Not using lsqkab very often, this might be a stupid question: How do you
know that version 6.0 _DOES_ include multiple conformations? Maybe it only
does not report their omission?
Tim
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Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Mon, 22 Dec 2008, Jose M de Pereda wrote:
Dear colleagues,
While using LSQKAB I have encountered what it seems a different behavior
between version 6.1 and 6.0.
If I superpose two structures with LSQKAB version 6.1 (included in
CCP4-6.1.0), residues with alternative conformations are not included for the
calculations. This is an example of the message in the log file:
- NO MATCH FOR WORKCD ATOM - 995CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 995CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 1009CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 1009CA A IN REFRCD FILE
The program completes the task normally, but it does not use the residues
with alternative conformations.
In contrast, LSQKAB version 6.0 (included in CCP4-6.0.2) uses the residues
with alternative conformations.
The documentation of LSQKAB does not have any reference about the treatment
of residues with alternative conformations.
This problem is not specific to a particular coordinates file. For example, I
can reproduce it using PDB entry 1QG3 and superposing residues 1127-1318 of
molecule A onto the same range of molecule B.
I would appreciate if someone could enlighten me whether this is a new
FEATURE of ver 6.1 or a BUG; and how can this be avoided (i.e. include
residues with alternative conformations for calculations).
Finally, I am running CCP4 6.1.0 in a Linux box with Suse 10.2 (Linux
2.6.18.8-0.10-default i686).
Happy holidays and happy New Year
Cheers
Jose
--
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Jose M de Pereda, PhD
Instituto de Biologia Molecular y Celular del Cancer (IBMCC)
Spanish National Research Council - University of Salamanca
Campus Unamuno s/n
E-37007 Salamanca, Spain
Phone: +34-923-294819
Fax: +34-923-294795
http://xtal.cicancer.org/
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