July 2011 - phenixbb - phenix-online.org

Re: [phenixbb] Validation question: R-factor (all) and # of unique reflections (all)
by Pavel Afonine 05 Jul '11

05 Jul '11

Hi Young-Jin, > I feel like I should calculate R(all). As mtz file is usually big, > how can I extract Fobs and Fmodel from phenix generated mtz file? If you feel you want it, then go ahead, and this command might be of help here: phenix.mtz.dump data.mtz --column-data-format=spreadsheet -c Yet another (easier) alternative is to run a dummy phenix.refine run like this: phenix.refine data.mtz model.pdb xray_data.r_free_flags.ignore_r_free_flags=true main.number_of_mac=1 strategy=none output.prefix=junk then take the reported R-factor (Rwork will be equal to Rfree, so take any of them), and discard the files. All the best! Pavel.

1 0

phenix.mr_rosetta: Inconsistent query numbering
by Pietro Roversi 05 Jul '11

05 Jul '11

Dear all, my run of phenix.mr_rosetta stops with: ******************* ERROR ENDING *************** Inconsistent query numbering ******************* ERROR ENDING *************** I attach script and logfiles. Any suggestions? Thanks Pietro

1 0

Ligand woes
by José Trincão 05 Jul '11

05 Jul '11

Hello all, I have been having very weird problems refining a structure with several ligands. The weirdest problem is that if I try to run ligand fit giving just the name of the ligands, no problem - it finds the ligands (FAD and MTE). I save the pdb with all the ligands in and phenix.refine complains that MTE is not recognised, I have to run ready-set. I do it. Run phenix.refine again, and now it complains with the following: Number of atoms with unknown nonbonded energy type symbols: 116 "HETATM18439 C1' MTE A3003 .*. C " "HETATM18441 C2' MTE A3003 .*. C " "HETATM18443 C3' MTE A3003 .*. C " "HETATM18444 O3' MTE A3003 .*. O " "HETATM18474 N9A FAD A3005 .*. N " "HETATM18475 C8A FAD A3005 .*. C " "HETATM18476 N7A FAD A3005 .*. N " "HETATM18477 C5A FAD A3005 .*. C " "HETATM18478 C6A FAD A3005 .*. C " "HETATM18480 N1A FAD A3005 .*. N " ... (remaining 106 not shown) Any help will be greatly appreciated. Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

3 2

NCS Restraints
by Yuri 01 Jul '11

01 Jul '11

Hi Pavel, >It's rather packing.. Say, if more than one copy packs in the > asymmetric >unit then you have NCS, roughly speaking.. So is it correct to say that in cases where you have 1 molecule per ASU, there will be no NCS only crystallographic symmetry?? > In other words, if for the same enzyme one crystal goes to 3.1 and > another 1.5 A could one have significant NCS but not the other? >I'm not sure I understood this... May some one else did? I was trying to understand if this phenomenon would be noticeable depending on the resolution only... You and Nathaniel pretty much answered this now... -- Yuri Pompeu

2 1

NCS restraints
by Yuri 01 Jul '11

01 Jul '11

Hello, I have some fundamental questions about NCS: 1- I think its somewhat of a consensus that at higher res. it should not be used to avoid missing out "real" detailed discrepancy. Is this true? 2- Should one try to use it in lower res data (3 A and worse)? 3- Is the presence of NCS macromolecule specific, or crystal specific? In other words, if for the same enzyme one crystal goes to 3.1 and another 1.5 A could one have significant NCS but not the other? Thanks or any clarification -- Yuri Pompeu

3 3