I'm sorry to have ignited more controversy. As seems somehow always
inevitable, I now find I can't recreate the problem I saw before: the
PDB file that yesterday looked squished (1a4x) now displays fine, so
it's likely there is no problem with how your code handles pdb
entries. It's rather embarrassing. I'm using 0.5.1-pre-1.
As far as building, using R 3 2 :H allows me to place helices whose
symmetry mates display correctly. I was taking Se sites from SHARP, so
it's likely coot was reading the symmetry from that PDB, rather than
the map. I may have stumbled on an obscure way to screw this up.
--James
On Oct 29, 2008, at 5:46 AM, Paul Emsley wrote:
Eleanor Dodson wrote:
Paul Emsley wrote:
James Whittle wrote:
Hi-
I'm trying for the first time to work with a structure in
spacegroup H32. Coot reads the CRYST card, but when I build a
helix, or look at a H32 PDB entry, the symmetry mates appear
squished. I know there is some discussion about handling this
spacegroup: do I need to change the CRYST line to get the
structure to display correctly?
<chuckle> what timing :-)
OK, so the answer is that Coot does not support such a spacegroup
symbol. You need to specify it as "R 3 2 :H".
Paul
Paul - you have to fix this - until such time as PDB depositions
return such a symbol. At the moment they have H32
Actually, at the moment they have "H 3 2".
For example, I tried 1B41 and that displays symmetry just fine, as
Kevin suggests. James, name an accession code that appears to have
squished symmetry (you are using the latest stable version, I take
it).
Fitting a helix is a different story though, I get a pdb file with a
rhombohedral spacegroup but hexagonal cell (which makes a mess of
the symmetry related coordinates of course). Both cell and
spacegroup for a "Fit Helix" molecule should be picked up from the
map/MTZ file - so I don't know what is going on there.
Paul.
