Dear Modeller team,
I have got a couple of questions about the more uncommon restraint types
that are available in Modeller (v62).
There is a rather big loop in my target structure for which no homology
derived restraints can be defined and which tends to protrude into the
vacuum in the resulting models.
I wanted to try 'user_distance' in order to get a more compact model but
failed in producing a correct restraints file.
test input file:
-----
.
.
set atom_types = 'CA'
pick_atoms pick_atoms_set=2, selection_segment='2:' '3:'
pick_atoms pick_atoms_set=3, selection_segment='10:' '11:'
set restraint_parameters = 3 1 1 27 2 2 0 0.0 0.010
make_restraints restraint_type='user_distance'
.
.
-----
restraints file:
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MODELLER5 VERSION: MODELLER FORMAT
R 3 1 1 27 2 2 0 11 0 0.0000 0.0100
R 3 1 1 27 2 2 0 11 0 0.0000 0.0100
R 3 1 1 27 2 2 0 20 0 0.0000 0.0100
R 3 1 1 27 2 2 0 20 0 0.0000 0.0100
.
.
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It appears to be a problem of pick-set 3. The numbers of atoms and
restraints are correct (also in more realistic examples) but the second
set of atom indices gets lost somewhere along the way.
My second bunch of questions concerns restraint feature 5 (distance
between gravity centers). What is the exact format of this restraint?
How are 'groups of atoms' defined in the rsr-file? Is it equivalent with
defining the gravity centers as pseudo-atoms and restraining the
distance between them?
Thanks a lot in advance!
Best wishes,
Karl
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Karl Gruber
Institute of Chemistry
KFU Graz
Heinrichstrasse 28 e-mail:
A-8010 Graz phone: (+43 316) 380-5483
AUSTRIA fax: (+43 316) 380-9850
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