RE: [ccp4bb]: Ligand B factor restraints in refmac

[Ian Tickle <I.Tickle@astex-technology.com>]

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Hi a quick look at the code reveals the following:

      SUBROUTINE CHECK_SIDE_OR_MAIN(ATOM_NAME,SIDE_OR_MAIN)
C
C---Checks if atom is side or main chain atom
      IMPLICIT NONE
      CHARACTER ATOM_NAME*(*),SIDE_OR_MAIN*(*)
C
      SIDE_OR_MAIN = 'S'
      IF(ATOM_NAME(1:4).EQ.'CA  '.OR.ATOM_NAME(1:4).EQ.'N   '.OR.
     &   ATOM_NAME(1:4).EQ.'C   '.OR.ATOM_NAME(1:4).EQ.'O   '.OR.
     &   ATOM_NAME(1:4).EQ.'H   '.OR.ATOM_NAME(1:4).EQ.'HA  ')
     &             SIDE_OR_MAIN='M'
      RETURN
      END

i.e. if the atom name is 'CA', 'N', 'C', 'O', 'H' or 'HA' then it uses the
main-chain restraints, all others are classed as side-chain atoms.  So if
you choose to call an atom in your ligand 'CA' (unwise I would suggest!),
then it will get the main-chain restraint.

-- Ian

-----Original Message-----
From: WeiruWang@lbl.gov [mailto:WeiruWang@lbl.gov]
Sent: 21 February 2003 23:45
To: ccp4bb@dl.ac.uk
Subject: [ccp4bb]: Ligand B factor restraints in refmac


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Hi everybody,
I'm refining whit refmac and trying to set restraints to the B factors
of my ligand molecule. According to the manual, "BFAC" keyword affects
the temperature factor restraints on amino acid (mainchain and
sidechain).  I wonder how the non-aa's are treated. Are they treated as
sidechain? mainchain? or to be set separately?

Thanks,

Weiru


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