In PyMol, I am selecting a subset of atoms from a pdb file, then saving
the results to a pdb file. I'm having trouble with spaces in ligand
atom names. For example, notice that the carbon listed below has a
space as the 4th character in the name, but after loading into pymol and
then saving, the space is now the first character. (By the way, I'm
doing "set pdb_retain_ids", "set retain_order" and "sort" before saving)
original:
HETATM 1689 AC5 AP5 A 215 ...
after pymol save to pdb file:
HETATM 1689 AC5 AP5 A 215 ...
I need to preserve the original spacing and the original atom name. I
noticed in a previous email that Warren suggested writing a python
script to convert spaces to underscores before loading in pymol. In my
case, after saving the file in pymol, I would then need to write a
second script to replace the underscores with spaces.
Can you change pymol so that it simply stores character array elements
12-15 as the atom name? That way, you can output the same characters
when saving.
Also, will pymol support PDBML/XML soon?
Thanks,
-Dan Farrell
Arizona State University
