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Weird Hydorgen refinement
by Yuri 23 Aug '11

23 Aug '11

Hello everyone. I was trying to refine my model anisotropically. I selected element NA or (chain A and not element H). I looked at the output pdb shows that hydrogens were being refined anisou as well as the protein. I believe its because technically they are also in chain A, but shouldnt the default be never refine H's anisotropically, especially at 1.5A ?. -- Yuri Pompeu

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autosol error in GUI
by r n 23 Aug '11

23 Aug '11

Hi all I downloaded the Phenix developing version 842, autosol gui running gave me the following error, "The key gui_output_dir is not in var_type_dict....command line wizzard needs conversion in the autosol.py script uing translating inputs or else in excluded inputs....wizard setVars routine needs this variable set". I have not had this error earlier version. any help? Thanks ram

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pdb conversion to 3.2 format
by Luca Pellegrini 23 Aug '11

23 Aug '11

Hi, I am trying to use iotbx.pdb_remediator to convert PDB atom names to 3.2 format (as suggested by Nat Echols in a recent post to Coot mail-list). Unfortunately I get the following error message: lp212-mp2281 58% iotbx.pdb_remediator file_name=refine.pdb output_file=refine_3.2.pdb_file Traceback (most recent call last): File "/usr/local/cctbx/cctbx_sources/iotbx/command_line/pdb_remediator.py", line 54, in <module> run(sys.argv[1:]) File "/usr/local/cctbx/cctbx_sources/iotbx/command_line/pdb_remediator.py", line 51, in run remediator.remediator(params) File "/usr/local/cctbx/cctbx_sources/iotbx/pdb/remediation/remediator.py", line 257, in remediator user_dict) File "/usr/local/cctbx/cctbx_sources/iotbx/pdb/remediation/remediator.py", line 95, in build_hash test=os.path.isfile), "rb") TypeError: coercing to Unicode: need string or buffer, NoneType found It looks like a python problem, but I am afraid my insight ends here. Can anyone tell me how to fix this, please? I am not sure if it matters, but iotbx_pdb_remediator was not in my phenix installation (PHENIX-1.7.1-743 on MacOSX 10.6.8), so I installed cctbx separately. Thanks! Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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MR problem
by intekhab alam 22 Aug '11

22 Aug '11

Hi there I have a data of heterotrimer protein complex at 2.9A resolution. One protein consists of two domains. I tried phaser as well as molrep which gives a solution with only one domain. Rotation function and translation function were found to be fine for these solutions. I tried to find missing domain of the protein after fixing one of the domain or the other partner proteins using whole part or various truncations of missing domain. I also tried to find and build missing domain using Rosetta with the solutions of Molrep or Phaser as template. But, there were no solutions, or the solutions are clashed with other domain or proteins. Furthermore, R and Rfree is 30 and 40, respectively, and I could not reduce them further. There was almost no electron density map in the empty space so that I could not model manually. Plz guide me ,how can i look for the missing domain in the protein. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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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 20 Aug '11

20 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 20 Aug '11

20 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 17 Aug '11

17 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 17 Aug '11

17 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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