Hi Nat, After the long discussion, mostly on CCP4BB, about riding H, which covered different H-bond lengths, it would be really good if the GUI and other Phenix documentation explained exactly how this is handled. I think using riding H as a geometry restraint during refinement should be standard practice, but I think 'interpreting' those H atoms in all but the very highest resolution X-ray structures is probably not good. Mark ________________________________________ From: Nathaniel Echols [[email protected]] Sent: Tuesday, October 05, 2010 3:56 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Problem with Molprobity analysis in phenix 1.6.4 On Tue, Oct 5, 2010 at 11:53 AM, Mark A Saper wrote:

If I take my well-refined structure as output by phenix (.pdb) and use it directly on the Molprobity web site, the clash score is much lower: 2.75 for 39 total bumps. Many of these involve residues or waters with high B factors. If I first remove all hydrogens from the phenix-refined .pdb file with a text editor, and upload it to the Molprobity web site, then add hydrogens, and then calculate clash score, the score is now 8.69 or 123 bumps for 14150 atoms. This is *identical* to what phenix calculates. Therefore, why doesn't phenix feed the refined coordinates directly into the Molprobity (probe) calculations? Has this change been made in one of the nightly builds?

There is a discrepancy in hydrogen bond lengths in Reduce versus the monomer library - I believe Reduce is using the distance to the center of the nucleus instead of the center of the electron cloud. phenix.refine will regularize the hydrogen geometry before refining the non-hydrogen coordinates, so it is correcting the bond lengths to be appropriate for X-ray refinement. It looks like they're getting stripped off and replaced when we run the clashscore calculations, so you end up with the longer bonds and thus more clashes. I think the consensus among the group was that these are more appropriate for interpreting (instead of refining) the model, but I'll double-check this with everyone. The GUI could at least be more explicit about how the calculations are done, however. (By the way, a clashscore of 8.69 is pretty decent anyway.) -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Hi Florian, a paper is coming in next Acta D that will be discussing it to some (more or less deep) extent: Joint X-ray and neutron refinement with /phenix.refine/ P. V. Afonine, M. Mustyakimov, R. W. Grosse-Kunstleve, N. W. Moriarty, P. Langan and P. D. Adams I hope it will be out in few weeks. In addition you can have a look: Acta Cryst. (2010). D66, 12-21 MolProbity: all-atom structure validation for macromolecular crystallography V. B. Chen, W. B. Arendall III, J. J. Headd, D. A. Keedy, R. M. Immormino, G. J. Kapral, L. W. Murray, J. S. Richardson and D. C. Richardson and J. Appl. Cryst. (2010). 43, 669-676 phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart and P. D. Adams (especially focusing on section 3.1.5). Probably we need a specific discussion and investigation on what's happening at that low (4A) resolution. I've never systematically looked into it. So you are hitting a bit of a gray area now. Pavel. On 10/6/10 6:56 AM, Florian Schmitzberger wrote:

Dear Mark,

I would be quite interested in opinions about the usage and assignment of hydrogens in the riding position for refinement too, especially at low resolution of around 4 A. How important are they for obtaining reasonable geometry at that resolution?

From what I could see in the phenix manual hydrogens should should not be included into NCS or TLS groups and are automatically excluded from them. Cheers,

Florian

Hi Maia, refinement of occupancies is probably the most documented topics in phenix.refine: http://www.phenix-online.org/documentation/refinement.htm#anch20 so your option number 1 is to check out this section of phenix.refine manual. The option number 2 is to send me your PDB file and tell which atoms you want to relate as alternative conformations in occupancy refinement, and I will send you back a working example (or I will ask more questions off-list if your inputs are not sufficient to produce the unique sugestion). Pavel. P.S.: I will not have internet access all day tomorrow (Friday) till late night. On 12/22/10 6:35 PM, Maia Cherney wrote:

Hi phenixers I need to connect the conformation A to a ligand 1 and the conformation B to a ligand 2. I need to get the group occupancies for conformation 1 and ligand 1 (group 1) and group occupancies for conformation B and ligand 2. I could not get the right groups together. Your selections in the groups does not provide for alternative conformations having different ligands.

Could you help me?

Maia