Dear all,
I am having a problem in validating my refined model with ADIT server from
RCSB. The problem is actually due to the space group.
Actually the data was processed in R3 space group. So, there are two
conventions for this space group (Hexagonal and Rhombohedral). I refined
the model with R3 using CNS because H3 is not acceptable by CNS. But,
actually the space group is H3 which I confirmed while checking for the
twinning using UCLA server and also when i tried to generate the symmetry
related molecules in COOT, it was not able to generate symmetry related
molecules properly (all bonds were broken). But when I replaced R3 with
H3, COOT was able to generate the symmetry related molecules properly
with no short contacts. Now when I wanted to validate the
final refined model using ADIT server (RCSB) with R3 space group, it gives
some close contacts with symmetry related molecule. When I checked in COOT
using R3, there was short contact due to symmetry related molecule
(remember the symmetry related was not properly generated by COOT in R3).
Then I checked the map in FRODO and actually there was no short contact.
So, I realized that actually the space group is H3 and not R3. And COOT
also showed no short contact with H3 space group group (remember, in H3,
COOT is able to generate symm. related molecule properly).
The problem is that when I tried to validate the model with ADIT server
with H3 space group, it is not able to do anything. Even after 24 hrs of
ADIT run, there was no oupput (not even error in loading the files).
When I checked the PDB statistics, actually there are 479 structures
submitted in RCSB with H3 space group. So, I am very much sure that some
(if not all) must have validated their refined model with ADIT in H3 space
group. Did anybody face this kind of problem.
For your kind information, my CRYST card is like this:
CRYST1 125.608 125.608 277.323 90.00 90.00 120.00 H 3 9
Any suggestions will be very helpful.
Thanking you.
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Yours Sincerely,
Shankar Prasad Kanaujia
Research Student
C/O - Dr. K. Sekar
Bioinformatics Center, Department of SERC
IISc, Bangalore - 12, INDIA.
Office Phone: 2469, 3059
Mobile: 9845631581
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