On Sun, Aug 16, 2015 at 3:56 PM, Eric Martz <ema...@microbio.umass.edu>
wrote:
> Dear Bob,
>
> Here are three possible bugs (minor ones).
>
> ITEM ONE:
>
> "select %a" fails to select altloc="a".
> "select %A" succeeds.
> I report this "in case" it is a bug.
>
>
Are there both "A" and "a"?
> Jmol Aug 13:
>
> $ print _version
> 1403016
> $ load =1bsz
> HYDROLASE 01-SEP-98 1BSZ
> PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLE
> INHIBITOR POLYETHYLENE GLYCOL
> found biomolecule 1: A
> found biomolecule 2: B
> found biomolecule 3: C
>
> $ select altloc="A"
> 74 atoms selected
> $ select altloc="a"
> 74 atoms selected
> $ select %A
> 74 atoms selected
> $ select %a
> 0 atoms selected
> $
>
>
$ load =1bsz as 1bsz.pdb
1bsz.pdb created
$ print {*}.altloc.pivot
{
"" : 4272
"A" : 74
"B" : 74
"C" : 10
}
> ITEM TWO:
> The doc, under Atom Expressions,
> under " RasMol biomolecular residue specifications"
> says:
>
> %altLoc %1 %A %?
>
> Either the doc needs revision, or %? is not working (should be same as
> "not %" I think)
>
> $ select %?
> script compiler ERROR: invalid model specification
> ----
> select %? <<<<
> $ select %*
> 4430 atoms selected
> $ select all
> 4430 atoms selected
> $ select %
> 4272 atoms selected
> $ select not %
> 158 atoms selected
> $ print 4272 + 158
> 4430
>
>
doc error.
> ITEM THREE:
> Note that the first line of the PDB TITLE field is truncated in the above
> report following the load command. Here are the first 3 lines of the PDB
> file with the lost portion in red:
>
> HEADER HYDROLASE 01-SEP-98
> 1BSZ
> TITLE PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX
> WITH
> TITLE 2 INHIBITOR POLYETHYLENE GLYCOL
>
>
>
Ah --- right -- because some files have the PDB number in columns starting
with column 72. But I can test for that in the HEADER record.
OK, that is fixed.
I have a major update in prep. Are you able to test it in the next days,
Eric?
Bob
> Best regards, Eric
>
>
>
>
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>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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