[phenixbb] Adding multiple conformers beyond 4

Dale Tronrud det102 at uoxray.uoregon.edu
Tue Sep 15 11:31:14 PDT 2009

   In my, several months old, entry 3EOJ I have a Bchl-a group
with 6 alternative conformations.  Actually they are composed
of three sets of two.  Certainly broke Coot when it first saw
it but Paul fixed it.  Shelxl has no problem with this.

   This model does present the larger issue that not all
alternative conformations are exclusive.  All the programs I've
seen assume that only one of each alternative is present in any
particular molecule.  This model is an example where within each
pair the conformations are exclusive, but the three pairs should
be combined combinatorially.

   This residue has conformations [a,b,c,d,e,f].  There can never
be bad contacts between atoms in conformations [a] and [b], [c]
and [d], and [e] and [f], but an atom in [a] could in principle
be too close to an atom in [c].

   A problem I have with all programs, yes even my own, is that
to define the plane of the conjugated system you need atoms
that are not disordered, atoms in [a], and atoms in [c].  Actually
there are four planes [*ac], [*ad], [*bc], and [*bd].

   To handle the PDB today you need to allow at least 6 conformations.
To handle them properly you need to do some deep recoding to
handle the combinatorials.

Dale Tronrud

Pavel Afonine wrote:
> Hi Ben,
> to allow so I will have to slightly change the code... I went through
> the whole PDB and did not find any item that has more than 3 or 4
> conformers (at the moment of coding this). So that made my choice for
> that temporary limitation of max=4 conformers (putting aside a number of
> cases of abusing altlocs to mimic multiple models MODEL-ENDMDL).
> Unfortunately, nothing is so permanent as temporary, so we have 4 since
> that -:)
> May I ask you: why you need to have more than 4 conformers? If it is
> really a bottleneck and stops you from doing something important right
> now, I can go ahead and fix it.
> Pavel.
> On 9/15/09 9:20 AM, Ben Mueller wrote:
>> I am a relatively new Phenix user and I am trying to see if it is
>> possible to push the number of conformers beyond 4. I tried to do so,
>> and I recieved the error message:
>> RuntimeError: Exceed maximum allowable number of conformers (=4).
>> Is there an easy (or difficult) way around this?
>> Thanks for your time,
>> Ben Mueller
>> Phillips Lab
>> Department of Biochemistry
>> University of Wisconsin - Madison
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