Hi George, hi Ben,

on a further thought... I think I have a work-around, may be not perfect but...

By default phenix.refine refines occupancies of atoms in alternative conformation (those having non-blanc altLoc identifiers in input PDB file), and those that have partial non-zero occupancies (for example, partially occupied ions, etc.). I think this is where the "max=4" assertion fires if you have more than 4 alternative conformations.

Now, say you have 16 models and you don't want to refine their occupancies (you can't anyway because of current "max=4" limit), then all you need to do is to set occupancies for each model to 1./16 or to whatever you like (make sure they add up to 1.; you can do it automatically using phenix.pdbtools) and turn OFF occupancy refinement:

phenix.refine model.pdb data.hkl strategy=individual_sites+individual_adp

I hope this will work just fine.

Please let me know if you have any questions or need any help with this. If you send me data/model files, I can make an example for you.

Pavel.

On 9/15/09 11:05 AM, George Phillips wrote:

Pavel,
Instead of 'abusing' the altlocs (one CAN think of this as alternative locations of the whole chain) if you have a convenient better way, we are listening....

George
George N. Phillips, Jr., Ph.D.

Professor of Biochemistry and of

Computer Sciences

University of Wisconsin-Madison

433 Babcock Dr. Madison, Wi 53706

Phone/FAX (608) 263-6142
On Sep 15, 2009, at 12:22 PM, 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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