Adding multiple conformers beyond 4
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
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 ------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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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 models? Pavel. 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 ------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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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
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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 ------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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In my, several months old, entry 3EOJ I have a Bchl-a group with 6 alternative conformations. Actually they are composed of three sets of two. Certainly broke Coot when it first saw it but Paul fixed it. Shelxl has no problem with this. This model does present the larger issue that not all alternative conformations are exclusive. All the programs I've seen assume that only one of each alternative is present in any particular molecule. This model is an example where within each pair the conformations are exclusive, but the three pairs should be combined combinatorially. This residue has conformations [a,b,c,d,e,f]. There can never be bad contacts between atoms in conformations [a] and [b], [c] and [d], and [e] and [f], but an atom in [a] could in principle be too close to an atom in [c]. A problem I have with all programs, yes even my own, is that to define the plane of the conjugated system you need atoms that are not disordered, atoms in [a], and atoms in [c]. Actually there are four planes [*ac], [*ad], [*bc], and [*bd]. To handle the PDB today you need to allow at least 6 conformations. To handle them properly you need to do some deep recoding to handle the combinatorials. Dale Tronrud 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 ------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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participants (4)
-
Ben Mueller -
Dale Tronrud -
George Phillips -
Pavel Afonine