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NCS Question
by Yuri 07 Jul '11

07 Jul '11

Dear PHENIX community, Could someone please point me toward a good paper on NCS? Cheers, -- Yuri Pompeu

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SA omit map
by Tjaard Pijning 06 Jul '11

06 Jul '11

Hi, I would like to generate an SA-omit Fo-Fc map for a ligand bound to protein. Using the GUI I selected the AutoBuild-Create Omit Map module and set the following : - data.mtz - protein.pdb (no ligand, no solvent) = start model - ligand.pdb (just ligand) = omit map atoms - omit map type = simulated annealing - omit region = omit around pdb The resulting map (/OMIT/resolve_composite_map.mtz) shows density for both the protein and the ligand. When I feed this into the CCP4 module FFT to generate an nF1-mF2 map (with n=1 and m=1) I still get density for both the protein and ligand. However I need only the ligand Fo-Fc density. What is the right way to do this ? Thanks, Tjaard Ing. Tjaard Pijning Research Assistant Protein Crystallography Group Nijenborgh 7 9747 AG Groningen The Netherlands (31)(0)50 363 43 85

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Re: [phenixbb] phenix.mr_rosetta: Inconsistent query numbering
by Thomas C. Terwilliger 06 Jul '11

06 Jul '11

Hi Pietro, There is something that phenix.mr_model_preparation cannot read in Japanin.hhr (attached): phenix.mr_model_preparation Japanin.hhr gives the same error. I'll copy Gabor Bunkoczi and see if he can help with this. All the best, Tom T >> 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 >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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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 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

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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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