[phenixbb] rotamers

Frank von Delft frank.vondelft at sgc.ox.ac.uk
Wed Mar 23 22:54:04 PDT 2011

Oh no!!  Please please please don't bring that hoary old canard of 
building in side-chains - it's Very Bad Practice, we don't build missing 
amino acids or ligands, do we, so why are sidechains different?  The 
"most likely rotamer" is still the WRONG rotamer:  if it were right, 
you'd see it.

CNS used to do this, but as far as I could tell it was an artefact 
because CNS could not refine a residue if not all atoms were present, so 
to truncate something you had to call it ALA.  That's obviously wrong, 
and phenix fixed this, thank god, and good riddance.

Now it's to come back...?  *sob*

As for theoption (b):  that sounds like a very valid criterion for 
placing a side-chain.  In fact, it's awesome - so why set occupancies to 
zero?  Phenix already deals with validly modelled atoms very 
effectively:  set occ=1 and relax the B-factor restraints.

(Sorry, you can tell I feel strongly... :)


On 23/03/2011 21:39, Pavel Afonine wrote:
>    Hi Ed,
> you are asking the right question.
> We discussed the issue of residue side chains partially or fully lacking
> density at PHENIX developers meeting last week. This was brought up by
> an industrial consortium user.
> Some people tend to chop them off (which I do not not not like), some
> let the refinement programs do what they want, and the programs stupidly
> tends to stick these sidechains in whatever density is available around
> (this is bad too).
> I think we decided that I have to do something about it, probably the
> following:
> - if a side chain lacks the density and the full rotamer search does not
> find any density, then a) set occupancies of affected atoms to zero, and
> b) move the side chain to the highest probable rotameric state that
> generates least clashes with surrounding atoms and may be still have
> some good density fit (even though it is a bad density). I will work on
> this. That's for sure.
> Pavel.
>> Does refine restrains side chain rotamers to, say, the closest one from
>> the rotamer dictionary or, perhaps, the starting coordinates (I find
>> this less likely, of course)?  I am particularly interested in what
>> would happen if a side chain is disordered and there is no strong
>> electron density to support a specific conformation.  Do I understand
>> correctly that the real-space refinement for the side chains is on by
>> default, which means that disordered side chains would tend to stay
>> within their biased density?
>> I apologize if I missed the description of this in the manual, just
>> point me to the right section then.
>> Cheers,
>> Ed.
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