April 2013 - phenixbb - phenix-online.org

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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Phenix version 1.8.2 released
by Paul Adams 26 Jun '13

26 Jun '13

The Phenix developers are pleased to announce that version 1.8.2 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights from this version: Ensemble refinement, updated hydrogen parameters in refinement and validation, mmCIF reading and writing, LLG maps output from refinement, ligand pipeline for automated solution of protein/ligand complexes, autobuilding starting from a very accurate but very small part of a model, CC* calculation from unmerged data, maximum entropy maps, and PDB editor. Graphical interface: ==================== - New GUIs: phenix.merging_statistics, phenix.pdb_editor General: ======== - Multiple bug fixes - phenix.refine, phenix.reduce, and MolProbity updated to use consistent, revised, electron-cloud centers for hydrogen positions as default (for X-ray) - also see MolProbity website for details: http://molprobity.biochem.duke.edu - mmCIF format now supported in place of PDB format for input to many programs - new commands: phenix.ensemble_refinement, phenix.ligand_pipeline, phenix.sort_hetatms, phenix.cc_star, phenix.pdb_editor, phenix.maximum_entropy_map Refinement: =========== - phenix.refine - support for LLG map type - uses Phaser to compute residual anomalous LLG map - best when used with group_anomalous strategy, which will flatten the LLG map around existing anomalous scatterers with refined f'/f''. - alternatively, anomalous_residual map type (similar but less sensitive) - automatic linking in refinement and pdbtools for residues in the same chain - enabled with automatic_linking.intra_chain=True; this includes carbohydrate linking to protein and between sugars, and covalently bound ligands. - optional output of mmCIF format model and data files - phenix.ensemble_refinement (new command): - New method for refining ensemble models - Combines MD simulation with X-ray restraints that simultaneously account for anisotopic and anharmonic atomic distributions. - For full description see: Burnley BT, Afonine PV, Adams PD, Gros P. 2012. Modelling dynamics in protein crystal structures by ensemble refinement. eLife 1:e00311. doi: 10.7554/elife.00311. Experimental Phasing and Model Building: ======================================== - phenix.autobuild: - now uses torsion NCS parameterization when NCS is used in refinement - building starting from a very accurate but very small part of a model: You can now use the keyword rebuild_from_fragments=True to start rebuilding from fragments of a model. You might want to use this if you look for ideal helices using Phaser, then rebuild the resulting partial model, as in the Arcimboldo procedure. The special feature of finding helices is that they can be very accurately placed in some cases. This really helps the subsequent rebuilding. If you have enough computer time, then run it several or even many times with different values of i_ran_seed. Each time you'll get a slightly different result. - Base-pairing in RNA building -- phenix.autobuild will now try to guess which bases in a model are base-paired, and if there is no positive sequence match to the model, the bases that are base-paired will be chosen to be complementary. You can set the cutoff for base pairing with the keyword dist_cut_base. - waters are automatically named with the chain of the closest macromolecule if you set sort_hetatms=True. This is for the final model only. - you can supply a target position for your model with map_to_object=my_target.pdb. Then at the very end of the run your molecule will be placed as close to this as possible. The center of mass of the autobuild model will be superimposed on the center of mass of my_target.pdb using space group symmetry, taking any match closer than 15 A within 3 unit cells of the original position. The new file will be overall_best_mapped.pdb. Molecular Replacement: ====================== - phenix.mr_rosetta - You can now give commands for Rosetta in mr_rosetta, including a command to specify where disulfide bonds are located - The Rosetta models are now identified by an ID number so that they have unique names - Default number of homology models to download is now 1 (was 5) - Default number of NCS copies (if ncs_copies=Auto) is number leading to solvent content closest to 50%; if ncs_copies=None then all plausible values of ncs_copies are tested. New commands: ============= - phenix.ligand_pipeline (new command): - combines Xtriage, Phaser, eLBOW, phenix.refine, AutoBuild, and LigandFit to automatically solve protein/ligand complexes - optional integration with Coot (parameter interactive=True) allows semi-interactive operation where more rebuilding is required - phenix.cc_star (new command): - combined assessment of model and data quality, as outlined in Karplus & Diederichs (2012) Science 336:1030-3. - summary also output by phenix.model_vs_data if additional unmerged_data keyword is specified - phenix.maximum_entropy_map (new command): - tool to compute maximum entropy map from map coefficients. The program reads input Fourier map coefficients and modifies corresponding synthesis using Maximum-Entropy Method (MEM). The MEM modified map is everywhere positive, smooth and is of higher resolution. The method uses is a modification of Gull & Daniell (1978) algorithm. - phenix.sort_hetatms (new command): - rearranges heteroatoms (ligands, waters, etc.) in a model so they are paired with the nearest macromolecule chain, similar to the PDB's processing of models - phenix.pdb_editor (new command): - graphical editor for PDB files, based on tree view of model hierarchy - perform common operations such as chain renaming, renumbering, manipulation of atomic properties, add/remove atoms Ligands: ======== - phenix.ready_set: - methyl rotations now automatic when adding explicit hydrogens (also in phenix.reduce) - more options adding deuteriums to a model have been introduced Miscellaneous: ============== - phenix.xtriage: - include merging statistics if unmerged intensities are used as input - phenix.maps: - added wavelength parameter and support for anomalous residual and Phaser LLG map coefficients For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Find Difference peaks and holes
by John Rose 03 May '13

03 May '13

Hi, I can't seem to find the "Find Difference peaks and holes" utility in the PHENIX 1.8.2-1309 distribution. I found it to be very useful. Can you tell me where it is hiding. Regards, John John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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ReadySet & phenix.refine problem: NAG-Asn with hydrogen atoms
by Zhijie Li 30 Apr '13

30 Apr '13

Hello, I am refining my structure with hydrogen atoms on (phenix 1.8.2-1309). The protein contains two Asn-linked GlcNAc. I noticed two problems with respect to the NAG-Asn linkage in the presence of hydrogen atoms: 1) After running ReadySet (to add hydrogen to the PDB ab initio), the H1 on the NAG is pointing to the amino group of Asn, ie, the NAG seems to be interpreted as in its alpha anomer instead of beta (should be GlcNAc beta1,N-Asn). This is not really a problem as it doesn't seem to affect the refinement. 2) The H21 in Asn is correctly removed by ReadySet, leaving only H22. However, if I send this PDB to phenix.refine, the refinement will fail almost instantly complaining that H22 of the Asn has an unknown nonbonded energy type symbol. But if I simply change the atom name of H22 to H21, the refinement will proceed to completion with no problem, only leaving an H21 at the position where H22 should be. I was not sure what caused this error. So I trimmed my PDBs down to the Asn and NAG only, and fed the small PDB to ReadySet and phenix.refine (with an eff file indicating the NAG-Asn linkage) and got the same behavior: H22 on Asn - error; H21 on Asn - OK. I hope someone can look into this. Thanks in advance. Zhijie

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SIGF in refinement
by Aksyuk, Anastasia (NIH/NIAMS) [F] 29 Apr '13

29 Apr '13

Hi, I was wondering how SigFobs values are used in phenix refinement and how important those are. I am asking in view of P1 space group with low redundancy or even cryo-EM map based Fobs. Maybe you can point me to a useful reference on likelihood targets. I feel lost in those that I have. Thanks, --Anastasia ------------------------------ Anastasia A Aksyuk, PhD Laboratory of Structural Biology, NIAMS Bldg 50, Room 1511, 50 South Drive MSC 8025 N.I.H., Bethesda, MD 20892-8025 tel 301 451-8247 e-mail: anastasia.aksyuk(a)nih.gov

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Re: [phenixbb] clashscore discrepancies
by Alex Theodossis 27 Apr '13

27 Apr '13

Dear phenixbb, I have carried out refinement using the latest version of PHENIX, which gives improved molprobity stats. However, these stats still do not match those porvided by the molprobity server: PHENIX output Molprobity server Existing H-model Electron-cloud H-model All atom clashscore 2.57 4.2 (81st perc) 3.25 (88th percentile) Rotamer outliers 0.7 1.14 1.14 Overall score 1.04 1/24 (89th perc) 1.16 (93rd percentile) Given that PHENIX is now giving me the best results and all scenarios give reasonable results I am less inclined to be concerned. However, I still find these inconsistencies rather puzzling and am curious to learn what is causing them. Thanks in advance.

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phenix.elbow: Best ploy to generate restraints files for similar compounds ?
by Phil Jeffrey 26 Apr '13

26 Apr '13

I've got homologues of small molecule compounds I want to generate restraints for. The changes I'm looking at are converting O to S and moving a substituent around on a phenyl ring. I expect them to have similar conformations overall. Is the best method to: 1. create a new PDB file of the homolog, change atom types and do some primitive modeling, assuming that the --opt method will fix geometry snafus ~or~ 2. use a SMILES string, edit the numbering of the PDB file and regenerate the restraints from that Thanks Phil Jeffrey Princeton

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clashscore discrepancies
by Alex Theodossis 25 Apr '13

25 Apr '13

Dear phenixbb, Have refined a 1.05A structure with riding hydrogen model in phenix v1.8.1-1168 and doing final validation. The molprobity statistics output by phenix include: all atom clashscore = 4.12 Rotamer outliers = 0.71% Overall score = 1.2 Put through the molprobity server I am given the option of analysing with existing hydrogen model, or replacing with the 'electron-cloud parameters' they recommend for X-ray crystal structures. The results end up being very different: existing H model: electron-cloud model: All atom clash score: 4.66 (78th percentile) 3.72 (85th percentile) Poor rotamers: 1.14% 1.14% Overall score: 1.28 (88th percentile) 1.20 (92nd percentile) While all three scenarios give acceptable statistics, I am surprised by the inconsistency in the results given by molprobity, even when using the same hydrogen model. I am also wondering whether I am using a suboptimal riding model in my refinement (generated using phenix ready-set). Can anyone advise on the reason for these inconsistencies (is it just due to differences in the version of molprobity being run in each case). Is there anything I should be doing differently? Thanks in advance. On 18 November 2012 12:36, Alex Theodossis <alex.theodossis(a)monash.edu>wrote: > Hi, > > I'm attempting to install the latest version of phenix on mac 10.5.8, > using the command line installer. > > Installation proceeds well until towards the end, where it hangs on: > > precompiling .py files > > I can leave it for up to an hour without any further progress, but upon > typing: > > ctrl+c > > The installation comes back to life and proceeds to completion. > > Can anyone advise as to what might be causing this and on how reliable > this installation is going to be? > > Thanks in advance. > > >

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Postdoctoral positions in structure and function of membrane proteins at the NIH
by Anirban Banerjee 25 Apr '13

25 Apr '13

Dear all, Will you please bring this to the attention of suitable candidates ? Postdoctoral positions in structure and function of membrane proteins at the NIH The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows to start from September, 2013 or later. The broad interests of the lab are in membrane protein structure and function. We will combine macromolecular crystallography with functional assays with detergent-solubilized and liposome-reconstituted proteins to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab is part of the Cell Biology and Metabolism (CBMP) program and is part of a large and diverse macromolecular crystallography and NMR community in the NIH campus. There is ample opportunity to interact with other scientific groups across a broad range of scientific disciplines. CBMP is part of the National Institute of Child Health and Human Development (NICHD). Our lab also has an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). The DC Metro area is a wonderful place to live, the weather is pleasant and the NIH is a vibrant international community. Candidates must be motivated and have a strong background in biochemistry and structural biology. Experience with protein expression, purification and crystallization is required. Prior experience in membrane protein biochemistry will be an added advantage. Candidates should hold a Ph.D. degree by the time they join and have no more than one year of postdoctoral experience at the time of applying. To apply, please send an email of interest to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future research interests. Best regards, Anirban

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install problem on Ubuntu 12.10
by Guan Hong Hsiang 25 Apr '13

25 Apr '13

Dear all: When I wanted to install phenix on my computer with ubuntu 12.10 (./install), the error message showed that "/usr/local/phenix-installer-1.8.2-1309/bin/install-from-binary:130:export:6 core : bad variable name. I am a newbie of phenix. Could anyone give me some suggestion? Thank you Hong-Hsiang

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