OK, I've added something to the coot wiki, basically wrapping the
rotamer name function and comparing strings. If different, rotamer info
is added to the list (adding a filter by residue type is an exercise for
reader) and a navigation dialog pops up with differences.
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#NCS_Rotamer_differences
Paul.
On 20/06/12 12:07, Luca Pellegrini wrote:
But I feel that this is a something of a proxy for the original question (which I took to
be "show me NCS related residues that have side-chains in different rotamers").
Yes, a Kleywegt plot for side chain rotamers. Possibly with the option to look
just at hydrophobic or polar residues. Rotamer differences in poorly ordered,
solvent-exposed polar side chains might not matter, but different rotamers in
in the hydrophobic core of the protein probably mean a modelling mistake.
Luca
The scripting function of interest in Coot is get-rotamer-name, but there is no
function provided to run this over a pair of chains and compare results.
Paul.
On 20/06/12 11:24, Eleanor Dodson wrote:
If you use the " superpose molecules" task, using LSQKAB , and fit molecule A
over molecule B say, asking for all atoms to be fitted, you will get a list of large
deviations for main and side , which should include all those residues with side chains
in different rotamers.
Eleanor
On 20 June 2012 10:22, Antony Oliver<[email protected]> wrote:
<forgive the cross-posting coot-bb/ccp4-bb>
Can I second that please? I am possibly in a similar situation -
2.8 Angstrom structure, 6 molecules in the asymmetric unit, refining with
ncs torsion restraint.
It would be very useful to identify which side-chains are in different
rotamers (without having to look at each and every side-chain).
Tony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ
email: [email protected]
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512
On 6/20/12 10:04 AM, "Luca Pellegrini"<[email protected]> wrote:
Hello,
Is there a way to flag up residues that have been modelled with different
side chain rotamers in two NCS-related molecules? I can use the NCS Ghost
Control tool to check individual residues but it would be useful to be
able to produce a list, so that one can zoom in on possible outliers.
Thanks,
Luca
Luca Pellegrini
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
Cambridge CB2 1GA - UK
Email: [email protected]
Tel: 0044-1223-760469
Fax: 0044-1223-766002
Sanger building, room 3.59
