The issue here is that "=" in this context is case-insensitive, with altloc or color or anything.
If you want to be case-sensitive, you need to use "like" select altloc like "A" Bob On Mon, Aug 17, 2015 at 5:16 PM, Eric Martz <ema...@microbio.umass.edu> wrote: > 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> > 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> >> 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 >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> -- >> 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 >> >> >> >> ------------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> Jmol-users mailing >> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > 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 > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > Jmol-users mailing > listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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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