- phenixbb - phenix-online.org

refinement for ligands with alternative conformation
by zhengyi＠msu.edu 22 Mar '11

22 Mar '11

Hello, I am working on the refinement of a structure about 2.8A, which the substrate ligand has an odd conformation. A blob of negative difference density about 4.8 sigma between the one portion of the ligand and the other. If I break down the ligand into two parts, the negative density disappears, however, one part of the ligands does not fit well. We suspect a mixture of conformations. Any suggestions would be appreciated on how to setup refinement for ligands with alternative conformation. Many thanks, Yi Zheng Department of Biochemistry Michigan State University

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Re: [phenixbb] "FOM" or HL coeffs from model?
by Dyda 21 Mar '11

21 Mar '11

Phoebe, >How can I get phenix to spit out not just PhiModel but an estimated FOM or fake HL coefficients (without experimental phases - just based on how badly my model agrees with FOBS)? And I'd like the weights in their own personal mtz column(s), not just precombined in a "weighte d phi" column.< can sigmaa do that for you from Fcalc (vector) and Fo (magnitude)? Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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B factor sharpening in twinned maps
by Mary Ho 21 Mar '11

21 Mar '11

I'm using phenix-1.7-650. When phenix.refine generates the detwinned maps with apply B-factor sharpening on and no value inputed, is the value the program uses for sharpening output anywhere? Thanks, Mary X. Ho Postdoctoral Associate Arnold Lab Rutgers

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changing the project directory
by Charisse Crenshaw 19 Mar '11

19 Mar '11

Hello, I have recently started a project whose folder was located on my desktop. I would like to move that folder off of my desktop as I've heard that having a messy desktop slows down one's computer. I moved the project directory somewhere else, and this resulted in Phenix not being able to find the project (understandably). So I moved it back to its original location and Phenix could then open the project. So, in an X11 shell, I copied the project folder to the new desired location, then changed the output directory in the Phenix main window to that new path. But when I clicked on the project again, the output directory that is indicated changes back to the original path. Now I am looking through the preferences etc for a way to change the path of the project directory within Phenix and I cannot. Can anyone tell me if this is possible and if so, how do I do it? Thanks, Charisse The Salk Institute for Biological Studies

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Refinement Strategy vs. R gap
by Yuri 17 Mar '11

17 Mar '11

Pavel, It seemed like I had to close the GUI window and reopen it for the default (automatic aniso/iso) to take effect. I ran a TLS with 5 groups and ended up with better statistics. Rwork 0.18 Rfree 0.239 -- Yuri Pompeu

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Refinement Strategy vs. R gap
by Yuri 17 Mar '11

17 Mar '11

Hello phenixers, I am refining a liganded structure at 2.1 and I am pretty far into my modeling. Rfree = .265 rwork= .20 My asu has 399 residues one prosthetic group (3178 atoms) and 236 HOH. I just want to do one last refinement round before submission and I am not sure about the strategy I should select as I am running into the following: I- If I refine individuals sites and real space (XYZ) and individual ADP with aniso/iso selection automatic my Rfree goes up slightly and Rwork drops to about .196. I also select optimize x-ray/ADp weight I should say. II- When I choose no XYZ refinement with anisotropic ADP for protein chain only with weight optimization Rwork plummets to 0.15 and Rfree also drops to 0.25. But my gap is now .10 !! I checked my log file and it looks like in default automatic individual ADP phenix.refine is picking all the residues to be anisotropic even though I would not try that at 2.1 A. Could someone point me in the right direction, there is probably something I am overlooking. Thank you -- Yuri Pompeu

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Peptides bonds in cyclic peptides
by Krzysztof Bzymek 16 Mar '11

16 Mar '11

Hi, I've been trying to refine a structure of a protein with a cyclic peptide bound to it. Adding LINK/CONECT to the pdb file works in coot but the bonds are not present after refinement in phenix. I tried creating a param file (I followed recommendations for making ASN/NAG bonds posted here a while ago, but changed the names of connected residues) and included it in refinement, but the bond was not formed and the amino and carboxy groups of respective amino acids were far apart. I also got a message after refinement that a cif file was not specified. What's the solution? Thanks, Chris

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Only one solution in AutoMR with very negative LLG
by Zhang yu 16 Mar '11

16 Mar '11

Hi, I am working on a DNA-protein complex, the protein apo structure is already known. Recently I got a dataset of the DNA-protein complex, I tried to find a solution by autoMR in Phenix with the known protein coordinate as template. I got only one solution with very negative LLG (around -4000), and after rigid body refinement, the both Rwork and Rfree is around 0.55. Was there anyone in the same situation as me? What does that mean if there is just one solution while with very high negative LLG? Thanks

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Need help in refining my twinned P6322(apparent) dataset
by John Pak 15 Mar '11

15 Mar '11

Hey Phenix community, Here are the details of my current situation - any assistance in the matter would be greatly appreciated as I've been struggling mightily for the past month trying to get this structure refined (to no avail). Details: -3.0 angstrom dataset from a membrane protein crystal -reduced in a P3 Bravis lattice using HKL2000 -Pointless and Xtriage suggest P622 symmetry -Solved structure via MR - ran Phaser in all P622 based space groups, found 1 convincing solution in P6322 (LLG ~110) which makes biological sense (1 monomer in ASU that lies on the screw axis to recapitulate the biological trimer) -31% sequence identical search molecule -no pseudotranslation (via Xtriage) Xtriage suggests that the P6322 dataset is nearly perfectly twinned (twin fraction = 0.49). Mindful of the fact that there are no twin operators for P6322, I'm thinking that the true space group is P321, P312 or P63 and I've tried a number of things listed below: 1. Refined in P6322 (simulated annealing+individual B). Missing side chains and incorrectly modelled loops apparent in maps. Start R=0.49, Rfree=0.5. Refinement stalls at R=0.41, Rfree=0.45 after building. 2. Ran Phaser in P312 (using unrefined model) - no solution. 3. Ran Phaser in P321 (using unrefined model). One nice solution (LLG ~220) - lattice looks very similar to P6322 crystal packing. Twin refinement in phenix using operator suggested by Xtriage (simulated annealing + individual B) results in R=0.38, Rfree=0.41 (no rebuilding performed). 4. Ran Phaser in P63 (using unrefined model). Three solutions (LLGs all ~210) - solution #3 looks very similar to P6322 crystal packing. Twin refinement in phenix using operator suggested by Xtriage of solution #3 gives R=0.37, Rfree=0.40 (no rebuilding performed). Solutions #1 and #2 do not give packing arrangements that look like the P6322 solution. Twin refinement of Sol 1 and 2 give higher R factors. So I'm at a loss as to which space group my crystal truly belongs to, and where I should be focusing my refinement. The maps all look similar before and after DM. Thanks for any assistance or recommendations that you might have! -- John E. Pak, Ph.D. Postdoctoral Associate, Stroud Lab Department of Biochemistry& Biophysics UCSF MC2240 Genentech Hall Room S414 600-16th St. San Francisco, CA 94158-2517 Lab #: 415-476-3937 Fax #: 415-476-1902 Cell #: 415-215-0048

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fwd: Re: Need help in refining my twinned P6322(apparent) dataset
by Nathaniel Echols 15 Mar '11

15 Mar '11

---------- Forwarded message ---------- From: "Van Den Berg, Bert" <Lambertus.VandenBerg(a)umassmed.edu> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Tue, 15 Mar 2011 08:01:42 -0400 Subject: Hi John, How do the maps look for cases 3 and 4? Are they great or are there obvious things to correct? Does your model have the correct sequence or is it that of the search model? I’m asking because your R’s seem reasonable to me after a first round of refinement and using a 30% identical search model for MR. So maybe there is no problem? Bert On 3/15/11 2:55 AM, "John Pak" <john.pak(a)msg.ucsf.edu> wrote: Hey Phenix community, Here are the details of my current situation - any assistance in the matter would be greatly appreciated as I've been struggling mightily for the past month trying to get this structure refined (to no avail). Details: -3.0 angstrom dataset from a membrane protein crystal -reduced in a P3 Bravis lattice using HKL2000 -Pointless and Xtriage suggest P622 symmetry -Solved structure via MR - ran Phaser in all P622 based space groups, found 1 convincing solution in P6322 (LLG ~110) which makes biological sense (1 monomer in ASU that lies on the screw axis to recapitulate the biological trimer) -31% sequence identical search molecule -no pseudotranslation (via Xtriage) Xtriage suggests that the P6322 dataset is nearly perfectly twinned (twin fraction = 0.49). Mindful of the fact that there are no twin operators for P6322, I'm thinking that the true space group is P321, P312 or P63 and I've tried a number of things listed below: 1. Refined in P6322 (simulated annealing+individual B). Missing side chains and incorrectly modelled loops apparent in maps. Start R=0.49, Rfree=0.5. Refinement stalls at R=0.41, Rfree=0.45 after building. 2. Ran Phaser in P312 (using unrefined model) - no solution. 3. Ran Phaser in P321 (using unrefined model). One nice solution (LLG ~220) - lattice looks very similar to P6322 crystal packing. Twin refinement in phenix using operator suggested by Xtriage (simulated annealing + individual B) results in R=0.38, Rfree=0.41 (no rebuilding performed). 4. Ran Phaser in P63 (using unrefined model). Three solutions (LLGs all ~210) - solution #3 looks very similar to P6322 crystal packing. Twin refinement in phenix using operator suggested by Xtriage of solution #3 gives R=0.37, Rfree=0.40 (no rebuilding performed). Solutions #1 and #2 do not give packing arrangements that look like the P6322 solution. Twin refinement of Sol 1 and 2 give higher R factors. So I'm at a loss as to which space group my crystal truly belongs to, and where I should be focusing my refinement. The maps all look similar before and after DM. Thanks for any assistance or recommendations that you might have! -- John E. Pak, Ph.D. Postdoctoral Associate, Stroud Lab Department of Biochemistry& Biophysics UCSF MC2240 Genentech Hall Room S414 600-16th St. San Francisco, CA 94158-2517 Lab #: 415-476-3937 Fax #: 415-476-1902 Cell #: 415-215-0048

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

15 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 15 Mar '11

15 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 11 Mar '11

11 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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