- phenixbb - phenix-online.org

Re: [phenixbb] number of cycles
by Maia Cherney 02 Mar '11

02 Mar '11

Hi, I am using now the latest phenix version and I am curious how to understand these lines: Flipped N/Q/H residues before refinement: A 28 HIS A 72 HIS A 141 GLN A 202 GLN A 296 ASN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 388 HIS Maia

4 4

[Fwd: Re: number of cycles]
by Maia Cherney 02 Mar '11

02 Mar '11

-------- Original Message -------- Subject: Re: [phenixbb] number of cycles Date: Tue, 01 Mar 2011 19:50:57 -0700 From: Maia Cherney <chern(a)ualberta.ca> To: Jeff Headd <jjheadd(a)lbl.gov> References: <40FBFA09-3C52-460A-A6A1-7D08F6496AD2(a)umich.edu> <AANLkTin=8_ddvihNSDyLp9k1iSpV9fVj6A2ndvoUTJ6O(a)mail.gmail.com> <0171D39299ABC14AAAA75ABABDD0BBB63868BF23AA(a)NIHMLBX12.nih.gov> <A8FA87FE-7DF1-48BE-AA44-E19BB7D0E6E0(a)crystal.harvard.edu> <4CAC89B8.9090909(a)lbl.gov> <4D12B58C.1030604(a)ualberta.ca> <4D12E866.9070602(a)lbl.gov> <4D138B20.5050001(a)ualberta.ca> <4D14E51F.2040305(a)lbl.gov> <4D164065.3050709(a)ualberta.ca> <4D165AE5.8090905(a)lbl.gov> <4D6C0DB1.5040003(a)ualberta.ca> <4D6C9271.6000301(a)lbl.gov> <4D6DA14C.6060806(a)ualberta.ca> <AANLkTi=GXvoGWsB+3+NNBNFvVtzc0Q0ag1Ln_U6FqHqO(a)mail.gmail.com> Thanks, Jeff. Though I don't see any clashes for any orientations. But this feature is really great. Jeff Headd wrote: > Hi Maia, > > Phenix.refine analyzes Asn, Gln, and His residues at each macrocycle > and determines which orientation is likely correct given the local > environment of the sidechain. The best orientation will have no steric > clashes and satisfy local H-bond donors/acceptors. In cases where > there are other model errors in the region of the sidechain and both > orientations clash significantly, you'll see the **PLEASE CHECK > MANUALLY** warning which indicates that there are likely multiple > misfit sidechains that need to be corrected, and refinement alone is > not powerful enough to escape the false minimum. > > If you want to turn this feature off, you can add main.nqh_flips=False > to your refinement call or > > main { > nqh_flips=False > } > > to your param file. However, we highly recommend leaving this option > on as it is an excellent diagnostic of model errors. > > If you have any further questions please let me know. > > Thanks, > Jeff > > On Tue, Mar 1, 2011 at 5:45 PM, Maia Cherney <chern(a)ualberta.ca> wrote: > >> Hi, >> >> I am using now the latest phenix version and I am curious how to understand >> these lines: >> >> >> Flipped N/Q/H residues before refinement: >> A 28 HIS >> A 72 HIS >> A 141 GLN >> A 202 GLN >> A 296 ASN >> ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** >> ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** >> A 353 ASN >> A 388 HIS >> >> Maia >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> > > >

1 0

Glycan Links/Restraints
by Damian Ekiert 02 Mar '11

02 Mar '11

Sorry to bring up an old topic again but I can't find any documentation of glycan refinement on the Phenix website and previous threads don't seem to answer my question. I am refining a structure with N-linked glycans. I have inserted several "apply_cif_link" records to my .eff file to define the glycan topologies (see below) and fed in a cif file for BMA. After fiddling for quite some time now, I have managed to get around all the error messages people have described previously to disappear. Yet, 1) none of my linkages appear to be enforced and 2) even the restraints on the individual sugars appear to be unenforced (or at least, insufficiently so). For example, some rings are rendered almost flat, or flipped into boat or otherwise distorted conformations, and glycosidic bonds stretch to >2 A. No obvious signs of trouble in the log file, running the latest version (1.7, also tried 1.6.4), but my glycans look terrible (despite some of the best density I have ever seen! :-) ) Any suggestions would be appreciated! Thanks, Damian Ekiert >From my .eff file: apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain X and resname NAG and resid 401 residue_selection_2 = chain A and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Y and resname NAG and resid 401 residue_selection_2 = chain C and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Z and resname NAG and resid 401 residue_selection_2 = chain E and resname ASN and resid 91 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain X and resname NAG and resid 402 residue_selection_2 = chain X and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname NAG and resid 402 residue_selection_2 = chain Y and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Z and resname NAG and resid 402 residue_selection_2 = chain Z and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname BMA and resid 403 residue_selection_2 = chain Y and resname NAG and resid 402 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain Y and resname MAN and resid 404 residue_selection_2 = chain Y and resname BMA and resid 403 }

3 6

Implementation of French & Wilson data correction?
by Joseph Noel 02 Mar '11

02 Mar '11

Hi All, Any pointers on implementing the new option in the latest build for French & Wilson correction? Does scala output negative intensities so that a proper scaling with this new option can be used? Also, what column labels should be used particularly for proper treatment of anomalous data? Can one use the labels output by scala? Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

9 13

Bay Area and Beyond Phenix User Meeting
by Paul Adams 02 Mar '11

02 Mar '11

Dear Colleagues, On Thursday March 17th, a Bay Area and Beyond Phenix User Meeting will be held at Lawrence Berkeley Lab. During the workshop, the Phenix developers will give lectures on the latest developments and Phenix usage. Half of the user meeting will be in the form of informal hands on sessions, allowing participants to work with the developers. Participants are encouraged to bring their own (reduced) data to be used during hands on sessions, but tutorial data will also be available. Due to the highly interactive format of the meeting there will be space for approximately 20 participants. If I have missed any of your colleagues on this invitation please feel free to pass on the message. To apply, researchers should send a email to NEchols(a)lbl.gov and PDAdams(a)lbl.gov by Monday March 7th. Unfortunately we are unable to provide any funds to support student travel to the meeting. Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology 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: Kathleen Moody [ KLMoody(a)lbl.gov ][ 1-510-495-2506 ] --

1 0

how to cut off side chain from a model
by crystallogrphy 02 Mar '11

02 Mar '11

Hi, I am refining a low resolution data (4.7A). I want to cut off all side chains from my model because they cannot be seen from the density. Phenix pdbtools can only keep the backbone, but cannot keep the Cbeta atom. What program I can use to cut off all the side chain, but keep the Cbeta atoms? Thanks!

9 13

ICSG 2011 early registration and abstracts submission open until March 4
by Tom Terwilliger 02 Mar '11

02 Mar '11

Dear Colleagues, We hope that you are planning to attend the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. Due to technical difficulties with the registration page, we have extended both the early registration and abstract submission deadlines. Abstract submission and early bird registration will now end Friday March 4th at 11:59pm EST. Please visit http://www.icsg2011.org for ICSG 2011 meeting and workshop registration details and to submit your abstract. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

1 0

Question about Adding Hydrogens
by Louis Lazar 02 Mar '11

02 Mar '11

All, I was curious if there is a way to add hydrogens to an individual residue. For example, rather than running the command: phenix.ready_set model.pdb, run something like: phenix.ready_set model.pdb resid=X or phenix.ready_set=resid 10 model.pdb Any thoughts/recommendations on the subject are greatly appreciated. Thanks in advance. Louis

6 9

ICSG 2011 Early Registration Deadline Feb 28, 2011
by Thomas C. Terwilliger 26 Feb '11

26 Feb '11

ICSG 2011 Abstract and Early Registration Deadline Feb 28, 2011 Dear Colleagues, We hope that you are planning to attend the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics, structural/chemical biology, and their impact on research in biology, medicine and disease. There are many speaking slots still open that will be chosen from submitted poster abstracts. We invite you to submit your abstract by February 28, 2011. Please also note that early registration will end on February 28, 2011, so we invite you to register now in order to take advantage of the reduced registration fee. In addition to the main ICSG meeting, there will be a whole day of free concurrent satellite workshops (May 10, 2011), including: Small Molecule Screening Workshop- This hands-on workshop will allow participants to screen a protein of their choice for binding of selected compounds, using thermal shift assays. Eukaryotic Gene Expression Systems Workshop - This workshop will provide participants with a detailed understanding of the state-of-the-art for production of eukaryotic proteins destined for biochemical, biophysical, and structural analyses. iSee: Interactive 3D Documents for the Dissemination of Structural Biology - This hands-on workshop will familiarize participants with the iSEE 3D graphical software which allows interactive viewing of 3 dimensional molecular structures and is currently used by journals such as Nature Structural & Molecular Biology and PLoS Biology and PLoS ONE. Workshop on NMR Methods for Structural Biology- This workshop will survey technologies for structure/function investigations of proteins, developed in (or in collaboration with) structural genomics projects, that are ready for widespread use by the wider biological community. Phenix Crystallography Software Workshop - This workshop will introduce the PHENIX software for macromolecular structure determination and the core algorithms that it uses. It will provide hands-on tutorials for crystallographers of all levels. Please visit http://www.icsg2011.org for ICSG 2011 meeting and workshop registration details and to submit your abstract. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

1 0

composite omit map problem
by Morgan Thompson 24 Feb '11

24 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

1 0

questions on refinement
by Hena Dutta 24 Feb '11

24 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

3 3

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

2 1

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

22 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/>

1 0

adding ligands to model
by Geoffrey Feld 22 Feb '11

22 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"

2 1

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

5 11

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 ======================

3 2

ReadySet
by riya doreen 19 Feb '11

19 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

2 1

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

1 0

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 ************************************************************************

2 1

Autosol question
by Laurie Betts 18 Feb '11

18 Feb '11

Dear Phenix developers, I am SO impressed with what AutoSol (thank you TT) did with some old heavy atom data sets I collected on tetragonal lysozyme some years ago; one was a single-site uranium derivative and the other a pretty dodgy mercury derivative and just the sequence. Neither had any separation of anomalous pairs, so it was totally MIR. In an hour and a half, there was a gorgeous map (not perfect mind you, CC = 0.85, but our students will not realize how much more work this would have been 20 years ago or even 10). I was just curious which statistic in the log file could be compared with the old fashioned "phasing power"? THanks Laurie Betts UNC Chapel Hill

2 2

Unrealistic number of waters found by phenix?
by Ina Lindemann 18 Feb '11

18 Feb '11

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-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

4 3

IUCr Travel Fellowships Available
by Gloria Borgstahl 18 Feb '11

18 Feb '11

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 ************************************************************************

1 0

EMBO 2011 Practical Course - Exploiting Anomalous Scattering - ESRF - 6 - 10 June 2011
by Daniele de Sanctis 17 Feb '11

17 Feb '11

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/ -- ἀρετή --------------------------------------- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

1 0

At what percentage of saturated peaks is acceptable?
by Jason 17 Feb '11

17 Feb '11

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 ======================

3 2

Fwd: Your message to phenixbb awaits moderator approval
by Francis E Reyes 17 Feb '11

17 Feb '11

I love how this bb denies large attachments.. I almost sent some sensitive data to the list! F Begin forwarded message: > From: phenixbb-bounces(a)phenix-online.org > Date: February 16, 2011 2:44:47 PM MST > To: francis.reyes(a)colorado.edu > Subject: Your message to phenixbb awaits moderator approval > > Your mail to 'phenixbb' with the subject > > Re: [phenixbb] phenix.refine: Sorry: Inappropriate value for > grid_step_factor: must be positive and non-zero. > > Is being held until the list moderator can review it for approval. > > The reason it is being held: > > Message body is too big: 932289 bytes with a limit of 40 KB > > Either the message will get posted to the list, or you will receive > notification of the moderator's decision. If you would like to cancel > this posting, please visit the following URL: > > http://phenix-online.org/mailman/confirm/phenixbb/83115d392956ed11e4b78631f… > --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

1 0

refinement with twinning
by alexander.singer＠utoronto.ca 17 Feb '11

17 Feb '11

Hi -- I have a twinned data set -- approximate twinning fraction of 0.4. I decided to try to try twinned refinement using phenix.refine in what would seem to be the appropriate manner -- from the "All Parameters" menu, I select twinning, hit "Run Xtriage now" on my mtz file, it gives me the input to the "Twin Law", I keep the rest of the values the same (gave no Anisotropy correction), hit OK, then run 3 cycles of refinement. The only thing is that the Rwork/Rfree values are really very good, almost too good to be true -- for my 1.7 A refinement, I have values of 12.4 and 14.8%, respectively for Rwork and Rfree. Is there anything that I may be doing wrong yielding R values which are artifically too low? Thanks for your help Alex -- Dr. Alex Singer C.H. Best Institute 112 College St. Room 70 University of Toronto Toronto, Canada, M5G 1L6 416-978-4033

2 1

how to move one domain of a protein in respect to another?
by Tatyana Sysoeva 16 Feb '11

16 Feb '11

Dear all, I am working with a protein which form homooligomeric assembly. Each subunit of the assembly consists of 2 subdomains. I would like to create chimeras with the subdomains moved with respect to each other, keeping the linkers. I am wondering what would be the easiest way to do this? Any suggestions are welcome! Sincerely, Tanya

3 3

phenix.refine: Sorry: Inappropriate value for grid_step_factor: must be positive and non-zero.
by Francis E Reyes 16 Feb '11

16 Feb '11

Hi all Refining a low res (~ 3.5A) structure using a reference structure that was solved to 3.0A. I get the following error right when the refinement starts =============================== refinement start ============================== Sorry: Inappropriate value for grid_step_factor: must be positive and non-zero. All instances of grid_step_factor in my .def are positive and non-zero (they should be defaults b/c I never changed them). Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 1

phenix.model_vs_data feature request
by Stephen Graham 16 Feb '11

16 Feb '11

Hi there, A simple feature request: Like most phenix programs, when run from the command line phenix.model_vs_data fails when it is passed an mtz file with multiple 'data' columns (i.e. Fs, F(+/-)s, Is). However, unlike say phenix.xtriage it doesn't tell you the list of possible column combinations and the correct keyword. Would it be possible to add this in? Thanks, Stephen -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

2 1

phenix.maps
by Jason 15 Feb '11

15 Feb '11

Hi everyone, I have noticed that the coefficient mtz file generated by phenix.maps can't not be loaded to coot (it can be read through the link in the GUI version once after process). I am using 1.7 version. Any suggestions? -- ====================== Jason Structural Biology Department University of Pittsburgh ======================

3 5

Help for pdb deposition
by qiang liu 14 Feb '11

14 Feb '11

Hi,Dear all, Maybe it's a simple question for you,because I am a beginner in crystallography. Recently I deposited a structure in the pdb and got a reply bellow. "The deposited structure factor file is incomplete. We failed convert the deposited mtz file to cif format. Please send me the correct SF file including h, k, l, F, SigmaF (and/or I and SigmaI)and test flags as an attachment." The mtz file I uploaded is map_coeffs.mtz after refinement.The column lables are listed. type column lable H H H K H L F 2FOFCWT P PH2FOFCWT F 2FOFCWT_no_fill P PH2FOFCWT_no_fill F FOFCWT P PHFOFCWT So how can I get the parameters for deposition in PHENIX? Any suggestions will be appreciated! Thank you very much. Qiang Liu

2 2

difference map
by intekhab alam 12 Feb '11

12 Feb '11

Hi i am trying to calculate a difference map ( ligand-native ) using isomorphous difference map program in phenix. I used the reflection files of ligand and native and phase information of ligand derived data. But the difference map donot fits the ligand, and appears as a circular chunk of density at sigma level 5. I calculated an omit map that clearly showed the presence of my ligand at the specific position. Is there anything wrong in my calculation. What alternate ways are there to improve my difference map. -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

4 7

'python' received an X Window System error.
by Rongjin 11 Feb '11

11 Feb '11

Hello, when I was running Phenix for model building, I encountered some error. Is this a bug? Thanks Rongjin Guan close failed in file object destructor: The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadIDChoice (invalid resource ID chosen for this connection)'. (Details: serial 1812949 error_code 14 request_code 53 minor_code 0) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadIDChoice (invalid resource ID chosen for this connection)'. (Details: serial 41593302 error_code 14 request_code 55 minor_code 0) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.)

3 3

Graduate Student Summer Internship
by Soisson, Stephen M 10 Feb '11

10 Feb '11

Hi Everyone, Merck Research Laboratories has an opening for a summer intern in the Structural Chemistry (X-ray crystallography) groups located in either Kenilworth, NJ or West Point, PA. The idea is to have someone comfortable with programming and mathematics to explore some computational ideas that can take advantage of the large parallel computing cluster at Merck (> 3000 cores). I am pasting the advertisement below - please note that the deadline is rapidly approaching. Interested applicants must apply through the link provided below. Please note that an advanced undergraduate with the appropriate cross-disciplinary skill set would also be considered for this position. Thanks- Steve Stephen M. Soisson, Ph.D. Structural Chemistry Site Lead, WP Merck Research Laboratories 770 Sumneytown Pike, WP14-1101 West Point, PA 19486 Phone: (215) 652-6185 Fax: (215) 652-9051 stephen_soisson(a)merck.com Job Description Graduate Structural Chemistry Internship 2011:CHE002969 Description Merck is a global health care leader with a diversified portfolio of prescription medicines, vaccines and consumer health products, as well as animal health products. Today, we are building a new kind of healthcare company - one that is ready to help create a healthier future for all of us. Our ability to excel depends on the integrity, knowledge, imagination, skill, diversity and teamwork of people like you. To this end, we strive to create an environment of mutual respect, encouragement and teamwork. As part of our global team, you'll have the opportunity to collaborate with talented and dedicated colleagues while developing and expanding your career. The X-ray Crystallography group of the Global Structural Chemistry Department within Merck Research Laboratories is seeking graduate interns for their summer internship program. The intern will be embedded in the Structural Chemistry/X-ray Crystallography group and will conduct research on a project relevant to drug discovery. The intern will also attend group meetings to gain a wider perspective of the role of structural chemistry within the discovery process in the pharmaceutical industry. The Global Structural Chemistry Department is an industry-leading research group with world class laboratory, synchrotron, and computational facilities. A suitable candidate has a science background with interest in x-ray crystallography and drug discovery. Not required, but a plus, would be experience in one or more of the areas of protein crystallization, X-ray diffraction theory and x-ray crystallography. Preference will be given to candidates having a strong math and/or physical science background with expertise in computers and computer programming. We are seeking graduate student with strong academic performance, communication skills, teamwork, and the ability to work in a multi-functional environment. This internship is offered at either of our research facilities in Kenilworth, NJ or West Point, PA. It is a paid 10-12 week internship targeted to start in June 2011. A weekly stipend will be provided. Housing and transportation to and from work are available for those interns meeting the housing distance guideline. **Please note when applying for this position, the candidate MUST upload a cover letter or a personal statement letter and a copy of your unofficial transcript along with your resume. Qualifications * Candidate is currently pursuing a graduate degree in a relevant field (biochemistry, biophysics, applied math, computer science, etc.). * Science background with an interest in drug discovery * Must have experience in x-ray crystallography and knowledge of programming tools such as Python, Perl or C. * Applicants must be currently enrolled in an academic program. * Applicants must be available for full-time employment for 10 - 12 weeks during the months of June - August 2011. To be considered for this position, please visit our career site at www.merck.com/careers to create a profile and submit your resume for requisition #CHE002969. Merck is an equal opportunity employer, M/F/D/V - proudly embracing diversity in all of its manifestations. Primary Location:US-NJ-Kenilworth Job Type:Intern Employee Status:Regular Number of Openings:1 Stephen M. Soisson, Ph.D. Structural Chemistry Site Lead, WP Merck Research Laboratories 770 Sumneytown Pike, WP14-1101 West Point, PA 19486 Phone: (215) 652-6185 Fax: (215) 652-9051 stephen_soisson(a)merck.com Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

1 0

How to locate and refine a ligand using anomalous scattering
by Jason 09 Feb '11

09 Feb '11

Hello everyone, I have a few crystals to be x-rayed next week. Before that I hope to get a clear idea about what I am doing (I am new to anomalous scattering). Facts: 1. The crystal is a protein co-crystallized with a ligand 2. The protein structure is known. 3. The ligand has a heavy atom bromide (absorption K-egde=13.47Kev) 4. Data resolution is ~3 angstrom Goals: 1. Locate the bromide position 2. Locate and refine the ligand Questions: 1. Do I need to carry out MAD experiment at 3 wavelengths or there is some other easier way since the protein structure is known (I am not expecting big change of the protein structure itself)? 2. Assuming I have the MAD data, what should I do next using phenix to achieve the two goals listed above? Here are some thoughts: - Using phenix.hyss to locate the anomalous scatterers - Using phenix.autobuild to build the protein model (which data set to use?) - Using coot to add ligands to the protein structure (Is the relative position between the protein and the ligand known based on phenix.hyss and phenix.autobuild?) - Using phenix.refine to refine the ligand+protein complex Thank you all for reading this. ====================== Jason Structural Biology Department University of Pittsburgh ======================

2 1

How to locate and refine a ligand using anomalous scattering
by Jason 09 Feb '11

09 Feb '11

Hello everyone, I have a few crystals to be x-rayed next week. Before that I hope to get a clear idea about what I am doing (I am new to anomalous scattering). Facts: 1. The crystal is a protein co-crystallized with a ligand 2. The protein structure is known. 3. The ligand has a heavy atom bromide (absorption K-egde=13.47Kev) 4. Data resolution is ~3 angstrom Goals: 1. Locate the bromide position 2. Locate and refine the ligand Questions: 1. Do I need to carry out MAD experiment at 3 wavelengths or there is some other easier way since the protein structure is known (I am not expecting big change of the protein structure itself)? 2. Assuming I have the MAD data, what should I do next using phenix to achieve the two goals listed above? Here are some thoughts: - Using phenix.hyss to locate the anomalous scatterers - Using phenix.autobuild to build the protein model (which data set to use?) - Using coot to add ligands to the protein structure (Is the relative position between the protein and the ligand known based on phenix.hyss and phenix.autobuild?) - Using phenix.refine to refine the ligand+protein complex Thank you all for reading this. ====================== Jason Structural Biology Department University of Pittsburgh ======================

3 2

using reference model for low resolution refinement
by crystallogrphy 07 Feb '11

07 Feb '11

Hi, I am refining a hexamer model using low resolution data (4.7A). I want to use a high resolution model (2.4A) which is a dimer as the reference model. The sequence identity is 100%. Does anyone know how to select the residue range from the reference model for my refinement? Thanks!

3 2

is new phenix.refine (1.7-650) comaptible with twinning refinement?
by fulvio saccoccia 05 Feb '11

05 Feb '11

Dear all, I have installed the new phenix version 1.7-650, but I have a doubt: is the real-space refinement within phenix.refine now compatible with twinning refinement?

2 1

ICSG 2011 Abstract Deadline Feb 28, 2011: International Conference on Structural Genomics
by Thomas C. Terwilliger 05 Feb '11

05 Feb '11

Dear Colleagues, We hope that you are planning to attend the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics, structural/chemical biology, and their impact on research in biology, medicine and disease. There are many speaking slots still open that will be chosen from submitted poster abstracts. We invite you to submit your abstract by February 28, 2011. Please visit http://www.icsg2011.org for ICSG 2011 meeting and workshop registration details and to submit your abstract. In addition to the main ICSG meeting, there will be a whole day of free concurrent satellite workshops (May 10, 2011), including: Small Molecule Screening Workshop- This hands-on workshop will allow participants to screen a protein of their choice for binding of selected compounds, using thermal shift assays. Eukaryotic Gene Expression Systems Workshop - This workshop will provide participants with a detailed understanding of the state-of-the-art for production of eukaryotic proteins destined for biochemical, biophysical, and structural analyses. iSee: Interactive 3D Documents for the Dissemination of Structural Biology This hands-on workshop will familiarize participants with the iSEE 3D graphical software which allows interactive viewing of 3 dimensional molecular structures and is currently used by journals such as Nature Structural & Molecular Biology and PLoS Biology and PLoS ONE. Workshop on NMR Methods for Structural Biology- This workshop will survey technologies for structure/function investigations of proteins, developed in (or in collaboration with) structural genomics projects, that are ready for widespread use by the wider biological community. Phenix Crystallography Software Workshop This workshop will introduce the PHENIX software for macromolecular structure determination and the core algorithms that it uses. It will provide hands-on tutorials for crystallographers of all levels. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

1 0

Phenix version 1.7-650 and Pymol
by Leonid Flaks 04 Feb '11

04 Feb '11

>On Tue, Feb 1, 2011 at 5:49 AM, Leonid Flaks<flaks at bnl.gov <http://phenix-online.org/mailman/listinfo/phenixbb>> wrote: >>/ Nat, As I reported minutes ago coot issue is solved. Now I clicked on pymol />>/ button - got an error: />>/ />/> /usr/local/crys/64/phenix-1.7-650/pymol/pymol.exe: error while loading />/> shared libraries: libXmu.so.6: cannot open shared object file: No such file />>/ or directory /> >That's a system library, and not something we distribute or otherwise >interfere with. Does PyMOL even work on the command line? > >thanks, >Nat Nat, pymol is installed as rpm binary and works fine from command line. The library in question is also installed from rpm: dunkin:/home/pxuser 104: rpm -qf /usr/lib64/libXmu.so.6 libXmu-1.0.5-2.fc13.x86_64 dunkin:/home/pxuser 105: rpm -q pymol pymol-1.3-3.20100705svn3911.fc14.x86_64 Could it be something like LD_LIBRARY_PATH or similar? To tell the truth my users are happy to have coot working but don't care too much about the pymol at the moment, so I would not put very high priority on this problem. By the way, I never received you reply - had to cut-and-paste from the web interface. I am subscribed to digest, which has not showed up yet. Thanks, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

5 8

Phenix version 1.7-650 and Pymol
by Leonid Flaks 02 Feb '11

02 Feb '11

On 02/01/2011 04:20 AM, phenixbb-request(a)phenix-online.org wrote: > Message: 11 > Date: Mon, 31 Jan 2011 16:37:14 -0800 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix version 1.7-650 and coot > Message-ID: > <AANLkTim6ux3V6FcfhXr_0vhNf2P9GWXfBh3aexbZcZ41(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: >> > Hi! >> > I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that >> > if I start coot from within phenix interface, most of the icons on the right >> > hand side of the coot window are not displayed. >> > There is a lot of messages like this: >> > >> > Error loading icon: Couldn't recognize the image file format for file >> > '/usr/share/coot/pixmaps/residue-info.png' > Okay, apparently we missed an important environment variable in the > script that launches Coot from Phenix - several library paths need to > be cleansed to prevent conflicting with the libraries we distribute. > The one we didn't know about (because it never caused problems before) > appears to be XDG_DATA_DIRS. The crude fix for this is to edit > $PHENIX/phenix/phenix/command_line/start_coot.sh and add this line at > the end of a list of "unset" commands: > > unset XDG_DATA_DIRS > > It'll be fixed in the next build too. If this doesn't totally solve > the problem, let me know - I'm going to unset several other paths too, > but those didn't appear to have any effect on our Fedora 14 machine. > > -Nat Nat, As I reported minutes ago coot issue is solved. Now I clicked on pymol button - got an error: /usr/local/crys/64/phenix-1.7-650/pymol/pymol.exe: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory So, looks like we need to unset more variables indeed ;-) Meanwhile I'll just keep clicking on buttons... All the best, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

2 1

AutoBuild fails using NFS on Snow Leopard
by Chris Richardson 02 Feb '11

02 Feb '11

I've been having a problem running AutoBuild jobs in NFS-mounted project directories on Snow Leopard. The jobs start ok, but typically fail in a build cycle with the error "File exists". The problem is reproducible, but the exact details of the failure are not - the point at which the error occurs changes from run to run. Identical jobs run to completion if the project directory is on a local disk or an AFP-mounted volume. My guess is that it's a file locking issue, or maybe some sort of race condition in file creation. Has anybody else experienced this and if so, is there a solution? The details are: OS X 10.6.6, mounting volumes by NFS from a variety of machines (Ubuntu 10.0.4, OS X 10.6.6 & 10.4), Phenix 1.7-650. Regards, Chris -----%<----{ Log Extract }----- Sorry, a subprocess has failed... END OF LOG FILE /work/nedu/foop/phenix_nedu_nfs/AutoBuild_run_3_/TEMP0/RUN_FILE_3.log : rd desired_run_number=self.desired_run_number) File "/common/app/phenix-1.7-650/phenix/phenix/autosol/wizard_command_line.py", line 132, in __init__ overwrite_defaults=False,desired_run_number=desired_run_number) File "/common/app/phenix-1.7-650/phenix/phenix/wizards/AutoBuild.py", line 83, in __init__ init_OutputDir=init_OutputDir,init_RunInstance=init_RunInstance) File "/common/app/phenix-1.7-650/phenix/phenix/autosol/AutoBaseExtend.py", line 613, in local_init quiet=self.quiet,OutputDir=self.OutputDir) #032107 OutputDir File "/common/app/phenix-1.7-650/phenix/phenix/autosol/RunWizardPDS.py", line 65, in __init__ self.ScriptPDS=ScriptPDS(workspace=workspace) File "/common/app/phenix-1.7-650/phenix/phenix/pds/ScriptPDS.py", line 29, in __init__ PhenixDataStorage.__init__(self, dirname) File "/common/app/phenix-1.7-650/phenix/phenix/pds/PDS.py", line 233, in __init__ os.mkdir(self.dirname) OSError: [Errno 17] File exists: 'PDS/AutoBuild_run_1_' Possibly this subprocess is run on a machine with different architecture than the main process? -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk 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.

3 4

Re: [phenixbb] Phenix version 1.7-650 and coot - SOLVED!
by Leonid Flaks 01 Feb '11

01 Feb '11

On 02/01/2011 04:20 AM, phenixbb-request(a)phenix-online.org wrote: > Message: 11 > Date: Mon, 31 Jan 2011 16:37:14 -0800 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix version 1.7-650 and coot > Message-ID: > <AANLkTim6ux3V6FcfhXr_0vhNf2P9GWXfBh3aexbZcZ41(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: >> > Hi! >> > I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that >> > if I start coot from within phenix interface, most of the icons on the right >> > hand side of the coot window are not displayed. >> > There is a lot of messages like this: >> > >> > Error loading icon: Couldn't recognize the image file format for file >> > '/usr/share/coot/pixmaps/residue-info.png' > Okay, apparently we missed an important environment variable in the > script that launches Coot from Phenix - several library paths need to > be cleansed to prevent conflicting with the libraries we distribute. > The one we didn't know about (because it never caused problems before) > appears to be XDG_DATA_DIRS. The crude fix for this is to edit > $PHENIX/phenix/phenix/command_line/start_coot.sh and add this line at > the end of a list of "unset" commands: > > unset XDG_DATA_DIRS > > It'll be fixed in the next build too. If this doesn't totally solve > the problem, let me know - I'm going to unset several other paths too, > but those didn't appear to have any effect on our Fedora 14 machine. > > -Nat Nat, Just to confirm - your fix worked! Thank you very much, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

1 0

(no subject)
by Shuchi 01 Feb '11

01 Feb '11

hello, i have solved one structure and after solving the average B factor of the model is 107 and average B factor from wilson plot of DATA is 85.5 . is this fine or i did some wrong while fitting and refinement. resolution is 3.0 Angstroms . -- vandana kukshal CSIR-senior research fellow X ray lab ,MSB division central drug research institute lucknow

2 1

Phenix version 1.7-650 and coot
by Leonid Flaks 01 Feb '11

01 Feb '11

Hi! I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that if I start coot from within phenix interface, most of the icons on the right hand side of the coot window are not displayed. There is a lot of messages like this: Error loading icon: Couldn't recognize the image file format for file '/usr/share/coot/pixmaps/residue-info.png' for png and svg files in the console window. I can see all of the icons if I start coot directly. I am using coot version 1.6.2-pre1 rev 3213 which is installed on 64-bit fedora 14 as a rpm file. I did not see this issue on a phenix version 1.6.4-476 with the same version of coot. Thanks, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

2 2

phenix.mr_rosetta paths
by Ben Eisenbraun 01 Feb '11

01 Feb '11

Hi, I'm testing Rosetta 3.2+PHENIX 1.7-650, and in the phenix.mr_rosetta output, I see: Checking rosetta paths: rosetta binary: /programs/l/rosetta/3.2/rosetta_source/bin/mr_protocols.default database_dir: /programs/l/rosetta/3.2/rosetta_database script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/public/electron_density pilot_script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/pilot/frank/ In the script directory, the C++ files were not built along with the regular Rosetta build. Do those need to be compiled for the target platform? Also, the pilot_script_dir is empty. Is there supposed to be something in there? Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

3 4

translation/rotation matrix
by Yogesh Gupta 01 Feb '11

01 Feb '11

Dear PhenixBB members, I calculated two maps one using 3 wavelengths Se to 4.2A, and 3 wavelength Ta to ~3.9A for ~100kDa protein in space group P62 with 1 molecule in A.U. These crystals are non-isomorphous. Ta MAD map is better than Se MAD map. There is no model available at this point. Is there a way to transform Se sites accurately to the Ta map? Thanks for your help. Yogesh -- -------------------------------------------------- Yogesh K. Gupta, Ph.D. Dept of Structural & Chemical Biology Mount Sinai School of Medicine Icahn Medical Institute 1 Gustave L. Levy Place, Box 1677 New York, NY, USA 10029 Tel:+1 212-659-8639 --------------------------------------------------

2 1

Re: [phenixbb] Phenix version 1.7-650 and coot
by Leonid Flaks 31 Jan '11

31 Jan '11

On 01/29/2011 03:00 PM, phenixbb-request(a)phenix-online.org wrote: > Message: 1 > Date: Fri, 28 Jan 2011 12:09:01 -0800 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix version 1.7-650 and coot > Message-ID: > <AANLkTini0jaSAh9KKv1xZGbtE4ABtdU2_G5KMxWP0c4p(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: >> I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that >> if I start coot from within phenix interface, most of the icons on the right >> hand side of the coot window are not displayed. >> There is a lot of messages like this: >> >> Error loading icon: Couldn't recognize the image file format for file >> '/usr/share/coot/pixmaps/residue-info.png' >> >> for png and svg files in the console window. I can see all of the icons if I >> start coot directly. I am using coot version 1.6.2-pre1 rev 3213 which is >> installed on 64-bit fedora 14 as a rpm file. I did not see this issue on a >> phenix version 1.6.4-476 with the same version of coot. > Could you please send me the complete console output from Coot under > these conditions: > > a) when launching from Phenix 1.7 > b) when launching from Phenix 1.6.4 > c)when launching from the command line? > > Very little has changed in the Coot-related parts of Phenix since > 1.6.4, so I'm not sure how it's possible for one to work but not the > other. In the past, errors like this were due to conflicts with the > shared libraries distributed with Phenix, but we largely reset the > environment when starting Coot to avoid the problem, and I'm pretty > sure we started that a year and a half ago. > > thanks, > Nat > Nat, first of all - my apologies for the incorrect report. It turned out this problem exists in phenix 1.6.4 under fedora 14 also - just nobody noticed it on the current setup! Fedora 14 is about 2 month old and we are coming out of the winter shutdown. We had a mixture of fedora 12 and 13 before and did not see that problem. Of course, python version has been changed to python-2.7 for Fedora 14. Console output for all 3 conditions are saved. I'll mail them to you directly - I don't want to flood the list. Thanks, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

1 0

cis peptides
by Timothy Springer 31 Jan '11

31 Jan '11

Is there an easy way to specify unwanted cis-peptides and remove them in refinement or with torsion dynamics or SA? Tim

3 3

Re: [phenixbb] Global refinement parameters - use statistical model for missing atoms
by Joseph Noel 31 Jan '11

31 Jan '11

Hi Pavel! Thanks for the reply. It does seem to be working though in the current version as long as I choose advanced level in the gui. Does it make sense though that it is lowering my Free-R? Also, the upshot is that the Fo-Fc maps are much flatter. I can see waters to build but only in the 2Fo-Fc sigmaa weighted maps so it does certainly seem to be doing something. Anyway, I look forward to the docs on it when you officially release it. Seems useful! Best- Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

1 0