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: ----- 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 . . -----

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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