Dear Mariah,
Recently I significantly improved an alpha-helical structure using
"restraints" in Phenix. Maybe, this will help you to improve your model
and get better Pymol "pictures". I copy the message I got from Phenix
people here, as many CCP4 users may also face such a situation.
> Hi Stefan,
>
>
>>> > > Is it possible to restrain refinement according to secondary >
>>> > structures in phenix?
>>>
>
> Yes, although it is a bit tedious at the moment.
>
> See the "Definition of custom bonds and angles" section here:
>
>
> https://www.phenix-online.org/download/documentation/phenix/development/refinement.htm
>
>
> You will need some way to figure out the hydrogen bonds (e.g. use DSSP,
> http://swift.cmbi.ru.nl/gv/dssp/). Then re-format the information
> like this:
>
> refinement.geometry_restraints.edits {
> bond {
> action = *add
> atom_selection_1 = resname XXX and resid 123 and name X
> atom_selection_2 = resname YYY and resid 124 and name Y
> distance_ideal = 2.1
> sigma = 0.02
> slack = 0.2
> }
> bond {
> action = *add
> atom_selection_1 = resname XXX and resid 125 and name X
> atom_selection_2 = resname YYY and resid 126 and name Y
> distance_ideal = 2.1
> sigma = 0.02
> slack = 0.2
> }
> }
>
> Ralf
>
Regards,
Stefan
Charlie Bond a écrit :
> Dear Maria,
>
> I can see that others have suggested how to manually change the
> secondary structure, but I have one comment:
>
> If a secondary structure detection algorithm doesn't assign those
> residues as 'strand' then this is probably (bugs notwithstanding) a
> feature of your model and you should also take care to look that the
> local structure (hydrogen bonding etc) makes sense at that point.
>
> While we shouldn't blindly accept the output of computer programs,
> altering their output to fit our preconceptions isn't necessarily a
> good idea either.
>
> Cheers,
> Charlie
>
>
> protein.chemist protein.chemist wrote:
>> Dear All,
>>
>> I have a question about PYMOL.
>>
>> I am trying to make a cartoon diagram of my protein showing the
>> secondary structural elements. However for some reasons it is not
>> showing the N terminal strand and showing that as a loop. Is there
>> any command for selecting a range of residues and showing them as a
>> strand or helix.
>>
>> Thanks for helping.
>>
>> Mariah
>>
>> --
>> Mariah Jones
>> Department of Biochemistry
>> University of Florida
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