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A question about the topallhdg.pro of xplorv3851

Isabelle Phan phan at bioch.ox.ac.uk
Fri Jan 15 05:58:18 EST 1999

liuxz at PUBMS.PKU.EDU.CN wrote:
> Hi,
> This question has been asked by someone else. But I do not
> see any answer which I would like to know too. Would someone
> please explain it on the mailinglist?  Thanks for any help.
> > Would someone please explain the term "ic" in the file topallhdg.pro,
> > which is new in v3851 ?
> >
> >   ic N C *CA CB  0.0 0.0  120.0  0.0 0.0


The IC command in X-PLOR is a carryover for its Charmm legacy.
ID stands for the Internal Coordinate manipulation commands.

My man pages say:

            Purpose of the various Internal Coordinate commands

Description :
        These commands are used to setup, modify and process the
internal coordinates of the molecule. This operation is very useful
in setting up atom coordinates whenever they are not known. This
occurs when a protein structure is built from scratch or when an
existing structure is modified. The modification can be simply a
conformational change, or a change in the residue sequence through
replacement, insertion, or deletion. Many of these modifications can
be processed within the program as it currently stands. Other more
difficult modifications can be facilitated by editing the internal
coordinate card file by using external programs.
        This facility is also useful as an analysis tool. Several
program use the output from IC tables for conformational analysis
(phi-psi maps, ring pucker, pseudorotational angles, solvent

Hope this answers your question

   Dr. Isabelle Phan                       phan at bioch.ox.ac.uk
   Oxford Centre for Molecular Sciences    http://www.ocms.ox.ac.uk/
   University of Oxford                    voice: 44-1865-275720
   OXFORD OX1 3QU, U.K.                    fax:   44-1865-275253

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