- phenixbb - phenix-online.org

Mar 15, 2011 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 Mar '11

14 Mar '11

Dear Users, The deadline for May/June 2011 Collaborative Crystallography proposals will be *Mar 15, 2011.* ---------------------------------------------------------------------------------------- Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for May/June 2011 allocation period, proposals must be submitted by *Mar 15, 2011.* The deadline for CC proposals for the time period July/Aug 2011 will be May 15, 2011. Regards, Banumathi Sankaran

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Jan 15, 2011 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 Mar '11

14 Mar '11

Dear Users, The deadline for March/April 2011 Collaborative Crystallography proposals will be *Jan 15, 2011.* ---------------------------------------------------------------------------------------- Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for March/April 2011 allocation period, proposals must be submitted by *Jan 15, 2011.* The deadline for CC proposals for the time period May/June 2011 will be March 15, 2011. Regards, Banumathi Sankaran

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B-factor discrepancy
by Yuri 14 Mar '11

14 Mar '11

I am refining a single-mutant structure at 2.1 A. The native was solved years ago by heavy atom phasing. The reported average B-factors for alpha carbons especially of the original structure were significantly lower than the ones I am seeing. around 15 vs. around 25. Has anyone any idea if this is perfectly fine and its simply something intrinsic to my crystals? Also at this resolution, should I try to refine any residues at all anisotropically? Thanks for the guidance

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XYZ refinement vs individual sites refinement
by Yuri 13 Mar '11

13 Mar '11

I am new to phenix and I am trying to probe two residues that are putative H-bond partners, after refinement they seem to be put in orientations that would make it impossible for them to be interacting with a ligand. My SA composite omit map may suggest that one of the Asn could be in a different position. My question: If I manually change its conformation is it wise to keep its position fixed during refinement to see what the new maps would look like? If so where would I do that under the real space or individual sites tab on GUI phenix? I am not sure what these 2 tasks accomplish exactly. Any guidance would be appreciated. Thanks Yuri Pompeu

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Fwd: XYZ refinement vs individual sites refinement
by Yuri 13 Mar '11

13 Mar '11

Thats better! thank you

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most appropriate map for ligand fitting/interaction with FMN
by Yuri 13 Mar '11

13 Mar '11

I am refinig a structure at 2.1 A. I have 2 questions: a) Is the best way to identify a ligand refining the protein and water molecules and at the end looking at the 2mfo-dfc and mfo-dfc maps? Or looking at a SA composit omit map? b) In almost every map i look at during refinement I see density that smears/joins my ligand (cyclopentenone type molecule) and flavin's isoalloxazine ring. Has anyone ever seen that? they seem to be 3.1 A apart? Thanks -- Yuri Pompeu

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Elbow problem
by Jerome Nwachukwu 11 Mar '11

11 Mar '11

Hi all: For some reason, phenix.elbow converts a specific double-bond (C=C) in my ligand to a single bond (C-C) and therefore generates a wrong .cif file. Is there away to avoid or correct this problem? Thank you, -Jerome Jerome C. Nwachukwu, PhD Kendall Nettles' Lab Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

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Binary Installation failure on Ubuntu
by Katherine Sippel 11 Mar '11

11 Mar '11

Hi all, I am trying to install the latest nightly build (dev-694) using the Kernel 2.6 (64-bit; Fedora Core 3) binary. The OS is Ubuntu 10.10 installed as a dual boot through Wubi. I get as far as configuring PHENIX components at which point it heaves out a binary.log file. I can send the whole file to anyone whose interested but it's a bit too large for the bb. The juicy bit is as follows... Could not find platform independent libraries <prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site How can I determine which libraries are missing? Thanks for any help you can provide, Katherine

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Average maps (*not* NCS averaging)
by Stephen Graham 11 Mar '11

11 Mar '11

Hi there, I'd like to average 2Fo-Fc maps from 2 (approximately) isomorphous data sets (one with ligand, one without) to see whether I get better density for some of the noisier bits of the structure. I don't want to do any kind of solvent flattening, histogram matching, cyclical averaging, etc; I just want to sum the equivalent pixels and divide by 2. Is it possible to do this easily using any of the phenix tools? It seems like all the required plumbing is there with get_cc_mtz_mtz or superpose_maps, but I can't find a phenix utility for averaging two superposed maps. 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

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Re: [phenixbb] [ccp4bb] Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
by Francois Berenger 11 Mar '11

11 Mar '11

Sorry, I forgot to mention about what is the .obj file I need. It is a pure ASCII geometric description of a polyhedra. Cf. http://en.wikipedia.org/wiki/Wavefront_.obj_file It looks rather easy to parse compared to some VRML file, for example. Thanks, F. Francois Berenger wrote: > Hello, > > What are the good software to do this? > > I already know of Pymol and Jmol. > > Both can export the result to a .obj file, which is interesting for > later processing. > > However, Pymol's algorithm is not exactly what Connolly described, > cf. > http://www.mail-archive.com/[email protected]/msg00179.html > > Also, Pymol will save the surface with some translation and rotation > which are not present in the PDB read in, which is a real pain. > > For Jmol, sometimes the surface is not a closed polyhedra, so > it is kind of useless for my purpose. > > I know of MSMS, but I don't think it is that robust (I read some source > code where someone was using MSMS, the source code had many dirty things > in order to try handling the apparently many cases where MSMS was > crashing). > > Is there something freely usable for research, using beta shapes > internally, for example? That should be a robust approach. > > A robust software would be much appreciated (not crashing, whatever > the PDB we give it as input). > Open source and not in Fortran would be heaven. ;) > > Thanks a lot for suggestions, > F.

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Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
by Francois Berenger 11 Mar '11

11 Mar '11

(was posted on CCP4 bb also) Hello, What are the good software to do this? I already know of Pymol and Jmol. Both can export the result to a .obj file, which is interesting for later processing. However, Pymol's algorithm is not exactly what Connolly described, cf. http://www.mail-archive.com/[email protected]/msg00179.html Also, Pymol will save the surface with some translation and rotation which are not present in the PDB read in, which is a real pain. For Jmol, sometimes the surface is not a closed polyhedra, so it is kind of useless for my purpose. I know of MSMS, but I don't think it is that robust (I read some source code where someone was using MSMS, the source code had many dirty things in order to try handling the apparently many cases where MSMS was crashing). Is there something freely usable for research, using beta shapes internally, for example? That should be a robust approach. A robust software would be much appreciated (not crashing, whatever the PDB we give it as input). Open source and not in Fortran would be heaven. ;) Thanks a lot for suggestions, F.

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automr renumbered all residues to 0 for final solution in dev-674
by Francis E Reyes 10 Mar '11

10 Mar '11

Is this fixed in a later version? 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

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Sorry, I meant judging by distances it is not experiencing interaction in the form of H-bonds. Which I think is concerning.

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Hi Pavel, What I meant it was just that the 2mFo-2DFc map looks really great and corroborates experimental data as far as the stereochemistry. But I dont understand ehy the carbonyl moiety of the ligand would be where it is now, no "driving force to be here". And when I look at my averaged kick and SA omit map it looks ambiguous. Any help?

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Hello everyone, I have this strucuture I solved by Molecular replacement. It is a single mutant of previously solved enzyme. I started refining it and fit the ligand in a way that gives me the experimental stereochemistry. The final map 2mFo-2DFc looks great. After further examination I noticed, I have a carbonyl that does not seem to be bound to anything !!! I started looking at my average kick and SA composit omit-map prior to modeling in the ligand and now I am really lost. Could anyone help? Thank you

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Important change in phenix.refine output: MTZ file with data and map coefficients
by Pavel Afonine 04 Mar '11

04 Mar '11

Hi Everyone, starting development version dev-686: http://www.phenix-online.org/download/nightly_builds.cgi phenix.refine does not output *map_coeffs.mtz file. Instead, it creates prefix_serial.mtz file (example: lysozime_001.mtz) containing four sections: - section 1: Original input data (Iobs or Fobs, and HL coefficients if provided) and flags (as supplied in input); - section 2: Experimental data used in refinement (labels: F-obs-filtered, SIGF-obs-filtered). This can be different from "Original data" due to Iobs->Fobs conversion (if input data are intensities) and outliers filtering; - section 3: Contains total model structure factors (labels: F-model, PHIF-model) used everywhere in refinement (for the formula, see: http://www.phenix-online.org/documentation/fmodel.htm). In the future, this section might be extended to explicitly list all contributions to Fmodel, such as Fcalc (corresponding to atomic model), Fbulk (bulk solvent contribution), and so on. - section 4: Fourier map coefficients (exactly the same as used to be in *map_coeffs.mtz file). This change is meant to reduce the confusion when people tended to use *map_coeffs.mtz file for refinement and PDB deposition, and facilitates the reproduction of refinement statistics (R-factors, for example). Also, thanks to Jeff Headd, by default phenix.refine now converts input intensities (Iobs) to amplitudes (Fobs) using French & Wilson method (Acta Cryst A34, 517, 1978), so no need to run a specific program (Truncate, for example) to do this. To see the content of a MTZ file use phenix.mtz.dump command: phenix.mtz.dump data.mtz Pavel.

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Geometry problem with sugars refined in phenix
by Tirumala Kumar Chowdary 03 Mar '11

03 Mar '11

Hi, I have refined a structure with NAGs linked to ASNs at 3 places in my structure. I used the right link definitions and the NAG definitions are from Phenix library. Phenix refined all the sugars right and made the right links between the NAGs. However, while submitting, PDB found problem with the geometry of NAGs linked to the ASN at two places. This is the issue -the atoms around C1 atom of the sugar molecule NAG A #810 and NAG A #1670 are on a plane and the C1 atom center is far off to be tetrahedral. Please, verify the chirality of C1 and provide the correct coordinates if necessary.- Any ideas on how to fix the geometry of these sugars will be of great help. Regularization and real space refine in Coot is not working or I don't know how to do it. I am looking for alternative ways to fix this problem. Thank You Tirumal

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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

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[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 >> >> > > >

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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 }

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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 ___________________________________________________________

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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 ] --

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how to cut off side chain from a model
by crystallogrphy 01 Mar '11

01 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!

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ICSG 2011 early registration and abstracts submission open until March 4
by Tom Terwilliger 01 Mar '11

01 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

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Question about Adding Hydrogens
by Louis Lazar 01 Mar '11

01 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

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ICSG 2011 Early Registration Deadline Feb 28, 2011
by Thomas C. Terwilliger 25 Feb '11

25 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

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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"

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 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

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 17 Feb '11

17 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 17 Feb '11

17 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 17 Feb '11

17 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 16 Feb '11

16 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 16 Feb '11

16 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 15 Feb '11

15 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 15 Feb '11

15 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 10 Feb '11

10 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.)

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