Hi Bernhard,
In coot, the chiral volume is computed from the ideal bond lengths and
angles using the unit cell trick already pointed out by George. (That's
because Ralf explained to me how to do it at a phenix code camp).
the esd is not defined in the monomer library. In coot, it is define by
this parameter:
volume_sigma_ = 0.2;
I believe that this is the same value as used in phenix.refine.
Paul.
Ralf W. Grosse-Kunstleve wrote:
Hi Bernhard,
In phenix.refine, the chiral volume is computed from the ideal bond lengths and
angles,
using the unit cell trick pointed out already by George:
uc = uctbx.unit_cell( [bond.value_dist for bond in bonds]
+ [angle.value_angle for angle in angles])
if (volume_sign.startswith("neg")):
return -uc.volume()
return uc.volume()
The esd isn't defined in the monomer library files. In phenix.refine it is
defined by
this parameter:
chir_volume_esd = 0.2
I believe this is the same value as used in refmac.
Ralf
----- Original Message ----
From: Bernhard Rupp <[email protected]>
To: [email protected]
Sent: Friday, April 3, 2009 9:21:03 PM
Subject: [ccp4bb] chiral volume target value
Dear All,
assuming the chiral volume definition with r() a Cartesian position vector
Vc = [r(N)-r(Ca)]*([r(C)-r(Ca)]x[r(Cb)-r(Ca)])
I always get about -0.65 A**3
Is this correct? Are there any target values?
In a SHELX manual I read + 2.5 for the chiral volume - seems to
be different.
(not to be confused with the pseudo-torsion target of +34 deg)
Thx, BR
