Michael,
PyMOL's PDB handling is an attempt to navigate a minefield of
incompatible standards which exist in the conventions of various
software packages. Amber in particular poses significant challenges, as
its PDB files are unusual.
Since version 0.90, PyMOL's behavior has changed. Nowadays,
your input data:
HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54
O
HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05
O
HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 11.05
O
HETATM 1314 XYZ NAP 164 30.554 66.174 18.275 1.05
O
HETATM 1314 LMN NAP 164 32.554 68.174 20.275 41.05
O
Would be returned as:
HETATM 1 OA22 NAP 164 28.315 61.969 12.250 0.00 31.54
O
HETATM 2 OA23 NAP 164 26.554 62.174 14.275 0.00 21.05
O
HETATM 3 ABCD NAP 164 28.554 64.174 16.275 0.00 11.05
O
HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05
O
HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05
O
END
...which does preserve atom names, but not the order. Note that
white-space in the atom names is not preserved (an inherent limitation
in PyMOL -- significant white-space within identifier is hell on users
and parsers).
Conventionally, atom names of length 3 or less are placed in the second
column, not the first -- so your "LMN " atom may cause trouble.
Also note that by some conventions, "2OA2" in a PDB file really means
atom "OA22". PyMOL used to work this way (up to 0.90). Nowadays
(v0.91+), "2OA2" is treated as "20A2" unless pdb_literal_names is on, in
which case the old behavior returns.
Note that in PyMOL, the PDB ATOM IDs are treated more as a property of
the PDB file than of the atoms themselves since TER records also have
unique IDs in that sequence and repeated MODELs sometimes do as well.
Furthermore, in your example, they are not unique (a mistake?).
However, I am trying to bend PyMOL around to meet your needs a bit
better.
Towards this end, I've created a new setting "pdb_retain_ids" which
preserves the original PDB serial numbers in the output file.
In future PyMOL versions, so long as
set retain_order, 1
set pdb_retain_ids, 1
set pdb_no_end_record, 1
The following behavior will be obtainable:
Assuming input of:
HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54
O
HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05
O
HETATM 1315 ABCD NAP 164 28.554 64.174 16.275 11.05
O
HETATM 1316 XYZ NAP 164 30.554 66.174 18.275 1.05
O
HETATM 1317 LMN NAP 164 32.554 68.174 20.275 41.05
O
You'll get an output of:
HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 0.00 31.54
O
HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 0.00 21.05
O
HETATM 1315 ABCD NAP 164 28.554 64.174 16.275 0.00 11.05
O
HETATM 1316 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05
O
HETATM 1317 LMN NAP 164 32.554 68.174 20.275 0.00 41.05
O
Which is as close as I think PyMOL is going to get...
Cheers,
Warren
--
mailto:[email protected]
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: [email protected] [mailto:pymol-users-
> [email protected]] On Behalf Of michael lerner
> Sent: Friday, September 26, 2003 8:44 AM
> To: [email protected]
> Subject: [PyMOL] why is PyMOL renaming my residues?
>
> Hi,
>
> If I load up a PDB file that looks like this:
>
> HETATM 1313 OA22 NAP 164 28.315 61.969 12.250
> 31.54 O
> HETATM 1314 OA23 NAP 164 26.554 62.174 14.275
> 21.05 O
> HETATM 1314 ABCD NAP 164 28.554 64.174 16.275
> 11.05 O
> HETATM 1314 XYZ NAP 164 30.554 66.174 18.275
> 1.05 O
> HETATM 1314 LMN NAP 164 32.554 68.174 20.275
> 41.05 O
>
> and then save it from PyMOL, the resulting PDB file looks like this:
>
> HETATM 1 2OA2 NAP 164 28.315 61.969 12.250 0.00
> 31.54 O
> HETATM 2 3OA2 NAP 164 26.554 62.174 14.275 0.00
> 21.05 O
> HETATM 3 DABC NAP 164 28.554 64.174 16.275 0.00
> 11.05 O
> HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00
> 41.05 O
> HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00
> 1.05 O
> END
>
> You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed
to
> 3OA2 and ABCD has been renamed to DABC. It looks to me like residue
> with a four-letter name is getting renamed.
>
> No .. wait .. it's a little stranger than that .. if I open up the
> second file (the one with DABC) and save *it*, I get this:
>
> HETATM 1 2OA2 NAP 164 28.315 61.969 12.250 0.00
> 31.54 O
> HETATM 2 3OA2 NAP 164 26.554 62.174 14.275 0.00
> 21.05 O
> HETATM 3 CDAB NAP 164 28.554 64.174 16.275 0.00
> 11.05 O
> HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00
> 41.05 O
> HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00
> 1.05 O
> END
>
> Note that ABCD went to DABC which went to CDAB, but OA22 went to 2OA2
> and stayed there. LMN and XYZ weren't touched.
>
> Is there a way to supress this behavior? It causes me a bit of
trouble
> when, e.g., my AMBER parameter files expect residues to have certain
> names.
>
> I'm not sure exactly when PyMOL decides to rename things .. if I
> shift-left-click on one of the residues in the first file (either
before
> or after saving), PyMOL says "You clicked NAP: /test1///164/OA23"
(i.e.
> it gives me the original name).
>
> thanks,
>
> -michael
>
> --
> michael lerner
>
>
>
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