On 07/27/2011 03:10 PM, Pavel Afonine wrote:

Hi Francois,

...

Is it possible to do

phenix.pdbtools model.pdb --geometry_regularization

but only allow sidechains to be corrected during the process?

no, sorry. This is something that I have no good excuse for, but I simply need to spend a day to make it clean: let atom selections, external restraints and CIF files, etc.

Right now there is a dirty way of doing this using phenix.refine:

Thanks for the workaround Pavel. However, I just wanted to know if it could be done using geometry only with phenix.pdbtools. If it was possible and fast, I or some colleague may have needed to wrap the functionality into some code as a compiled library. Maybe I should rather look for some tool that can add sidechains to a backbone model (without introducing clashes in the process). Thanks a lot, Francois.

step 1: create a dummy data file:

phenix.fmodel model.pdb high_res=5 type=real r_free=0.1 label=f-obs

step 2: run phenix.refine:

phenix.refine model.pdb data.mtz strategy=individual_sites main.bulk_sol=false main.number_of_macro_cycles=20 refine.sites.individual=sidechain wxc_scale=0

"strategy=individual_sites": requests to refine coordinates only; "main.bulk_sol=false": turns off bulk-solvent correction and scaling; "main.number_of_macro_cycles=20": asks for "many" macro-cycles to achieve convergence; "refine.sites.individual=sidechain": asks to refine side chain atoms only; "wxc_scale=0": turns off X-ray term, since refinement target is T = wxc * wxc_scale * Txray + wc * Trestraints, and wc=1 by default.

Note, atoms selection syntax used in "refine.sites.individual=sidechain" is very flexible , you can be very specific about selected atoms. The are examples in docs.

Pavel.

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On 07/28/2011 03:39 AM, Nathaniel Echols wrote:

On Tue, Jul 26, 2011 at 11:48 PM, Francois Berenger wrote:

...

Thanks for the workaround Pavel. However, I just wanted to know if it could be done using geometry only with phenix.pdbtools. If it was possible and fast, I or some colleague may have needed to wrap the functionality into some code as a compiled library.

Maybe I should rather look for some tool that can add sidechains to a backbone model (without introducing clashes in the process).

Try PULCHRA (http://www.pirx.com/pulchra/index.shtml) - since it is open-source, we distribute it with Phenix (phenix.pulchra). My guess is it won't be able to avoid all clashes for a poor starting structure, but it is incredibly fast,

I like to encounter such tools: 0.049s to rebuild side-chains of 1M6T as a test case. That's really fast yes. :)

and it can even start from C-alpha coordinates alone. It appears to only work with a single chain at a time, but a little bit of scripting will fix that problem.

Thanks for the suggestion Nathaniel. Regards, Francois.

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