[phenixbb] Adding multiple conformers beyond 4

George Phillips phillips at biochem.wisc.edu
Tue Sep 15 10:58:17 PDT 2009


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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