I think the LSQKAB change at Line 291(old)/Line 300(new) DOES introduce
new and possibly incorrect logic.
I haven't looked at all the code, but this one change does seem to
substitute a check that chain, residue number, and atom name (only 3
characters; incorrect) match [OLD] for a check that chain, residue
number, atom name (4 chars, correct), insertion code (correct, assuming
that the insertion codes and residues numbers in the two proteins are
lined up correctly), AND ALT CODE match [NEW].
The alt code match is, I suspect, a bug, in exactly the situation that
Jose provided: one protein may have them, but the other may not (or may
have different ones). One should perform the alignment such that the
protein (residue) without alt codes aligns onto the other protein
(residue) with the "A" alt code; to discard the residue pair is simply
because alt codes don't match is not correct. [I don't want to start a
discussion on whether instead the program should use that alt code with
the highest occupancy, though that also should be fine; if occs are
equal, then pick "A".)
Dave
David Borhani, Ph.D.
D. E. Shaw Research, LLC
120 West Forty-Fifth Street, 39th Floor
New York, NY 10036
[log in to unmask]
212-478-0698
http://www.deshawresearch.com
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On
> Behalf Of Kevin Cowtan
> Sent: Monday, December 22, 2008 11:39 AM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1
>
> 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?r
> 1=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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