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: [log in to unmask]
>> 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: [log in to unmask]
http://sb.web.psi.ch
****************************************
|