[phenixbb] Adding multiple conformers beyond 4

Pavel Afonine PAfonine at lbl.gov
Tue Sep 15 11:27:48 PDT 2009

Hi George, hi Ben,

thanks a lot for explaining! Yes, I'm well aware of multi-model 
refinement/building works and even myself was involved into one:

Acta Cryst. (2007). D63, 597-610. "Interpretation of ensembles created 
by multiple iterative rebuilding of macromolecular models".

The "proper" way would be to enable using multiple models in 
phenix.refine (those defined with MODEL-ENDMDL cards). Currently this is 
not possible, but allowing it is in our to-do list. There is a number of 
technical issues that we need to address first (and some of them are not 
entirely up to me to re-solve: ed. Ralf's PDB interpretation procedure).

Yes, using altLoc identifiers solves the problem indeed, although the 
under-the-hood calculations become extremely inefficient, but again, you 
are right, it works (see remark below for potential issues!).

I can go ahead and remove "max=4" limitation.

One remark. Recently I went through the whole PDB and tried to 
re-compute the reported statistics (R-factors, for example) for all 
entries containing multiple models. You can do it using 
phenix.model_vs_data tool:

phenix.model_vs_data model.pdb data.hkl

So, the observation is: more models your PDB file contains, less 
reproducible the R-factors. The obvious reason for this is  the 
precision filed for occupancy in PDB file, which is 1.00. This means if 
you have 16 models, then you report occupancy as 0.06 and NOT 1./16 = 
0.0625. So the rounding errors are the issue here. What if you have 200 


On 9/15/09 10:58 AM, George Phillips wrote:
> Pavel,
> Ben and I are here now, so here is your response from both of us.
> We are trying to do complete ensemble refinements like we used to do 
> with CNS.  8 or even 16 (or more)copies of the whole protein tends to 
> give the best R-free. See the article below.  
> We can recompile if you tell us what needs to be changed (or give us 
> some clues where to look), but we need a lot more than four.  Clearly 
> this is not the normal use of this feature, but it works.  We are 
> getting drops in Rfree from your test examples in phenix even with four.
> Levin et al.  Structure, 15: 1040 (2007).
> 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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