Hi Paul,
Can changing the CELL of the moving molecule after
doing an SSM cause problems if one is interested in lattice contacts
of the moving molecule ? Will symmetry related copies of the moving
molecule now use the cell of the reference molecule ?
If so, this is a real issue for some of the things I am trying to do
(detecting if differences in conformation are influenced by different
lattice interactions). Is there any way of preventing this from
happening ?
Thanks
Andrew
On 20 Dec 2010, at 17:25, Paul Emsley wrote:
On 20/12/10 14:55, David Komander wrote:
Dear all
I have noticed a (related?) CRYST1 problem/bug/feature.
superposing 2 molecules in 2 different cells, and saving the moved
molecule, changed the CRYST1 record of the saved file to the one
from the reference molecule.
original pdb
CRYST1 60.400 72.150 133.010 90.00 90.00 90.00 P 21 21 21
SCALE1 0.016556 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013860 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007518 0.00000
after coot SSM and save_as
CRYST1 69.675 39.000 36.255 90.00 111.69 90.00 C 1 2 1
SCALE1 0.014352 0.000000 0.005709 0.00000
SCALE2 0.000000 0.025641 0.000000 0.00000
SCALE3 0.000000 0.000000 0.029684 0.00000
this generates very funny results in PyMol. Changing the CRYST
record after saving to the original cell seems to fix this, but
surely the CRYST record should stay the same upon loading and
saving a pdb-file?
I wonder if this is to do with me? I am running coot on a MBP, snow
leopard, and just upgraded to the latest version of everything
using the latest builds from Bill Scott. Let me know if I have left
out some crucial information.
Hello David,
Yes, saving and loading a file should not change the CELL card.
Which version are you using?
$ coot --version-full
This code was updated in rev 3272.
After SSMing, the moving molecule should match the CELL, SCALE and
ORIGx cards of the reference molecule.
Paul.
