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Validation question: R-factor (all) and # of unique reflections (all)
by Young-Jin Cho 05 Jul '11

05 Jul '11

Hi everyone, While I am trying to deposit, I am faced with several things that I am not sure: FYI. I am in the <Refinement Statistics> section (Auto Dep Input Tool) in the PDB bank. Most values are came from pdb file that was made from phenix.refine but it asks me "R-factor (all)" that satisfy the limits established by high & low resolution cut off and "number of unique reflections (all)". My simple question is if phenix has those kind of information, if so where I can find them. Another question is if I changed water (deletion or changed occupancy) based on 'precheck', should I run phenix.refine again to get R/Rfree values in correct? I am not sure if these are captured by PDB automatically or not. (seemingly they do like that at this point but not 100% sure yet.) With many thanks~ Young-Jin

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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.

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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

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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

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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

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NCS restraints
by Yuri 30 Jun '11

30 Jun '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

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phenix.ligand_identification problem
by Andrzej 29 Jun '11

29 Jun '11

Dear All, I'm having problem with running ligand_identification script. All well up to the point where the ligand library is created and then for each ligand following error is displayed: Running job sequence 13, ligand 14, in /share/scratch/an... Sorry, resolve was not able to finish on the first cycle I suspect it has something to do with resolve size but there is no keyword like resolve_size for ligand_identification. I've tested my input files with 1.7.1-743 and dev-738 release - same results. Thanks in advance for the support! Regards, Andrzej -- Dr. Andrzej Lyskowski (andrzej[.]lyskowski[(a)]acib[.]at) ACIB Austrian Centre of Industrial Biotechnology GmbH Petersgasse 14, A-8010 Graz, Austria http://acib.at/ c/o IMB Institute of Molecular Biosciences, University of Graz Humboldtstraße 50,III/194, A-8010 Graz, Austria http://strubi.uni-graz.at/ +43 316 380 1993 tel +43 316 380 9897 fax

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Phenix.refine and Unusual residues
by Haytham Wahba 27 Jun '11

27 Jun '11

Version: 1.7 Release tag: 650 Platform: intel-linux-2.6-x86_64 linux User: haytham why phenix does not recognise ACT, PO4 Sn and Br (unusual residue) as you see in this part in the Log file.. (see below) Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" SN SN E 1 " occ=0.70 residue: pdb=" SN SN E 2 " occ=0.20 --------------------------------------------------------- when i try to refine specially the Tin atom (not other, ACT,...) in coot after phenix.refine. coot display ((no restraints Found,...lablabla)) ----------------------------------------------------------- this is the PDB (what is the wrong with that) HETATM 3552 O HOH S 361 11.670 -4.327 9.559 1.00 34.14 O TER 3553 HOH S 361 HETATM 3554 OXT ACT C 1 10.133 -3.417 7.937 1.00 20.00 O HETATM 3555 C ACT C 1 9.911 -2.331 7.357 1.00 20.00 C HETATM 3556 O ACT C 1 10.897 -1.607 7.183 1.00 20.00 O HETATM 3557 CH3 ACT C 1 8.550 -1.912 6.905 1.00 20.00 C TER 3558 ACT C 1 HETATM 3559 OXT ACT C 2 10.700 -2.628 9.985 1.00 20.00 O HETATM 3560 C ACT C 2 10.962 -1.952 11.000 1.00 20.00 C HETATM 3561 O ACT C 2 11.756 -2.461 11.809 1.00 20.00 O HETATM 3562 CH3 ACT C 2 10.364 -0.601 11.240 1.00 20.00 C TER 3563 ACT C 2 HETATM 3564 SN SN E 1 6.346 -4.396 -16.894 0.70 20.00 SN TER 3565 SN E 1 HETATM 3566 SN SN E 2 6.492 -2.146 -14.779 0.20 20.00 SN TER 3567 SN E 2 HETATM 3568 SN SN F 1 10.186 0.632 6.366 1.00 30.00 SN TER 3569 SN F 1 HETATM 3570 P PO4 G 1 5.763 10.047 -3.974 1.00 30.00 P HETATM 3571 O1 PO4 G 1 6.960 10.924 -4.190 1.00 30.00 O HETATM 3572 O2 PO4 G 1 4.531 10.872 -4.101 1.00 30.00 O HETATM 3573 O3 PO4 G 1 5.758 8.978 -5.017 1.00 30.00 O HETATM 3574 O4 PO4 G 1 5.835 9.456 -2.607 1.00 30.00 O TER 3575 PO4 G 1 HETATM 3576 P PO4 G 2 9.060 -4.976 -17.812 1.00 30.00 P HETATM 3577 O1 PO4 G 2 10.418 -5.179 -18.415 1.00 30.00 O HETATM 3578 O2 PO4 G 2 8.223 -4.116 -18.710 1.00 30.00 O HETATM 3579 O3 PO4 G 2 8.412 -6.316 -17.597 1.00 30.00 O HETATM 3580 O4 PO4 G 2 9.172 -4.280 -16.485 1.00 30.00 O TER 3581 PO4 G 2 HETATM 3582 BR BR H 1 9.484 11.317 -29.959 1.00 20.00 BR TER 3583 BR H 1 END

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Difference Map positive peaks in release dev-798
by Yuri 27 Jun '11

27 Jun '11

I was wondering if anything changed (weights or something) in the way the difference maps are calculated? I just ran refinement on a 1.3 structure and a hexacoordinated Mg2+ ion has significant positive density peak even at occupancy 1.0. I had not noticed that before. My ligand also does have positive peaks, but refine gives it a .91 occupancy. I wonder if I am missing some parameter cif file or some definition that would make the positive peaks decrease? Thank you -- Yuri Pompeu

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NCS error in Phenix 1.7.1-743
by Ngan Nguyen Bich 26 Jun '11

26 Jun '11

Dear, Thank Nat for your quick reply, I will try the new nightly build and see what happen. I hope it will fix my problem. Ngan

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