Hello Tim,
I vaguely remember differences between X-PLOR/CNS, TNT, REFMAC and
WHAT_CHECK, especially for the carbonyl carbon-oxygen bond lenghths, but
also some other values. I can't tell you anymore what the actual
differences were. REFMAC and TNT use libraries that define directly the
bond lenghths (etc.) and their SDs, whereas X-PLOR/CNS uses an
energy-parametrization of bond lengths (etc.). Differences come either
from a wrong assignment of atom types (like aromatic C, sp3-hybridized
C, ...) to the atom names of amino acids, or wrong parametrizaiton, or
from using more up-to-date values for specific bond lenghts. Especially,
the carbonyl bond mentioned above seems to be non-optimal in the
original Engh & Huber library, compared to values derived from atomic
resolution crystal structures of proteins. Given the numbers of atomic
resolution protein structures in the data bank, I think, it would be a
good idea to derive a new Engh & Huber type set of stereochemical
parameters directly from protein structures.
Best regards,
Dirk.
Tim Gruene wrote:
Hello,
I would love to learn how "differently" one can implement the difference
between two numbers? Or are you referring to 'versions'?
Cheers, Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Wed, 14 Mar 2007, Dirk Kostrewa wrote:
Dear John,
I don't know how different the RMSD values are, and whether the
calculated estimates are with or without hydrogen atoms (this can make
a difference). In principle, both programs use the Engh & Huber
stereochemistry library, but I've observed in the past that different
programs used slightly different "implementations" of this library,
resulting in different RMSD values, although they should all be the
same ...
Good luck,
Dirk.
john kryst wrote:
Hi ccp4bb !!!
Does the rmsd estimation (for eg. rmsd_bonds ) depends on the program
we use
??
Example : shifting from Refmac to CNS. There appears to be an
increase in
rmsd of bonds even without refining the structure in CNS. Is the
estimation
methods are different or am i doing something wrong !!
Thanks for your valuable inputs.
regards
john
--
****************************************
Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
****************************************
--
****************************************
Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
****************************************
