OK. I can easily work around it. But at first it confused me when I
tried %a. I didn't think to try %A until days later. So it would be good
to document that this atom expression %X is case sensitive, while
"altloc =" is not (or maybe you want to change that to be consistent?).
Thanks! Eric
On 8/17/15 5:41 PM, Robert Hanson wrote:
perhaps, but
/The value of _atom_sites_alt.id <http://atom_sites_alt.id> must
uniquely identify a record in the ATOM_SITES_ALT list. Note that this
item need not be a number;*it can be any unique identifier.*/
So just because at this point in time all are upper case, it can, in
principle, be upper or lower case. I would rather not change the
behavior. People who write their own PDB files could distinguish A
from a.
Bob
On Mon, Aug 17, 2015 at 11:17 AM, Eric Martz
<ema...@microbio.umass.edu <mailto:ema...@microbio.umass.edu>> wrote:
Hi, Bob,
1. YES I will be very interested to test a new release in the next
few days.
2. I think the largest number of altlocs is 22 (A-V) in 1zir. The
altloc stats were kindly updated for all entries by Jaime Prilusky:
http://oca.weizmann.ac.il/reports/altLocations.txt
So I don't think there has ever been a need for distinguishing
altlocs by upper vs. lower case (unlike chains). Numerals are also
permitted as altloc IDs (2plt, 1tal) so there are at least 36
permissible IDs available.
So I think the case independence of altloc=A/altloc=a is what we
want, and %a should find %A (but currently does not).
-Eric
On 8/17/15 9:26 AM, Robert Hanson wrote:
On Sun, Aug 16, 2015 at 3:56 PM, Eric Martz
<ema...@microbio.umass.edu <mailto: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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--
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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