script to output a large number of peptide files for 
use in gaussian, but I need to preserve the atom
order in the output file.

I am not a python expert, but it seems like it should be in 
exporting.py..  But it is not obvious where the atom reordering is done.

Thanks,
Bob

RE: [PyMOL] Atom Ordering when Saving

[Warren L. D. <wa...@de...>]

Hi Robert,

	Actually, PDB atom ordering is deep inside the C core. I just
glanced at the code...it should be possible to add this capability, but
it is not a trivial task.  There's currently no way to force PyMOL to do
this, and it may or may not make it into the next version.

	For the time being, I can only suggest a workaround, which
requires overwriting the B-factor field:

alter all,b=ID/100.0
save test.pdb

Now you can reorder the output PDB file based on the B-factor field.  It
should be possible to write a short Python script which does this, while
at the same time renumbering the PDB.

For example:

f=open("test.pdb")
l = f.readlines()
f.close()

l = filter(lambda x:x[0:6] in ('HETATM','ATOM  '),l)
l = map(lambda x:(float(x[60:66]),x),l)
l.sort()
l = map(lambda x:x[1],l)
c=1
ll = []
for a in l:
   a = a[0:6] + "%5d"%c + a[11:]
   c = c + 1
   ll.append(a)

g=open("reorder.pdb","w")
g.write(string.join(ll,''))
g.close()
   
Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano
Principal
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Robert
Havlin
Sent: Saturday, May 17, 2003 10:26 AM
To: pym...@li...
Subject: [PyMOL] Atom Ordering when Saving

I was curious how I might prevent Pymol from re-ordering the atoms when 
saving to a pdb file.
I am using a .pml script to output a large number of peptide files for 
use in gaussian, but I need to preserve the atom
order in the output file.

I am not a python expert, but it seems like it should be in 
exporting.py..  But it is not obvious where the atom reordering is done.

Thanks,
Bob



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