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 can get. Problem is how to parameterise info you have.
The main problem with phi/psi is that there is no functional form
that can be easily implemented and would make chemical sense
VDW repulsions take to some degree into account phi/psi but not
completely. You can add restraints explicitly where you want
using for example distance restraints in refmac. See for example
www.ysbl.york.ac.uk/refmac/data/refmac_news.html
It is only for refmac. I am sure that other programs like
phenix.refine, shelxl and cns have their own implementations to deal
with these cases.
regards
Garib
On 7 Nov 2007, at 18:19, Edward A Berry wrote:
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 atoms in a residue, and perhaps with the residues
before and after?
Otherwise positional refinement would in fact tend to drive
the residues into the rama-allowed region?
Might it be a good idea to use torsion restraints, or
intra-residue vdw repulsion, in the last stage of refinement
after calculating an unbiased ramachandran plot;
especially in low-resolution problems where we need all the
restraints we can get?
Ed
