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> > 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
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