- phenixbb - phenix-online.org

composite omit map problem
by Morgan Thompson 23 Feb '11

23 Feb '11

Hi, I am having trouble generating a composite omit map using the AutoBuild GUI. I am using Phenix version 1.7-650 on Ubuntu and I am able to run AutoBuild to make a simulated annealing composite omit map using my experimental data .mtz file and a reasonably refined model (R/R-free of 24/29% at 3.3 Angstrom). However, when I load the map - resolve_composite_map.mtz - into Coot (version 0.6.1) along with the starting model it looks terrible. There is quite a bit of density between each molecule within the ASU but very little density surrounding the model itself. However, I am able to open any of the .mtz_OMIT_REGION_XX files and they look really good. Any suggestions? Thanks, Morgan Biochemistry Department Dartmouth College

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questions on refinement
by Hena Dutta 23 Feb '11

23 Feb '11

Hello, I have a question on refinement of macromolecules. I like to apply 180 degree rotation to the side chain of a particular residue about a particular bond and see, which one (before or after applying rotation) agrees well with the observed x-ray data (based on R factors and electron density map). Can someone advise, what could be the best way to do this? I like to do the same operation on multiple structures which are already refined. Regards, hena

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phenix find tls groups
by Kendall Nettles 23 Feb '11

23 Feb '11

is there a command line interface to have phenix find TLS groups ? Best regards, Kendall Nettles

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Deadline March 1, 2011: Travel Fellowships for XXII IUCr Congress, Madrid, August 22-31, 2011
by Gloria Borgstahl 21 Feb '11

21 Feb '11

Please visit the USNC/Cr website for more information. *http://sites.nationalacademies.org/pga/biso/IUCr/*<http://sites.nationalacademies.org/pga/biso/IUCr/>

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adding ligands to model
by Geoffrey Feld 21 Feb '11

21 Feb '11

Greetings, I have a few structures I am trying to refine that have density for ligands, and I'm having trouble getting phenix to refine them properly. There are two unique scenarios, so I'll go in order of difficulty. 1) There are non-water solvent molecules (i.e. probably PEGs) that are here and there in the structure. I used phenix.elbow with SMILES notation to build the requested ligands and placed / real space refined them into the density using COOT. Now I cannot get phenix to refine the structure, every time I get the message "Number of atoms with unknown nonbonded energy type symbols: XX Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). where XX can be any variation of a number, depending on how I set up the phenix.refine run. This is what I've tried: a) adding the .cif files into my .def file I'm using for refinement parameters b) adding the .cif files on the command line c) running phenix.ready_set to generate .cif files for the unknown ligands and then inputing the .cif files from that on the command line d) running phenix.elbow with --add_all and the pdb to generate .cif files for unknown ligands, then doing as in (c) from the command line None of these seem to get phenix.refine to skip the error mentioned above and start refining. There are 3 different ligands, one of which is repeated 4x, but each has its own chain number in the same chain (I've even tried them each with their own unique chain). Any advice on getting these ligand restraints into phenix so it will happily refine? 2) I have an intramolecular crosslink in another structure, basically I crosslinked two cysteines with 1,3-dichloroacetone, giving a Cys-S-CH2C(=O)CH2-S-Cys linkage. How can I get restraints for this crosslink so it will refine as one covalent chain? So far, I've placed the acetone in between the two Cysteines, but it would be nice for it to be a part of the chain so I can refine it in real space, the density is not so good since the crosslink adds flexibility to the bond as apposed to just a disulfide. Any ideas here? I thought maybe the best way to do it is to just modify one of the cys to contain the extra atoms and call it a new residue, then add bond restraints for the 2nd link, however, then I'm still stuck with the extra hydrogen. Thanks! Geoff -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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automating setting up parallel refinement jobs
by Kendall Nettles 19 Feb '11

19 Feb '11

Dear PHENIX developers, I'm writing to ask if it would be possible to automate the following: What we do now is a series of parallel throw away refinements to test for different parameters. So I will set up 12 folders with the same data and different parameter files (and all the same file names). On top of individual sites and adp I would add: 1=nothing (control) 2=ncs=True 3=fix_rotamers = True 4=flip_peptides = True 5=nqh_flips = True 6=individual_sites_real_space 7=tls with 3 groups per monomer 8=tls with 6 groups per monomer 9=tls with 9 groups per monomer 10=tls 1 with 12 groups per monomer 11=tls 1 with 15 groups per monomer 12=tls 2 with 20 groups per monomer I then launch all of them with a script that sends it to a cluster. After reviewing results, we combine parameters for one job that we keep. So here is my feature request: I would love to have a GUI interface to generate the folders and parameter files, where you would select a list of common parameters, and a list of parameters to populate 1/ job, instead of having to set up each one as a separate job. I think this would really speed things up for your industrial users. I'm working on 20 structures of the same protein with different ligands, and expect to spend maybe 8 hours generating TLS groups and editing the 240 parameter files. A GUI interface would make it 10 or 20 minutes! I don't see a way to select different TLS groups. I really prefer to test different ones myself for comparison, at least to convince myself that the auto selection is superior. We see big differences from optimizing TLS group number. Right now I am asking TLSMD to generate all these tls files, copying them to my desktop, copying to parameter files. Help! All the best, Kendall

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isomorphous difference map
by Jason 19 Feb '11

19 Feb '11

Hello everyone, I have two data sets, one for apo form and the other is co-crystalized with ligandl. Both data sets has P1211 space group; resolution is about ~3.5Angstrom. Unit cell: Apo: 105.22, 266.26, 110.63 90.00, 108.12, 90.00 Ligand: 104.60, 264.74, 109.98, 90.00, 106.33, 90.00 When I try to create an isomorphous difference map using phenix GUI, an error message pops up: crystal symmetry mismatch between different files. Anyone could tell me what's the problem and how to solve it? ====================== Jason Structural Biology Department University of Pittsburgh ======================

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ReadySet
by riya doreen 18 Feb '11

18 Feb '11

Hi Everyone, I am having trouble refining a structure that has 2*-deoxy-thymidine-5*-triphosphate (three letter id is TTP). My PDB file has exactly the same number and names for the atoms as described in the cif file (TTP.cif). ReadySet recognizes TTP but crashes with a warning that it could match only 21 out of a total of 29 atoms. What am I missing here ? I can overcome the problem by renaming TTP to some random name and generating a new cif file with phenix.elbow but why can't I use the standard TTP.cif file ? Thanks

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X-ray facility Scientist at MRC LMB, Cambridge, UK
by A Leslie 18 Feb '11

18 Feb '11

X-Ray Facility Scientist MRC Laboratory of Molecular Biology Cambridge £26,022 – £31,758 We wish to recruit an Investigator Scientist to join the MRC Laboratory of Molecular Biology X-ray facility in Cambridge, UK. You will provide support for a range of projects involving X-ray crystallographic data collection both in-house and at synchrotrons. You would also be responsible for optimising the performance of the in- house X-ray facilities, liaising with maintenance engineers and helping to train new users. The position requires extensive travel to synchrotrons both in UK and abroad. You should have a PhD in a relevant subject and experience in X-ray crystallographic data collection. Your salary will be supported by a flexible pay and reward policy, 30 days annual leave entitlement, an optional MRC final salary pension scheme and excellent on-site sports and social facilities. Applications are handled by the RCUK Shared Services Centre; to apply please visit our job board at https://ext.ssc.rcuk.ac.uk and complete an online application form. Applicants who would like to receive this advert in an alternative format (e.g. large print, Braille, audio or hard copy), or who are unable to apply online should contact us by telephone on 01793 867003, Please quote reference number IRC14067. Closing date: 16th March 2011 For informal enquiries please email: andrew(a)mrc-lmb.cam.ac.uk

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AutoMR error
by Erik R. Kish-Trier 18 Feb '11

18 Feb '11

Hi, I am getting the following error from AutoMR, which I am fairly certain is due to the deficiencies of my machine: Python(2624) malloc: *** mmap(size=1665024000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug While using the prior release of phenix, I was able to get a similar job to complete, which makes me curious. I am running phenix 1.7-650 (GUI) on an Intel Mac with 4GB of RAM and OS 10.6.6. Any suggestions? Thanks! Erik On Feb 17, 2011, at 11:29 AM, <phenixbb-request(a)phenix-online.org<mailto:[email protected]>> <phenixbb-request(a)phenix-online.org<mailto:[email protected]>> wrote: Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org<mailto:[email protected]> To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org<mailto:[email protected]> You can reach the person managing the list at phenixbb-owner(a)phenix-online.org<mailto:[email protected]> When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Re: At what percentage of saturated peaks is acceptable? (Mischa Machius) 2. Re: At what percentage of saturated peaks is acceptable? (Ed Pozharski) 3. Unrealistic number of waters found by phenix? (Ina Lindemann) 4. Re: Unrealistic number of waters found by phenix? (Folmer Fredslund) 5. Re: Unrealistic number of waters found by phenix? (Felix Frolow) 6. EMBO 2011 Practical Course - Exploiting Anomalous Scattering - ESRF - 6 - 10 June 2011 (Daniele de Sanctis) 7. IUCr Travel Fellowships Available (Gloria Borgstahl) ---------------------------------------------------------------------- Message: 1 Date: Wed, 16 Feb 2011 20:42:55 -0500 From: "Mischa Machius" <machius(a)med.unc.edu<mailto:[email protected]>> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org<mailto:[email protected]>> Subject: Re: [phenixbb] At what percentage of saturated peaks is acceptable? Message-ID: <91F63968-BF15-47B4-A15E-FB73279AD18C(a)med.unc.edu<mailto:[email protected]>> Content-Type: text/plain; charset=us-ascii I would recommend taking two passes; a low-resolution pass with short exposures and a high-resolution pass with longer exposures. Then merge the two, and you've got a complete dataset. If applicable, take three or more passes. MM On Feb 16, 2011, at 8:39 PM, Jason wrote: Hi, I have a technical question that is not related to phenix, but I hope some expertise around may help me out. I am intending to increase the exposure time to gain some resolution. At the same time I do not want too many over exposed peak. The question comes to at what percentage of the saturated peaks is acceptable? Many thanks. ====================== Jason Structural Biology Department University of Pittsburgh ====================== _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb ------------------------------ Message: 2 Date: Wed, 16 Feb 2011 20:45:47 -0500 From: Ed Pozharski <epozh001(a)umaryland.edu<mailto:[email protected]>> To: PHENIX user mailing list <phenixbb(a)phenix-online.org<mailto:[email protected]>> Subject: Re: [phenixbb] At what percentage of saturated peaks is acceptable? Message-ID: <1297907147.30587.17.camel@thunderclap> Content-Type: text/plain; charset="UTF-8" If you start losing completeness at low resolution, just collect a low resolution pass (i.e. exactly the same frames but with short exposures). Be mindful of radiation damage though. On Wed, 2011-02-16 at 20:39 -0500, Jason wrote: Hi, I have a technical question that is not related to phenix, but I hope some expertise around may help me out. I am intending to increase the exposure time to gain some resolution. At the same time I do not want too many over exposed peak. The question comes to at what percentage of the saturated peaks is acceptable? Many thanks. ====================== Jason Structural Biology Department University of Pittsburgh ====================== _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb ------------------------------ Message: 3 Date: Thu, 17 Feb 2011 08:52:26 +0100 From: Ina Lindemann <lindema2(a)staff.uni-marburg.de<mailto:[email protected]>> To: phenixbb(a)phenix-online.org<mailto:[email protected]> Cc: heinea(a)mailer.uni-marburg.de<mailto:[email protected]> Subject: [phenixbb] Unrealistic number of waters found by phenix? Message-ID: <20110217085226.106944rzydtyujeo(a)home.staff.uni-marburg.de<mailto:[email protected]>> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Hi, I am refining a crystal structure of a protein with 198 amino acids at 1.59 A resolution. I have used the function Update waters in phenix. After visual inspection of the found water molecules I deleted some of them, but there are still 334 water molecules left which show reasonable electron density. Many of them interacts just with other water molecules and not with the protein. I calculated the average B of water molecules = 26.3 and protein = 12.6. Now I am wondering if the number of water molecules and their average B value is to high with respect to the protein and would be very pleased about your answers. With best regards, Ina Ina Lindemann Philipps-Universit?t Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908 ------------------------------ Message: 4 Date: Thu, 17 Feb 2011 09:14:41 +0100 From: Folmer Fredslund <folmerf(a)gmail.com<mailto:[email protected]>> To: PHENIX user mailing list <phenixbb(a)phenix-online.org<mailto:[email protected]>> Subject: Re: [phenixbb] Unrealistic number of waters found by phenix? Message-ID: <AANLkTimXZUDZQMxf70jRSMPxi+=9dFKHB6OAoVV6wGuw(a)mail.gmail.com<mailto:[email protected]>> Content-Type: text/plain; charset=ISO-8859-1 Dear Ina Have a look here (from the CCP4BB) http://www.mail-archive.com/[email protected]/msg19631.html Best regards, Folmer Fredslund 2011/2/17 Ina Lindemann <lindema2(a)staff.uni-marburg.de>: Hi, I am refining a crystal structure of a protein with 198 amino acids at 1.59 A resolution. I have used the function Update waters in phenix. After visual inspection of the found water molecules I deleted some of them, but there are still 334 water molecules left which show reasonable electron density. Many of them interacts just with other water molecules and not with the protein. I calculated the average B of water molecules = 26.3 and protein = 12.6. Now I am wondering if the number of water molecules and their average B value is to high with respect to the protein and would be very pleased about your answers. With best regards, Ina Ina Lindemann Philipps-Universit?t Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb ------------------------------ Message: 5 Date: Thu, 17 Feb 2011 10:23:58 +0200 From: Felix Frolow <mbfrolow(a)post.tau.ac.il> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Cc: heinea(a)mailer.uni-marburg.de Subject: Re: [phenixbb] Unrealistic number of waters found by phenix? Message-ID: <D3ACED80-CB0C-4043-BB4A-CF8E8A936195(a)post.tau.ac.il> Content-Type: text/plain; charset=iso-8859-1 Dear Ina Lindemann These are problems of the rich people... Be happy and why not, after all your resolution is ~1.6 A I would say that you have not enough water molecules. In such resolution and such molecular size I would expect about 2 or even 3 water molecules per residue. So you are missing 198*2-334=62 water molecules. As a frequent reviewer I would not let a paper describing such structure to pass! ;-) ;-) Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfrolow(a)post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Feb 17, 2011, at 09:52 , Ina Lindemann wrote: Hi, I am refining a crystal structure of a protein with 198 amino acids at 1.59 A resolution. I have used the function Update waters in phenix. After visual inspection of the found water molecules I deleted some of them, but there are still 334 water molecules left which show reasonable electron density. Many of them interacts just with other water molecules and not with the protein. I calculated the average B of water molecules = 26.3 and protein = 12.6. Now I am wondering if the number of water molecules and their average B value is to high with respect to the protein and would be very pleased about your answers. With best regards, Ina Ina Lindemann Philipps-Universit?t Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb ------------------------------ Message: 6 Date: Thu, 17 Feb 2011 16:23:16 +0100 From: Daniele de Sanctis <de.sanctisd(a)gmail.com> To: phenixbb(a)phenix-online.org Subject: [phenixbb] EMBO 2011 Practical Course - Exploiting Anomalous Scattering - ESRF - 6 - 10 June 2011 Message-ID: <AANLkTikigUeBYgzF9wuJg7z5jTkZcKO0sh8j+AGUWDf6(a)mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Deadline in 10 days!! DEADLINE TO APPLY FEBRUARY 28th COURSE ANNOUCEMENT EMBO 2011 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 6 - 10 June 2011 The EMBO 2011 Practical Course on Exploiting Anomalous Scattering in Macromolecular Structure Determination will be hosted by the ESRF in Grenoble, France from 6 to 10, June 2011. The course aims to impart the theoretical and practical basis for the 3-dimensional structure determination of bio-macromolecules using Anomalous Dispersion techniques (SAD & MAD) to young scientists who intend to apply these methods in macromolecular crystallography. Through a series of lectures, software demonstrations, practicals on the ESRF beamlines and tutorials, participants will get insights into all aspects of the structure determination process including beamline instrumentation, data collection and processing, heavy atom substructure determination, phasing and model building. There will also be sessions focusing on automated structure solution procedures and newer methods. Additional sessions will include presentations of distinguished structures solved with these techniques. Confirmed invited speakers include: G. Bunkoczi, A. Cameron, D. Chirgadze, Z. Dauter, P. Evans, M. Grininger, T. Gruene, W. Kabsch, S. Panjikar, N. Pannu, A. Popov, H. Powell, L. Sazanov, G. Sheldrick, T. Terwilliger, C. Vonrhein The number of participants is limited to 20 and the deadline for application is February 28th, 2011. Additional information, course programme and instructions to apply to the course can be found in the course webpages: http://cwp.embo.org/pc11-03/ -- ????? --------------------------------------- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869 ------------------------------ Message: 7 Date: Thu, 17 Feb 2011 10:42:00 -0600 From: Gloria Borgstahl <gborgstahl(a)gmail.com> To: phenixbb(a)phenix-online.org Subject: [phenixbb] IUCr Travel Fellowships Available Message-ID: <AANLkTik3EecaF_MB8avPPs5jZbVWjoA+s__6k067mDAD(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Please see the attachment The deadline is 15 days away. ************************************************************************ Gloria Borgstahl Eppley Institute for Cancer Research and Allied Diseases 987696 Nebraska Medical Center 10732A Lied Transplant Center Omaha, NE 68198-7696 http://sbl.unmc.edu Office (402) 559-8578 FAX (402) 559-3739 Professor Hobbies: ?Protein Crystallography, Cancer, Biochemistry, DNA Metabolism, Modulated Crystals, ?Crystal Perfection Interests: ?Manga, Led Zeppelin, Cold Play, piano, BRAN, RAGBRAI, golf and lately superspace groups ************************************************************************

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