This sounds similar to something I reported.
http://www.mail-archive.com/[email protected]/msg01827.html
The problem I had was, after saving, CRYST1 was modified to the
reference but SCALE cards were kept as original. This was the cause of
the distorted view in pymol. I wonder if this is still the same bug from
August. And my fix, too, was manually modifying the SCALE[1-3] cards.
Engin
On 12/20/10 6:55 AM, 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.
sorry if this should have come up before but I could not find it in the
archives.
best
david
On 16 Dec 2010, at 23:07, Bosch, Juergen wrote:
Dear BB,
I finked my MacPro (Snow Leopard)ti the latest and greatest version of Coot
0.6.2-pre-1 (revision 3290) [with guile 1.8.7 embedded] [with python 2.7.1
embedded]
and found out that I can not display any symmetry related molecules anymore.
Coot complains about a problem in the CRYST card.
Is this a feature or a know bug ?
Any help Paul ?
Thanks,
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry& Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/
___________________________________
David Komander
MRC Laboratory of Molecular Biology
Hills Road, Cambridge CB2 0QH, UK
http://www2.mrc-lmb.cam.ac.uk/groups/dk/
http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/d-komander
--
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111
