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Hi George, hi Ben,<br>
<br>
thanks a lot for explaining! Yes, I'm well aware of multi-model
refinement/building works and even myself was involved into one:<br>
<br>
Acta Cryst. (2007). D63, 597-610. "Interpretation of ensembles created
by multiple iterative rebuilding of macromolecular models".<br>
<br>
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).<br>
<br>
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!).<br>
<br>
I can go ahead and remove "max=4" limitation.<br>
<br>
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:<br>
<br>
phenix.model_vs_data model.pdb data.hkl<br>
<br>
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
models? <br>
<br>
Pavel.<br>
<br>
<br>
On 9/15/09 10:58 AM, George Phillips wrote:
<blockquote
cite="mid:6260662F-C796-48F9-A354-C5954522E8B6@biochem.wisc.edu"
type="cite">Pavel,
<div><br>
</div>
<div>Ben and I are here now, so here is your response from both of us.
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Levin et al. Structure, 15: 1040 (2007).</div>
<div><br>
</div>
</div>
<div><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
<div>
<div>George N. Phillips, Jr., Ph.D.</div>
<div>Professor of Biochemistry and of</div>
<div> Computer Sciences</div>
<div>University of Wisconsin-Madison</div>
<div>433 Babcock Dr. Madison, Wi 53706</div>
<div>Phone/FAX (608) 263-6142</div>
</div>
<div><br>
</div>
</span><br class="Apple-interchange-newline">
</div>
<br>
<div>
<div>On Sep 15, 2009, at 12:22 PM, Pavel Afonine wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">Hi Ben,<br>
<br>
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 -:)<br>
<br>
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.<br>
<br>
Pavel.<br>
<br>
<br>
On 9/15/09 9:20 AM, Ben Mueller wrote:
<blockquote
cite="mid:8b6123580909150920j52a7c0faw9ec29762e4aa66fb@mail.gmail.com"
type="cite">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: <br>
<br>
RuntimeError: Exceed maximum allowable number of conformers (=4).<br>
<br>
Is there an easy (or difficult) way around this?<br>
<br>
Thanks for your time,<br>
<br>
Ben Mueller<br>
<br>
Phillips Lab<br>
Department of Biochemistry<br>
University of Wisconsin - Madison<br>
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