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phenix.merging_statistics and resolution shells
by Murpholino Peligro 17 Sep '14

17 Sep '14

can I specify the ranges of the resolution shells in phenix.merging_statistics? (something like "XSCALE-word" RESOLUTION_SHELLS=) and how many resolution shells are ok? 10, 15, 20?

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LABELIT and MOSFLM version
by Ngoc Anh Thu Ho 16 Sep '14

16 Sep '14

Hello, labelit.index command cannot start Mosflm and gives an error, which reads: "MosflmVersionError: mosflm versions after 7.0.9 not supported” Other than that, indexing seems to be working fine. Can this be fixed or updated somehow? I’m using the latest Phenix 1.9-1692 and Mosflm 7.1.0 (with iMosflm 7.1.1). Best regards, Thu

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calculate CC*
by wei xia 15 Sep '14

15 Sep '14

Hi all:I have a set of data indexed with XDS (space group P222). When I use phaser, the MR solution was in space group P212121.I then changed the space group of mtz file to P212121 using phenix Reflection file editor and did the refinement. Now I use phenix to calculate CC*, in which I input unmerged data (from xds, P222) and merged data (mtz file, P212121) and final pdb file.It turned out to be "incompatible symmetry" error. Are there any easy ways to get the calculate CC* running?Thanks! Wei Xia

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Re: [phenixbb] [ccp4bb] Autobuild in specific area
by Terwilliger, Thomas Charles 14 Sep '14

14 Sep '14

Hi Foggy, This is a situation that autobuild does not address very well yet. Yes, you want rebuild_in_place=False. And yes, if you do that it will remove your model and rebuild it. It will also try to build into the remainder of the map. In practice, you already have pretty much the best that autobuild is going to produce. Delete the protein A chains that autobuild built, and put in your original protein A. Now you have your original model plus whatever autobuild was able to build. An alternative is: select "consider_main_chain_list=True" . This will take your input model A and at each step it will check to see if parts of that model are better than any other model that it has built. This can help for keeping the input model that you put in. All the best, Tom T ________________________________ From: CCP4 bulletin board [CCP4BB(a)JISCMAIL.AC.UK] on behalf of Zhang Foggy [foggyccp4(a)GMAIL.COM] Sent: Saturday, September 13, 2014 10:40 AM To: CCP4BB(a)JISCMAIL.AC.UK Subject: [ccp4bb] Autobuild in specific area Hi, All, I am trying to use Autobuild to build a protein-protein complex model. I obtained partial phase solution (protein-A) through MR, and can see some density of protein-B near protein-A. I would like to use Autobuild to build protein-B model into this area. I load data file, initial density map file, sequence file (both of protein A and B), and protein A model, and run Autobuild. However, The "rebuild-in-place" function confused me a lot, no matter I set it to True or False. When I set to True, it only rebuilt protein A model without adding any additional residues; while I set it to False, it deleted the input protein-A model, and rebuilt a new one... Could somebody tell me how to build the protein B model with keeping the input protein A model in Autobuild? Thanks. [https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif] Foggy

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Autobuild in specific area
by Zhang Foggy 13 Sep '14

13 Sep '14

Hi, All, I am trying to use Autobuild to build a protein-protein complex model. I obtained partial phase solution (protein-A) through MR, and can see some density of protein-B near protein-A. I would like to use Autobuild to build protein-B model into this area. I load data file, initial density map file, sequence file (both of protein A and B), and protein A model, and run Autobuild. However, The "rebuild-in-place" function confused me a lot, no matter I set it to True or False. When I set to True, it only rebuilt protein A model without adding any additional residues; while I set it to False, it deleted the input protein-A model, and rebuilt a new one... Could somebody tell me how to build the protein B model with keeping the input protein A model in Autobuild? Thanks. Foggy

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phenix rosetta installation
by Dan Lin 12 Sep '14

12 Sep '14

Hi all: This is kind of a silly problem, but I'm trying to get phenix.rosetta_refine running on my computer and I am having some difficulty getting rosetta.build_phenix_interface to run. I'm getting a permission denied error in the os.symlink(python_lib, lib_link_name) line in rosetta_build_phenix_interface.py script and presumably I could fix this by changing the write permissions to wherever this points to, but I don't know where. Could anybody point me towards the folder that needs to fixed? Thanks, Dan

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restraints for dna planarity
by John Lee 12 Sep '14

12 Sep '14

Hi, I'm refining a low resolution structure of a dna-protein complex (3.7A) & wondering if someone could help me with setting restraints in Phenix to maintain the base-pair planarity of the dna? With the restraints I have, even with a reference model, I'm getting 'puckering' of the base-pairs. Although the h-bonding distances seem to hold over time, I can't seem to find a way to keep the planarity intact. Thanks in advance for your help. -John

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Phenix-Rosetta integration tests fail with Rosetta MPI on RHEL 6.3
by Sina Masoud-Ansari 12 Sep '14

12 Sep '14

Hi there, I'm wondering anyone has managed to successfully run Phenix with Rosetta MPI on Red Hat Enterprise Linux 6.3 or similar? I currently have a non-MPI build of Rosetta that passes all of the tests in phenix_regression.wizards.test_command_line_rosetta_quick However when running these tests with the MPI build of Rosetta the following tests fail: Running test_relax ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax/test_relax.log test_relax/test_relax_current.log ================================================================= Running test_relax_double ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax_double/test_relax_double.log test_relax_double/test_relax_double_current.log ================================================================= Running test_relax_no_sol ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax_no_sol/test_relax_no_sol.log test_relax_no_sol/test_relax_no_sol_current.log I have attempted to attach an archive of the logs. I'm working with Rosetta 3.5, more recent versions of Rosetta fail other tests in phenix_regression.wizards.test_command_line_rosetta_quick , please see https://www.rosettacommons.org/node/3721 for details. Rosetta 3.5 was compiled with GCC 4.4.6 using OpenMPI 1.6.4 Any help or advice is appreciated. -- Sina Masoud-Ansari Centre for eResearch 409.G21 24 Symonds Street University of Auckland e: s.ansari(a)auckland.ac.nz p: +64 9 3737599 ext 89369 w: http://www.eresearch.auckland.ac.nz

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phenix refine geometry restraints
by George Devaniranjan 12 Sep '14

12 Sep '14

Hi, I was trying to restrain the N-CA-C angle to 110.0 I updated the .def file as follows: angle { action = *add atom_selection_1 = name N atom_selection_2 = name CA atom_selection_3 = name C angle_ideal = 110.0 sigma = 2 I got the following: Sorry: More than one atom selected: "name N" Number of selected atoms: 86 I tried using N in quotes and it doesn't work either but the example in the website had this(below), what am I doing wrong? resname ALA and (name ca or name c or name n or name o) Thank you

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refinement for non-standard DNA base
by John Cheong 11 Sep '14

11 Sep '14

Hi, I have 5-fluoro-Uracil in my DNA:protein complex. I modeled 5-F-dU into the map, ran eLBOW for geometry file and did refinement. After the refinement, 5-F-dU is not connected to the neighboring nucleotides and the phosphate oxygens are rotated to wrong positions. Can anyone teach me how to refine with non-standard DNA base ? Any help or advice would be appreciated. John

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