Hi Jennifer,
Doebbler wrote:
I am running Coot 0.5.2 on an intel Mac 10.5.6. I am trying to
visualize the symmetry related molecules for a small inorganic molecule
in spacegroup P 21/C. If I load the file into swiss PDB viewer or
Mercury, the symmetry operators show that I have 4 molecules in my unit
cell and a pretty orderly looking packing scheme. Coot, however, does
not seem to like the P 21/C spacegroup. I changed the CRYST1 line to read
CRYST1 25.000 6.082 11.308 90.00 100.04 90.00 P 1 21/c 1
Indeed. That is what I would have done. The space group symbol in the
PDB file should match the xHM symbol in syminfo.lib
If I go to Draw->cell and symmetry-> master switch: show symmetry
related atoms-> yes
I get a very cramped unit cell with many more than just 4 molecules
within.
Well that is a surprise. You should definitely only see 4. "Cramped"
as in crowded I presume you mean. I imagine that Coot at least got the
cell correct.
(I presume (because of your scripting competence) that it wasn't
something trivial like inadvertently displaying the symmetry for other
molecules also)
I tried to ask coot what it thinks my spacegroup and symmetry
operators were to reconcile this result with those of mercury and swiss
viewer.
It recognizes the spacegroup as P 1 21/c 1.
coot> (show-spacegroup 0)
"P 1 21/c 1"
As it should be.
If I then ask coot to show-symmetry I get the following
coot> (show-symmetry 0)
Backtrace:
In current input:
8: 0* (show-symmetry 0)
<unnamed port>:8:1: In expression (show-symmetry 0):
<unnamed port>:8:1: Unbound variable: show-symmetry
ABORT: (unbound-variable)
:-( There is no command to output the symmetry operators. I'll make a
note to add one.
I'm stumped - I don't know what is going on. If you have a shelx .ins
file for this molecule, I'd be curious to know if it was displayed
correctly.
Paul.
