May 2015 - phenixbb - phenix-online.org

mmCIF file must contain at least one data block
by Ursula Schulze-Gahmen 18 Dec '15

18 Dec '15

I am getting this thie error message mmCIF file must contain at least one data block when trying to run readyset or phenixrefine I cannot find anything wrong wqith my input files. What is the problem? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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Refinement with new mtz.file
by Aleksandar Bijelic 14 Jul '15

14 Jul '15

Dear CCP4 user and experts, I refined (with PHENIX) a 3.0 A dataset obtaining Rfree of about 0.24 (with good geometry according to Ramachandran, Beta Outliers, etc.) .... Everything seems to be ok (especially in relation to the resolution) .... because the mtz.file I used was quite old and I cannot find my xscale.hkl file, I processed the data set again (this time with optimizng and polishing) and received a "better" file according to almost everything (resolution limit, I/sigma, CC(1/2), Rmeas), thus I used this new mtz.file and put it in my last refinement step (the refinement which led to the above mentioned Rfree = 0.24). Suprisingly, the refinement starts at Rwork = 0.18 and Rfree = 0.19 but ending up with 0.20 and 0.22, respectively. So I wanted to know if this is usual? I was expecting my data to become slightlly better but what is irritating me is the starting R-values of the refinement and that it get worse during refinement. Maybe I did something wrong? Is it reasonable to replace the mtz.file with a new one in the last refinement step or should I start the refinement from the scratch? In the sake of completeness, I deleted the header of the used pdb.file because of the R-flag error which occurs, since Phenix reconizes that the pdb.file was already used with other Rflags. Sorry, but I am still a beginner in this field, so I would be very grateful if somebody could explain me this situation and my mistake and if I need to start refinement from the beginning. Thank you in advance! Best Regards. Aleksandar -- ------------------------------------------- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 A-1090 Wien Tel: +43 1 4277 52536 e-Mail: aleksandar.bijelic(a)univie.ac.at --------------------------------------------

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Problems running phenix.rosetta_refine
by Klose, Thomas 04 Jun '15

04 Jun '15

Dear all, I was trying to set up phenix.rosetta_refine to test it for the refinement of a 4.5Å structure. I installed the latest phenix release and compiled the latest rosetta version (2015.19) using rosetta.build_phenix_interface. However, when I try to run phenix.rosetta_refine I get the following error message: …. Generating 5 models on 4 processors... DEBUG dumping error message ERROR: Rosetta exited with status 1 stderr output: Sorry: Wrong map type requested: %%map_type%% Allowed format is: [p][m]Fo+[q][D]Fc[kick][filled] where [p] and [q] are any numbers (optional), [m] and [D] indicate if the requested map is sigmaa (optional), Fo and Fc are Fobs and Fcalc, [kick] is for Average Kick Map (optional), [filled] is for missing Fobs filled map. Examples: 2mFo-DFc, 3.2Fo-2.3Fc, mFobs-DFcalc_kick, 2mFobs-DFcalc_filled, Fc, 2mFobs-DFcalc_kick_fill, anom, anom_diff, anomalous_difference, Fo ERROR: PhenixInterface::calculateDensityMap() : error writing map ERROR:: Exit from: src/core/scoring/cryst/PhenixInterface.cc line: 1122 This happens with our actual data as well as test data that I downloaded (PDB: 1yip). Any help in solving this problem would be greatly appreciated. Thanks, Thomas

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Help with using FFT map coefficients tool
by Emilia C. Arturo (Emily) 04 Jun '15

04 Jun '15

Hello. I'd like to generate a map appropriate for viewing in PyMOL, using a model and structure factors downloaded from the PDB. But I'm unable to do so, and perhaps you can help me figure out what I might be doing wrong: To generate the map, I did the following using the phenix GUI (version 1.9-1692): 1. I used Reflection tools > Import CIF structure factors to convert the .cif format structure factors for PDB id 1J8U to an mtz file. 2. Then, to configure the job to generate the CCP4 map, I loaded this mtz file, but when I did that I got the following error: "This reflections file does not appear to contain any suitable map coefficients" I went through the same steps again for two other PDB ids, this time generating the mtz file by either letting phenix do it from a PDB id, or by supplying the tool with both a .cif file with structure factors and a pdb model file. I get the same error. Has anyone any advice? Regards, Emily.

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Negative density
by mohamed noor 03 Jun '15

03 Jun '15

Dear all After refinement, there is a single negative peak in my map where nothing is modeled. What does it mean? Thanks.

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alternate side chains conjugated with water molecules
by Jorge Iulek 31 May '15

31 May '15

Dear all, I have a 1.70 A resolution dataset in which I observe, with certain confidence, that some (few) side chains are alternated with waters. Though managing to tie occupancies of each alternate side chain with a water molecule to give an overall occupancy of 1.00, phenix refine still pushes them (water from side chain) apart as if there were bumping restraints (but their occupancies sum up to no more than 1.00). The closest to this I could find is: http://www.phenix-online.org/pipermail/phenixbb/2009-May/013354.html But I could not find how to turn off specific bumping restraints. I would be thankful if someone could point me to the recipe to do this. Jorge

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Low resolution refinement - rotamers and Ramachandran
by mohamed noor 29 May '15

29 May '15

Dear developers I am refining a low resolution structure (3.8 A). After I fix most of the outliers (red bars) in Coot, phenix.refine is causing my structure to be worse than the start with 13 % Ramachandran outlier and 13 % rotamer outlier. Secondly, when I used phase_and_build to build my model, my R/Rfree is around 30/35 with atoms from some residues missing. When I fill them in with Coot, fix the outliers above and re-refine, R/Rfree jumps to 36/42 and the rmsd angles are too high (2.9). I have already used weight optimization and NCS. Am I doing something wrong? Thanks.

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reference model restraints by segid
by jp d 28 May '15

28 May '15

Hi,I am having trouble getting phenix to used segid's in reference model restraints when my reference and target pdbs both don't use chain ID's.phenix quits with this message: *** Adding Reference Model Restraints *** Sorry: chain ' ' in /home/path/removed/agnref2.pdb contains one or more errant TER cards. Please remove and try again. my definition file looks like this:refinement { main { reference_model_restraints = True } reference_model { file = two.pdb } } refinement.reference_model.reference_group { reference = segid A16S selection = segid A16S } (above about 50 more times) this was on versions 1.9-1692 , dev-2016 and dev-2056 any suggestions ?thanksjpd

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riding hydrogen model
by Filip Qbukarski 27 May '15

27 May '15

Dear phenix community I am currently refining a 1.75A structure and wanted to usethe riding hydrogen model in pehnix.refine. From what I found in the manual andprevious discussions on the mailing list and if I understand well, using ridingHs is advised for every resolution and the way of doing this in phenix.refine is notRefmac-like but instead I should 1) put Hs using ReadySet, 2) select the‘riding’ option for Hs and 3) use the PDB containing the H coordinates fordeposition, even though they were not individually refined. In this case theircontribution to scattering is also taken into account (which makes sense),which is a different way of treating riding Hs compared to Refmac, if Iunderstand well. Would it be possible to comment on this and in case I got thingswrong, correct?In fact for my structure, after adding the Hs prior to refinement using ReadySet and using theriding option, I actually got Rfree dropping by 1% (from 19.5 to 18.5) and better clash score (~0.5 according to Molprobity). Thanks in advancebestFilip

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