On May 18, 2006, at 3:37 p, Bob Hanson wrote:
Rolf Huehne wrote:
At least in the PDB format file they are "A","B" for 1VWH. Since I am
not used to read mmCIF files I couldn't figure out yet if they were
changed to "1","2" there. Since the following characters
'*1234ABCDEFGHIJKLMNOPQRSTUVXYZ
are currently used as altLoc indicators throughout the PDB
database it
would not be obvious how these are mapped to numbers.
Hmm, you can have altloc "*", eh? Then we will have to take out
%*
and change that to
%?
But, really, this "*" and "'" business appears to have been
abandoned or maybe just never implemented. Jaime Prilusky has
gathered information for the ENTIRE PDB database at http://
bip.weizmann.ac.il/oca-bin/altloc and http://bip.weizmann.ac.il/oca-
docs/altLocations.txt, and they always start with ABC or 123 or
sometimes an odd alphabetic character. So the statement, "are
currently used as altLoc indicators throughout the PDB database" is
not quite correct. Do you know of cases where this is * or '?
(maybe outside the context of mmCIF?)
My pivot table tells me there are 7174 models in the database with
altlocs. Of these, 78 are of the type "123", 7092 are of the type
"ABCDE", and 4 have a mix. Eric has looked, and many of these
numerical or odd ones are mistakes. Of the ABC type, the vast
majority are just "AB", a few more are "ABC", and then we have some
others. 1mx5 uses Y and Z only, for instance. So those would be
"conformation 1 (Y) and conformation 2 (Z).
None use * or ', even though those might be officially allowed. My
guess is that they are NOT actually being allowed.
it appears that any 'non-blank' character is allowable as an altLoc:
"
If an atom is provided in more than one position, then a non-blank
alternate location indicator must be used as the alternate location
indicator for each of the positions. Within a residue all atoms that
are associated with each other in a given conformation are assigned
the same alternate position indicator.
"
while the current set of pdb files may be restricted to alphanumeric
altLocs, it might be unwise to ignore the rest. other than mapping
logic (what number would * map to anyway?), are there other problems
with allowing the full range?
tim
--
Timothy Driscoll em: [EMAIL PROTECTED]
Virginia Bioinformatics Institute ph: 540-231-3007
Bioinformatics I im: molvisions
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