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matplotlib
by Ed Pozharski 21 Aug '11

21 Aug '11

This is really a rather esoteric issue, but I feel I need to mention this to save someone, depending on the situation, anywhere between five minutes of googling or two hours of hair-pulling. In a nutshell, phenix gui may in some circumstances screw up other programs that use matplotlib. I can't track down which specific phenix gui action causes it, but it's safe to assume that whenever matplotlib libs are used the subsequent calls to logarithmic scale plots (and likely other things) throw this error TypeError: coercing to Unicode: need string or buffer, dict found The solution is to erase the ~/.matplotlib/fontList.cache. The likely cause is that phinix gui calls on bundled matplotlib which is different from one I have installed (not to mention that I am using Lucid (because it's LTS) which has python 2.6 and not the 2.7 that is bundled with phenix). However, it still writes into the same ~/.matplotlib folder, thus I end up with incompatible data. Certainly, the problem will be gone when matplotlib gets bumped up to 1.0.1 in next Ubuntu release. This is yet another example of why the standalone installation approach is ideologically objectionable on modern Linux. But of course, the practical advantage gained by not having to package the software for any possible OS flavor/version users may choose outweighs the lower risks of package incompatibility and the reduced size of the packaged product. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs

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formyl-methionine
by Yuri 19 Aug '11

19 Aug '11

Hello Everyone, Stupid question. I see density at my N-terminus that really looks like formyl-Met. I want to model it and refine. I notice REEl has FME ligand for the formyl-methionine, but I dont want to treat it as a "ligand" since it is covalently attached to SER 2. What is the best way to modify the MET residue? Cheers -- Yuri Pompeu

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Definition of "Saenger Class"
by jens j birktoft 19 Aug '11

19 Aug '11

Hi All, Could somebody direct me to "saenger class" definitions used in base-pair restraints for DNA/RNA. Cheers Jens *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft e-mail: birktoft(a)nyu.edu <jens.knold(a)gmail.com> New York University, Dept. Chemistry Phone: 212-749-5057 *

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phenix.phaser multiple pdbs
by G Y 17 Aug '11

17 Aug '11

Dear all, I am writing a bash script for running phenix.phaser automatically on an ensemble of multiple pdbs. These pdbs have been superimposed by other tools before running phaser. The following is what I wrote for the ensemble part in params.eff file: ensemble { model_id = a1 coordinates { pdb = model1.pdb pdb = model2.pdb pdb = model3.pdb pdb = model4.pdb rmsd = None identity = 0.9 } It runs well. When it finished, I want to confirm that it really run MR on all four models or on a ensemble of these models. However in .log file, I found at the refinement part it shown me: ---------- REFINEMENT ---------- There is 1 solution to refine Refining solutions 0% 100% |==| DONE Configuring ensembles --------------------- PDB file # 1: model1.pdb This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 **************************** Does this mean that phenix.phaser only run MR with the first model? Does it due to the way I wrote in my params.eff file? What would be the correct way? Many thanks! best, G

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changing project directory
by Jens Kaiser 16 Aug '11

16 Aug '11

Hi all, I have project data on external hard drives. As I use several different file systems, and mount the drives in random order, I cannot rely on the device being mounted in the same mount point. In order to keep paths consistent, I link the project directories into my home. This used to work fine. I recently created a project, and phenix seemed to have used the real path instead of the link-path (That's not the problem, yet). I tried to manually edit ~/.phenix/project_db.phil, but it still tries to write in a non-existing directory. A naive 'grep -R "disk-1" ~/.phenix' did not reveal any obvious file either. Where can I change the directory associated with a project {per,con}sistently? Thanks for your time, Jens

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nucleic acid secondary restraints breaking in 1.7.1-743
by Francis E Reyes 16 Aug '11

16 Aug '11

Hi all Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 67, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 112, in __init__ hbond_params=self.params.hydrogen_bonding) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/__init__.py", line 494, in create_hbond_proxies log=log) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/__init__.py", line 286, in hydrogen_bond_proxies_from_selections log=log) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/base_pairing.py", line 415, in create_hbond_proxies if distance_values[i][2] != '_': IndexError: tuple index out of range When specifying a single base pair when using secondary_structure nucleic acids restraints Any ideas? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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modelling of disordered protein
by intekhab alam 16 Aug '11

16 Aug '11

Hi I solved an RNA polymerase structure in its native as well as in complex with chemical ligands (2.5A and C2 space group). The structure has been solved by MR a protein having 60% identity. The ASU has a monomer and dimer. Recently i complexed this RNA polymerase (protein A) with a highly flexible protein B and got the crystal. These crytsal also have C2 space group (resolution 2.3A) having similar cell parameters but has psudotranslation (17.34%). I tried MR using rosetta. HHpred server selected one of my deposited structure in PDB (3NAI 100% identity) as template. Rosetta MR gave 2 solutions one of which is dimer-monomer arrangement while the other one is a trimer. The values of these solution are below. Solution 1: trimer REMARK Log-Likelihood Gain: 10662.548 REMARK RFZ=16.5 TFZ=14.4 PAK=0 LLG=959 TFZ==23.2 RFZ=0.0 TFZ=48.9 PAK=0 LLG=3195 TFZ==55.6 (& TFZ==52.6) LLG+=(3191 & 7008) LLG=7024 TFZ==72.0 LLG=10663 TFZ==90.1 Solution 2: Monomer and dimer in ASU REMARK Log-Likelihood Gain: 2120.965 REMARK RFZ=39.7 TFZ=21.9 PAK=0 LLG=811 TFZ==37.7 LLG=2121 TFZ==43.6 REMARK ENSEMBLE ensemble_1 EULER 204.07 178.91 204.37 FRAC 0.499 Map and model fits well in both the cases with R and R free 26 and 30% respectively. My queries: 1. which one will be the correct solution? Is it possible that the protein B has resulted in the trimeric arrangement? 2. i cannot find any continuous 2Fo-Fc map for proteinB, but there are some continuous density at 0.7 which is very ambiguous. how can i improve the map so that i can model some fragments of my proteinB (protein B is of 73 amino acids and is predicted to be highly flexible and disordered. ((biochemical as well as bioinformatical analysis done )) I already have tried autobuild but it fails to build even a partial fragment of the proteinB. Kindly suggest how to proceed , or how can i prove the presence of protein B in the structure. Regards INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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LigandFit error
by Priit Eek 14 Aug '11

14 Aug '11

Hi, I'm getting this error when trying to run LigandFit from the GUI: The key gui_output_dir is not in var_type_dict…this means the command-line Wizard needs a conversion in the ligandfit.py script under 'Translating inputs' or else in excluded_inputs or else the Wizard SetVars routine needs this variable set Is this a bug? I am using the 64-bit dev-842 version on OS X 10.7 Lion. Best regards, Priit

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Unexpected Occupancy refiniement for ligands...
by Yuri 13 Aug '11

13 Aug '11

Hey, So I am finishing up a model at 1.5 A and I tried to refine my ligands (3) and waters (468) in addition to altloc residues. The residues refine as expected e.g OccA + OccB = 1.0 and all atoms in A have OccA and all the atoms in B have OccB. My ligands on the other are being refined as the following: HETATM 6867 C1 MLA L 3 32.357 -28.612 7.978 0.93 23.77 C C HETATM 6868 O1A MLA L 3 31.209 -28.949 7.502 0.85 24.79 C O HETATM 6869 O1B MLA L 3 32.454 -28.160 9.141 0.70 22.70 C O HETATM 6870 C2 MLA L 3 33.553 -28.727 7.095 1.00 25.46 C C HETATM 6871 C3 MLA L 3 34.774 -28.070 7.627 0.92 28.45 C C HETATM 6872 O3A MLA L 3 34.830 -27.664 8.808 1.00 30.15 C O HETATM 6873 O3B MLA L 3 35.775 -27.948 6.840 1.00 30.23 C O HETATM 6874 HC21 MLA L 3 33.321 -28.281 6.139 1.00 30.56 C H HETATM 6875 HC22 MLA L 3 33.760 -29.776 6.943 1.00 30.56 C H Each atom is getting an individual occupancy assigned, which physically is impossible :) Any light? Could it be my selection syntax? Corrigendum: I think I sent a bug email last night about an error when writing mtz files in refinement. It was an accident. My naming convention was bad, thats why it crashed. Sorry -- Yuri Pompeu

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R/Rfree discrepancy Phenix vs Refmac
by Sabine Schneider 12 Aug '11

12 Aug '11

Hello, I am refining a structure at 2.1A solved by MR. For curiosity I'm testing things like 'shaking' coordinates, simulated annealing, refinement Refmac vs Phenix and so on, to see what influence that has on stats, maps etc. For instance after MR I did a bit of shaking the coordinates with pdbset (noise 0.1), followed by simulated annealing in Phenix. Phenix states after SA: Start R-work = 0.2671, R-free = 0.2992 Final R-work = 0.2312, R-free = 0.2666 When I use the output pdb of phenix directly in Refmac (with same mtz as input for Phenix) Refmac tells me: Initial R factor 0.2392 R free 0.2887 So I am quite puzzled about the discrepancy. Or can someone tell me if I made an error in reasoning somewhere? Thanks a lot for the help! Sabine

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