> 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 <[log in to unmask]> 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: [log in to unmask]
>> tel (office): +44 (0)1273 678349
>> tel (lab): +44 (0)1273 677512
>>
>>
>>
>>
>> On 6/20/12 10:04 AM, "Luca Pellegrini" <[log in to unmask]> 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: [log in to unmask]
Tel: 0044-1223-760469
Fax: 0044-1223-766002
Sanger building, room 3.59
|