[phenixbb] Adding multiple conformers beyond 4 -- a possible work-around

Pavel Afonine PAfonine at lbl.gov
Tue Sep 15 11:47:06 PDT 2009

Hi George, hi Ben,

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

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.


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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