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<[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
>
>
>
>
>
>
>
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