In case it helps, you can see the diffs between the 6.0.2 version and
the 6.1 version here:
http://www.ccp4.ac.uk/ccp4bin/viewcvs/ccp4/src/lsqkab.f.diff?r1=text&tr1=1.51&r2=text&tr2=1.42.2.2&diff_format=h
The obvious changes seem to be some code from Clemens to make sure that
insertion codes match. I can't see anything obviously wrong with that
code though.
Jose M de Pereda wrote:
Hi Tim,
Not a stupid question at all. This is how I came to think that version
6.0 uses atoms with alternative conformations:
If I do the same superposition (with a pdb file that contains
alternative conformations) with LSQKAB version 6.0 and 6.1:
1) Version 6.0 reports 110 atoms "to be refined" and does not report any
error or warning. The loggraph contains data for the residues with
alternative conformations.
2) Version 6.1 reports 97 atoms "to be refined", and it reports 13 atoms
as "no match for workcd atom [...]". The loggraph does NOT contain data
for the residues with alternative conformations.
Based on that, I have assumed that version 6.0 does include atoms in
alternative conformations (in fact, it seems to take into account each
conformations independently).
Bye
Jose
On 12/22/2008 4:31 PM Tim Gruene wrote:
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
--
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
--
------------------------------------------------------------
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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