August 2008 - phenixbb - phenix-online.org

phenix.twin_map_utils AssertionError
by hari jayaram 14 Aug '08

14 Aug '08

Hi I am trying to run the following command phenix.twin_map_utils data.file=cy_p10_2_28.1_unique1.mtz model.file=cy_p10_2_28.1.pdb obs_labels=F_p10-2,SIGF_p10-2 free_flag=FreeR_flag When I run phenix.twin_map_utils from phenix version 1.3 final or from the newest cci_aps. I get the following AssertionError ( see below). I think my mtz file is kosher because phenix.refine with the twin_law option handles it well and I can refine with a twin law. Is there something wrong in the syntax or the file. I am attaching the log file with the Assertion Error to this email. Thanks for your help Hari Overall and bulk solvent scale paranmeters and twin fraction estimation ======================================================================= Traceback (most recent call last): File "/Users/hari/cci_apps_sources/mmtbx/mmtbx/command_line/twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/Users/hari/cci_apps_sources/mmtbx/mmtbx/twinning/twin_map_utils.py", line 306, in run out=log) File "/Users/hari/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 946, in __init__ assert self.f_obs.indices().all_eq( self.free_array.indices() ) AssertionError

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phenix pdp files and coot - FIXED
by nihmmayerm 13 Aug '08

13 Aug '08

Hi, The problem was that coot choked on the TER and BREAK lines in the PDB, once I removed these 0.4.1 reads the phenix PDBs fine. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I've just finished refinements with latest version of phenix (/phenix-1.3-final/build/mac-intel-osx/bin/phenix) in which I used riding hydrogens added with reduc (Molprobity) version and TLS - so I have anisou records - and a bunch of acs. When I open files in coot (coot/0.4.1/bin/coot) I see only 1 chain (I have a dimer chain A and B) and no solvent or other heteroatoms. The file displays fine in pymol - but I want to rebuild with coot. Any ideas ? I'm using the SBGrid install of coot, and a local installation of phenix. Thanks - Mark

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phenix pdp files and coot
by nihmayerm 13 Aug '08

13 Aug '08

Hi, I've just finished refinements with latest version of phenix (/phenix-1.3-final/build/mac-intel-osx/bin/phenix) in which I used riding hydrogens added with refine (Molprobity) version and TLS - so I have anisou records - and a bunch of acs. When I open files in coot (coot/0.4.1/bin/coot) I see only 1 chain (I have a dimer chain A and B) and no solvent or other heteroatoms. The file displays fine in pymol - but I want to rebuild with coot. Any ideas ? I'm using the SBGrid install of coot, and a local installation of phenix. Thanks - Mark

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Segmentation fault with twin-law refinement
by hari jayaram 13 Aug '08

13 Aug '08

Hi I have discovered that my data in the P3 spacegroup is potentially twinned. Truncate and phenix.xtriage indicate that the twin fraction is pretty high ( between 0.35 and 0.42). I am still new to twinned data refinement and still dont know which twin law to pick from the three possibilities for P3 that xtriage lists. I am emailing because , Regardless of the twin law I try , phenix.refine crashes with a Segmentation fault on my Mac Pro leopard 10.5.2 running phenix. 1.3b-rc6 The command that ends with a Python crash and segmentation fault is Command used: phenix.refine cy_p10_2_28.1.pdb cy_p10_2_28.1_unique1.mtz simulated_annealing=true model.ncs refinement.main.ncs=true --overwrite refinement.ncs.excessive_distance_limit=None strategy=group_adp+individual_sites twin_law='-h,-k,l' refinement.input.xray_data.labels=F_p10-2,SIGF_p10-2 > phenix_run2_mhmkl_simulanneal.log phenix.xtriage outputs Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | -h,-k,l | M | 0.100 | 0.406 | 0.407 | 0.393 | | h,-h-k,-l | M | 0.071 | 0.426 | 0.439 | 0.458 | | -k,-h,-l | M | 0.090 | 0.411 | 0.417 | 0.415 | ------------------------------------------------------------------ Can you tell me if there is something I am doing wrong . Thanks a tonne for your help Hari Jayaram Postdoc , Brandeis University

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phenix.reduce
by Mayer, Mark (NIH/NICHD) [E] 13 Aug '08

13 Aug '08

Hi, Does phenix.reduce correctly handle pdb files with alt confs? I ran reduce on such a file ang got a warning that only A was used, and when i checked output there were no H on AC B residues. I then sent file to Molprobity server, ran reduce, and now there are H on residues for both ACs. I'm doing this so I can refine with riding hydrogens. Thanks MLM

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secondary structure restraints
by Nikos Pinotsis 11 Aug '08

11 Aug '08

Dear all, I am refinining a 3.5 A structure where several of fragments are already determined in higher resolution (similar to the case I found below). In addition a large part of the structure is quite disordered (two out of four chains). I found a reply about a year ago that secondary structure restraints are not implemented in phenix, is there any new developements that can help the refinement in low resolution? (I have already employed NCS other common posibilities). thank you in advance for any help and best regards Nikos >/ On May 4, 2007, at 5:10 PM, Pavel Afonine wrote: />/ />>/ Hi Jianghai, />>/ />>/ I see several possibilities to think about or/and try out: />>/ />>/ 1) Fix the coordinates of atoms in the domains for which the high />>/ resolution structure is available and refine the rest; />>/ 2) Refine the domains for which the high resolution structure is />>/ available as rigid bodies and for the rest refine individual parameters; />>/ 3) There is no specific option in phenix.refine to restrain the />>/ secondary structure elements, however there is a tedious way of doing />>/ this (according to Ralf) by defining custom bonds and angles between />>/ specific atoms forming the secondary structure motifs. Look />>/ "Definition of custom bonds and angles" in the latest CCI Apps />>/ phenix.refine documentation for technical details. />>/ />>/ You can perform "1)" and "2)" in ONE refinement run by combining />>/ several refinement strategies and using specific selections for />>/ refinable parameters. />>/ />>/ Overall, at 3.8A resolution the refinement of individual atomic />>/ parameters (coordinates, B-factors) is questionable. I would consider />>/ to try to refine group parameters for B-factors (trough TLS or/and />>/ group B (like one B per residue)) and try to switch between rigid />>/ body refinement of smaller fragments of your model and refinement />>/ individual positional parameters or mix of individual and rigid body />>/ refinement. />>/ />>/ Also, I will think about making a specific option for automatic />>/ generation of secondary structure restrains. However, given the />>/ amount of work it may require this option will not appear in near future. />>/ />>/ Pavel. />>/ />>/ />>/ Jianghai Zhu wrote: />>>/ Hi all, />>>/ />>>/ I am refining a low resolution structure (~3.8 A). For some of the />>>/ domains in the structure, we already have high resolution />>>/ structures. Despite of some conformational changes in some loops, />>>/ the core structures should be the same. I am wondering if it is />>>/ possible to restrain the secondary structures in phenix.refine. />>>/ />>>/ Thanks. />>>/ />>>/ Jianghai/ -- --------------------------------- Dr. Nikos Pinotsis Section of Structural Biology Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London SW3 6JB, UK Tel: +44 20 7153 5453 / 5447 --------------------------------- The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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dihedral error
by Simon Kolstoe 08 Aug '08

08 Aug '08

phenix.refine keeps on stopping with the error: AssertionError: Conflicting dihedral restraints: tor id: var_002 1. definition from: residue: DRG, conformer A 2. definition from: residue: DRG, conformer A atoms: " CB DRG A 500 " " OG1 DRG A 500 " " PAL DRG A 500 " " OAF DRG A 500 " It is for a phospho-threonine residue whose dictionary I made in PRODRG. I've tried all the different charge states of the phosphate however phenix gives the same error every time. Any ideas? Thanks, Simon

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ncs in phenix.autobuild
by wang kaituo 07 Aug '08

07 Aug '08

Hi all, I failed in running phenix.autobuild. The end of the logfile said : ______________________________________________________ Build cycle 2 of 11 method:rebuild ...Using simple_ncs_from_pdb to find NCS Residues expected: [62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74] Residues found : [] ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Did not find expected residues in get_xyz_list _____________________________________________________________ The two ncs chain sequence is not exactly same , some sidechain missing and some connectivity not well. But the residue 62-74 is there in both chains. Have the ncs group to be exactly same to find NCS? how can i fix this? ps: phenix.simple_ncs_from_map works well with my pdb. using the ncs_spec file also not works many thanks kaituo

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riding hydrogens
by Jianghai Zhu 06 Aug '08

06 Aug '08

Hi, I used phenix.reduce to add riding hydrogens. After phenix.refine, the structure got a good score from MolProbity. However, if I stripped the riding hydrogens from the structure and let MolProbity to add hydrogens before the analysis, I got a much worse score, especially the clash score. Does phenix.refine refine the hydrogen positions? -- Jianghai

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DNA restraints
by jens j birktoft 06 Aug '08

06 Aug '08

Hi, Is there a way to restrain selected hydrogen bonds between base pairs during the refinement of DNA structures ? CNS has something like DNA_RNA.def if I remember correctly and I am looking for something of that nature. Cheers Jens -- Jens J. Birktoft - e-mail: jens.knold(a)gmail.com slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 use 212-749-5057 for ALL phone calls

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