Re: Problems optimizing when BLK residues are present

[Cláudio Soares <>]

Dear Modeller developers and users

	We have been using MODELLER for quite a while (since version 4.0) and we
have now encountered two problems that I would like to share with you.
These problems are of different nature and the first one is the most
important one. I am referring to problems using MODELLER version 6.0 under
i386 Linux.

1) We have proteins with non-standard co-factors, or simply co-factors that
do not exist in the topology files (one example is FMN). When we derive the
structure of the protein without the co-factors with standard optimisation
procedures (such as refine 3), the structures come out all right with good
Ramachandran plot and low values of the optimisation function. However,
when we add these co-factors as BLK residues, the results are quite
different, with much more Ramachandran violations and generally higher
values of the objective function (which is not directly comparable between
the two cases, but even so, the numbers are substantially different). This
is an observation from a set of runs and its seems statistically
significant. Another supporting evidence for a less good optimisation in
these cases is the observation that loop regions (not defined by
homology-derived restraints) are much similar between different generated
models when BLK residues are included than when they are not. Do you think
that this is a consequence of using BLK residues or a bug in the code?

2) When adding our own restraints to the homology derived restraints, the
program crashes with segmentation fault. An example follows:


-----------------------------------------------COMMAND FILE-------------------
INCLUDE
SET ATOM_FILES_DIRECTORY = './'
SET ALNFILE = 'align2d.pir'
SET KNOWNS = '1ar1' 
SET SEQUENCE = 'aa3'

SET HETATM_IO = on
SET WATER_IO = on
SET HYDROGEN_IO = on

SET STARTING_MODEL = 1
SET ENDING_MODEL = 1

CALL ROUTINE = 'model'

SUBROUTINE ROUTINE = 'special_restraints'
  READ_RESTRAINTS FILE = 'my_rest.rsr', ADD_RESTRAINTS = on
  RETURN
END_SUBROUTINE

STOP
-----------------------------------------------------------------------------


------------------------------MY_REST.RSR------------------------------------
MODELLER5 VERSION: MODELLER FORMAT
R    3   1   1   1   2   2   0  10  11       1.5000    0.0100
-----------------------------------------------------------------------------

This is a bond between two atoms, one belonging to a BLK residue and
another one belonging to an haem. The same happens if any of the residues
is a BLK residue. The same happens also when we use "USER FORMAT" instead.
We tried to do this procedure in MODELLER 4.0 and it
worked. It seems to be a bug then.


Could you please help us with this? Thank you very much.

Cláudio


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Claudio M. Soares                  |
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