thanks Tim. I have been using different "AltLoc" values (A,B) and
different "Atom name" values (HOH,CA) but the problem seems to be which
value to set for the "Residue name" field. Assigning different
residues numbers would seem to lose the distinction between partial and
alternate occupancy. The ins file seems to have no problem with the
pattern
RESI CA
PART 1
CA ..
PART 2
O ..
PART 0
On 05/14/2014 11:01 AM, Tim Gruene wrote:
Dear Alastair,
I think that refinement programs usually interpret chain ids A, B, ...
the way shelxl uses PART 1, 2, ... and a blank chain ID corresponds to
PART 0.
You may have to assign different residue numbers to CA and HOH, but I
think this is also the case for shelxl.
Does this resolve your problem?
Best,
Tim
On 05/14/2014 07:48 PM, Alastair Fyfe wrote:
On the subject of not (willfully) contaminating the pdb database, any
suggestions on the following are appreciated. I am refining the solvent
structure of some RNAs. Inspection of difference and anomalous
difference maps suggests that some closely-spaced positions are
alternately taken by distinct entities with partial occupancy. One
pattern suggests partial occupancy by a Ca++ ion with a nearby site
partially occupied by water (confirmed by an anomalous peak only for the
former). I am refining this with shelxl and expressing this in the ins
file is straightforward (and I'd like to express much gratitude for the
multi-core version of shelxl!). However it's not clear to me how to say
this in PDBese : choosing the HETATM residue name as either HOH or CA
and assigning alternate positions with HOH and CA in the atom name field
seems to make trouble for pdb reader software, eg mmdb.
thanks,
Alastair Fyfe
