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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