[modeller_usage] pseudo-atom usage?

[Daniel Rigden <>]

Hi all

Can anyone help with an example of the use of additional restraints
involving pseudoatoms?  I've read the relevant sections of the manual

http://salilab.org/modeller/manual/node99.html
http://salilab.org/modeller/FAQ.html#8

and it's still not clear to me.  The FAQ has this example of a
user-added restraint

  SET ATOM_IDS 'CA:35:A' 'CA:40:A'
  ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 10.0 0.1

How to define pseudo-atoms instead of single real atoms?

Alternatively, if the restaint were added in a file, how to specify
defined pseudo-atoms within the format?

R Form Modality Feature Group Numb_atoms Numb_parameters 0 Atom_indices
Parameters
R    3   1   1   1   2   2   0  437   28       1.5000    0.1000

In my case, I'd like to make a helix (which I'll define as a pesudoatom)
in a large insertion pack better, more compactly against the rest of the
protein.  Has anyone any experience with similar situations?

Many thanks in advance

Daniel Rigden


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Dr Daniel John Rigden                     Tel:(+44) 151 795 4467
School of Biological Sciences             FAX:(+44) 151 795 4414
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