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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