I wrote:
Isn't it the case that vdw interactions are turned off
between atoms in a residue, and perhaps with the residues
before and after?
No it is not the case, at least in refmac5 and SHELLXL.
Thanks to those who clarified this.
Jim Naismith's earlier post, which I had not seen, suggests
a b
SHELXL does not provide torsion angle restraints. As far as I can tell,
the normal procedure using REFMAC and PHENIX.REFINE is to refine with
torsion angle restraints applied to side-chains but not to the psi and
phi angles (all three programs have ways of keeping peptide units
approximately pl
I could not say about other program but in refmac there are intra
residue vdw repulsions if atoms are at least two bonds are apart.
If atoms are only two bonds apart then vdw distance is reduced and it
can be controlled.
I do agree that at lower resolution you should use as much info as
you
Bernhard Rupp wrote:
Dear All,
I wonder about the exact use of torsion restrains and the effect
on phi/psi/w validation.
a) does refmac restrain phipsi at all (except vdw repulsion
which does not bias them otherwise)?
Isn't it the case that vdw interactions are turned off
between ato
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Bernhard Rupp
Sent: 07 November, 2007 16:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] torsion restraints and phi/psi
Dear All,
I wonder about the exact use of torsion restrains and the effect
on phi/psi/w validation.
I think in r
Dear All,
I wonder about the exact use of torsion restrains and the effect
on phi/psi/w validation.
I think in refmac, omega is restrained with a 1-4 dihedral or
planarity, cis when the proper LINK statement is invoked - no
questions there.
In literature I find remarks like 'usually not restrain
