Jianghai, a couple of examples: 1) phenix.refine data.hkl model.pdb strategy=rigid_body+individual_sites This will refine the whole model as one rigid body, plus individual coordinates of all atoms (all B-factors will be fixed). 2) phenix.refine data.hkl model.pdb strategy=rigid_body+individual_sites sites.rigid_body="chain A" sites.rigid_body="chain B" sites.individual="chain C" sites.individual="chain D" This will refine domains A and B as two separated rigid bodies (no refinement of individual coordinates for A and B), plus this will refine individual coordinates all atoms in domains C and D (all B-factors will be fixed). 3) phenix.refine data.hkl model.pdb strategy=rigid_body+individual_sites+individual_adp sites.rigid_body="chain A" sites.rigid_body="chain B" sites.individual="chain C" sites.individual="chain D" Same as above (example "2)") plus refinement of individual B-factors for all atoms. 4) phenix.refine data.hkl model.pdb strategy=rigid_body+individual_sites+group_adp sites.rigid_body="chain A" sites.rigid_body="chain B" sites.individual="chain C" sites.individual="chain D" Same as example "2)" plus refinement of group B-factors for all atoms (one B-factors per residue). Analogously, you can specify which B-factors you want to refine individually and which ones you want to refine as group B. You can do this in any combination with the examples above. Check the Documentation for more examples, including those using TLS (using TLS in combination with group B (as it is uniquely implemented in phenix.refine) could be a good option to try out at 3.8A). Please let me know if you have more questions. Cheers, Pavel. Jianghai Zhu wrote:

Hi, Pavel,

Thanks for the suggestions. How do I do rigid body refinement for parts of the structure (or fixing) and do individual parameters refinement for the rest of the structure? I didn't find anything in the document.

Jianghai

+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

On May 4, 2007, at 5:10 PM, Pavel Afonine wrote:

...

Hi Jianghai,

I see several possibilities to think about or/and try out:

1) Fix the coordinates of atoms in the domains for which the high resolution structure is available and refine the rest; 2) Refine the domains for which the high resolution structure is available as rigid bodies and for the rest refine individual parameters; 3) There is no specific option in phenix.refine to restrain the secondary structure elements, however there is a tedious way of doing this (according to Ralf) by defining custom bonds and angles between specific atoms forming the secondary structure motifs. Look "Definition of custom bonds and angles" in the latest CCI Apps phenix.refine documentation for technical details.

You can perform "1)" and "2)" in ONE refinement run by combining several refinement strategies and using specific selections for refinable parameters.

Overall, at 3.8A resolution the refinement of individual atomic parameters (coordinates, B-factors) is questionable. I would consider to try to refine group parameters for B-factors (trough TLS or/and group B (like one B per residue)) and try to switch between rigid body refinement of smaller fragments of your model and refinement individual positional parameters or mix of individual and rigid body refinement.

Also, I will think about making a specific option for automatic generation of secondary structure restrains. However, given the amount of work it may require this option will not appear in near future.

Pavel.

Jianghai Zhu wrote:

...

Hi all,

I am refining a low resolution structure (~3.8 A). For some of the domains in the structure, we already have high resolution structures. Despite of some conformational changes in some loops, the core structures should be the same. I am wondering if it is possible to restrain the secondary structures in phenix.refine.

Thanks.

Jianghai

+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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What should I use for sigma?

I'd try 0.1 as a start, which is fairly tight. If the refinement is well behaved you could try increasing the sigma at the later stages. Ralf

Hi Jianghai,

Thanks. Just curious, how do you weight the distance off the ideal value by 1 sigma, 2 sigma, and 3 sigma?

Sorry, I'm not sure what you mean. Could you please explain some more what you'd like to do? Ralf