- phenixbb - phenix-online.org

Alternate conformation occupancies sum more than 1
by Mikalai Lapkouski 15 Nov '12

15 Nov '12

Hello, I was refining the 1.2 A structure. After refining occupancies there are several residues with alternate conformers for which the sum of the occupancies is greater than one. For example: GLY A 197 O Occupancy sums to 1.14 MET B 17 CB Occupancy sums to 1.03 TYR B 142 CD1 Occupancy sums to 1.04 TYR B 142 CZ Occupancy sums to 1.01 GLY B 197 O Occupancy sums to 1.23 The density is defined nicely for them, do you know what can be the problem of why the sum could be more than 1? Thank you Mikalai

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Restraints file for a new amino acid residue
by Agnes Thiane Pereira Machado 14 Nov '12

14 Nov '12

Hi We are trying to refine a protein structure with a (covalently) modified residue. The colosest discussion to our problem is: http://www.phenix-online.org/pipermail/phenixbb/2010-August/015629.html We ran: phenix.elbow --residue SSC ourmodel.pdb And read the due cif file at phenix refinement. The residue by itself is OK, but we were not able to perform the peptide bond between C and N. How to complete the .cif file such that it has due restraints for the peptide bond with this modified residue? Agnes

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Off topic: Anomalous signal
by ash.k＠aol.com 14 Nov '12

14 Nov '12

Dear all, I am sorry for this off topic question in the bb. I have good looking but poorly diffracting (3.8-4 A) crystals of SeMet derivative. Mass spec confirmed that Se incorporation is 100% and I got a very good energy scan for Se too. I properly selected the peak, inflection and remote wavelengths for the data collection. But, I do not see anomalous signal in the data collected. Processing in HKL2000 does not show any resolution dependance of Chi square and also xtriage says that the anomalous resolution limit is only up to 8-9A. Is it something usual for the kind of diffraction I am getting or something else is going on? I have 5/200 methionine residues in the sequence. Worst case I can think of is that all the Met side chains are disordered ! Any help would be highly appreciated.. AK

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den_refine on cluster
by Michael Thompson 13 Nov '12

13 Nov '12

Hi All, Apologies if this is a naive question, but I would like to run DEN refinement and I notice the documentation says that it runs optimally on a machine with at least 30 processor cores. Is there any way to run DEN refinement on a SGE cluster as a batch job using something like run_command="qsub" as can be done with autobuild, etc.? Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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Simulated anneal
by Qiang Chen 13 Nov '12

13 Nov '12

Hi all, I have a 3.05Å structure. I refine it to Rwork=25.2 Rfree=28.81. I use Molprobity to check the structure. The clash score is 100th and Molprobity score is 99th. I was suggested to run simulated anneal to help reduce Rwork and Rfree. I tried Cartesian and Torsion and different seed. The best result I got is: torsion anneal, start_temp=2500,final_temp=300, random_seed=4250146. The Rwork:25.8, Rfree=31.2. I checked the new model and found that some places in a domain were not correctly traced. The density for that domain is not good and have several flexible loops. My question is: does simulated anneal always work and reduce Rwork/Rfree? At the final stage of refinement, does it necessary to use simulated anneal again? Thanks! yamei The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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phenix.pdbtools - renumber specific chains
by Antony Oliver 12 Nov '12

12 Nov '12

Apologies if this has been covered before - but can someone point me to a way of renumbering only specific chains (i.e. F, G, H etc). I have tried using phenix.pdbtools with either selection = "chain F or chain G or chain H" or keep "chain A or chain B or chain C or chain D" - but in both cases phenix renumbers every single residue! With thanks, Antony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

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Setting up MR_Rosetta
by Julio Lenin 08 Nov '12

08 Nov '12

Hello guys, I am currently trying to setup MR_Rosetta but I am running into some trouble. When I run the tutorial for Defensin HNP-3 from the GUI I always get an error during the ... process (see image at this dropbox link). I know that my path for phenix and rosetta are correct since I can run the phenix_regression.wizards.test_command_line_rosetta_quick and phenix_regression.wizards.test_command_line_rosetta_quick test_rosetta_rebuild. If I try to trace down the error, I can only get the same info that I got from the GUI error message (vide supra). As additional info, here are somme details of my setup: MacBookPro 4,1 running OS 10.6.8 Core2Duo 2.5 Ghz 6 Gb RAM Rosetta 3.2 compiled with flags bin mode=release Phenix 1.8.1-1168 And my input settings for the GUI run (dropbox) Now, this might just be confusing but there was one command line test that my setup failed: phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta The error is kinda cryptic (see dropbox copy of the error) but it seem to be a discrepancy in the scoring results not a missing program or any other kind of misconfiguration. Of course, I might be wrong. Any advice? Best regards. -- Lenin Domínguez-Ramírez "And for all the current and rather silly emphasis on structural biology,understanding enzymes means understanding catalysis and catalysis is concerned with kinetics, not structure: as Jeremy Knowles aptly remarked, studying the photograph of a racehorse cannot tell you how fast it can run." Cornish-Bowden, 1995 Lenin Domínguez-Ramírez, PhD "What are we to think of an organism that loses practically all of its cellular water at ordinary temperatures and pressures and ceases to metabolize, but upon being rehydrated resumes all of the characteristics it previously exhibited?...we should be reluctant to call such an organism dead (unless we are willing to entertain the possibility of its resurrection) because it resumes an active life upon simple restoration of water."

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Sugar refine in phenix
by Jan van Agthoven 05 Nov '12

05 Nov '12

Hi everyone, This is a basic question. I would like to refine the sugar ends of my protein. The sugar polymers are made of NAG and BMA and whenever I use phenix.ready_set and subsequently phenix.refine it results in a structure of disconnnected sugar monomers. Indeed the cif file generated by phenix.ready_set does'nt give any geometry constraints for connecting the monomers. How do create a cif file that tells phenix.refine how to refine the sugars? Thanks, Jan

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ligand fitting, density and refinement
by Terwilliger, Thomas C 02 Nov '12

02 Nov '12

Hi Huaidong, I'm not quite sure exactly what you did...could you possibly elaborate a little? My confusion comes from two things. First, this phrase: "did the refinement with the output files from ligandfit", is confusing to me because I would not think that you would want to use any output files from ligandfit except for the ligand PDB file. Second, I agree, I can't see why ligandfit would find good density for your ligand if it is not present in a difference map calculated from the original data. All the best, Tom T ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of 张怀东 [zhanghuaidong(a)hust.edu.cn] Sent: Thursday, November 01, 2012 8:11 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Ligandfit_SigmaF_obs Hi,Tom T We followed the instruction after the ligandfit, and did the refinement with the output files from ligandfit. The electron density for the ligand is clear, but in the refinement with the original mtz file, the density is not there. So how to explain the difference? Is this a bug? Thanks! Huaidong > -----原始邮件----- > 发件人: "Terwilliger, Thomas C" <terwilliger(a)lanl.gov> > 发送时间: 2012年11月1日星期四 > 收件人: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> > 抄送: > 主题: Re: [phenixbb] Ligandfit_SigmaF_obs > > Hi Ed, > > Yes, good point. I will be changing the way the wizards read in and store reflection data (sometime soon I hope!) and at that point this should be moot because the wizards won't write out dummy intermediate files. > > All the best, > Tom T > > ________________________________________ > From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Ed Pozharski [epozh001(a)umaryland.edu] > Sent: Thursday, November 01, 2012 9:44 AM > To: PHENIX user mailing list > Subject: Re: [phenixbb] Ligandfit_SigmaF_obs > > On Thu, 2012-11-01 at 14:23 +0000, Terwilliger, Thomas C wrote: > > The sigma values are not useful, and are just set to 1.0 in that file. > > Tom, > > I've seen this issue before, and I am just wondering what could be the > rationale to reset sigmas to 1.0? Seems like one would have to code for > this to happen, and even if the sigma values are not used for map > generation, why isn't the column simply omitted but instead replaced > with obviously incorrect values? > > Ed. > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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Ligandfit_SigmaF_obs
by 张怀东 01 Nov '12

01 Nov '12

Hello, I am a newcomer. I need help. I have done phenix.ligandfit, and the result contained a mtz file named resolve.mtz. While sigma_F_obs in the file are all 1.0. Is there something wrong with the file? Is this a bug? Could I do phenix.refine with the resolve.mtz added R_flag, next? sincerely, Huaidong Zhang

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refining with f' and f" values
by Subhani Bandara 01 Nov '12

01 Nov '12

Hi Everyone, I have a structure with heavy metals which I would like to refine anomalous scattering factors. I could get the f' and f" values from Autosol, when I gave the atom name and wavelength. But when I ran refinement with anomalous scattering giving .mtz file and pdb file from pHENIX refinement I got the error "Invalid combination-F-obs not anomalous, provide anomalous reflections or fix all f" values. Then I used reflection file editor of GUI to create a mtz file that has anomalous data using the original reflection file and the mtz file of refinement. But still it gives an error. I must be doing something wrong, but cannot figure out what that is. Thanks in advance for any help. Subhani

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Rwork Rfree Bonds Angles
by Hexi Zhang 01 Nov '12

01 Nov '12

Dear All, During Phenix refinement, it request the Rwork and Rfree graduately decrease (at least no increase). But there is no request that the Bonds (should be RMS?) and the Angles (should also be RMS?) should graduately decrease. Am I right? I am looking forward to getting your reply. Hexi

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"H" atom refining occupancy with previous altconf residue in sequence
by Alexander Scouras 31 Oct '12

31 Oct '12

After a series of residues (1+) with alternate conformations, the H atom of the next residue seems to lock its occupancy to that of the final conformation of the previous residue. Hence I'm getting several H's with 0.1-0.5 occupancy on single conformation residues, where the entire rest of the residue has occupancy 1. This happens after every altconf series, and showed up in two separate structures I've worked on this week. Within a series of 2+ residues with altconfs, the H's refine correctly with their altconf groups. So it isn't just that all subsequent residue's H's are getting overridden. This behavior seems to have started with 1.8.1-1168, or at least previous refinements of the same structure didn't do this. 64 bit build on Retina MBP running OS X 10.8.2. I couldn't google any reference to this behavior, so assuming it's a new bug I can send along source files. Below I've pasted a couple residues from one of my PDBs. I added a ***** to mark the offending H with the wrong occupancy. -Alex Scouras ATOM 668 N CMET A 29 -17.970 6.464 59.720 0.21 10.72 N ANISOU 668 N CMET A 29 1641 1300 1133 -328 -379 -50 N ATOM 669 CA CMET A 29 -17.578 5.189 60.316 0.21 9.05 C ANISOU 669 CA CMET A 29 1545 882 1012 -248 -350 -140 C ATOM 670 C CMET A 29 -17.248 5.317 61.797 0.21 7.83 C ANISOU 670 C CMET A 29 1363 666 947 173 -134 166 C ATOM 671 O CMET A 29 -17.496 4.395 62.578 0.21 7.92 O ANISOU 671 O CMET A 29 1187 751 1071 371 -145 338 O ATOM 672 CB CMET A 29 -16.376 4.609 59.573 0.21 9.09 C ANISOU 672 CB CMET A 29 1561 834 1059 -243 -283 -203 C ATOM 673 CG CMET A 29 -16.681 4.210 58.145 0.21 9.05 C ANISOU 673 CG CMET A 29 1529 756 1154 -28 -331 -235 C ATOM 674 SD CMET A 29 -18.049 3.042 58.009 0.21 13.05 S ANISOU 674 SD CMET A 29 2356 1325 1279 -218 -284 -50 S ATOM 675 CE CMET A 29 -17.505 1.757 59.124 0.21 12.06 C ANISOU 675 CE CMET A 29 1866 1485 1232 -630 -667 420 C ATOM 676 H CMET A 29 -17.333 6.878 59.318 0.21 12.87 H ATOM 677 HA CMET A 29 -18.320 4.557 60.216 0.21 10.86 H ATOM 678 HB2CMET A 29 -15.671 5.275 59.551 0.21 10.91 H ATOM 679 HB3CMET A 29 -16.069 3.819 60.044 0.21 10.91 H ATOM 680 HG2CMET A 29 -16.916 5.004 57.640 0.21 10.86 H ATOM 681 HG3CMET A 29 -15.894 3.794 57.761 0.21 10.86 H ATOM 682 HE1CMET A 29 -18.164 1.059 59.140 0.21 14.48 H ATOM 683 HE2CMET A 29 -16.666 1.409 58.813 0.21 14.48 H ATOM 684 HE3CMET A 29 -17.401 2.130 60.002 0.21 14.48 H ATOM 685 N MET A 30 -16.667 6.445 62.187 1.00 6.77 N ANISOU 685 N MET A 30 1361 564 647 -30 -56 18 N ATOM 686 CA MET A 30 -16.416 6.699 63.606 1.00 7.66 C ANISOU 686 CA MET A 30 1362 946 601 -42 -173 2 C ATOM 687 C MET A 30 -17.759 6.724 64.367 1.00 7.62 C ANISOU 687 C MET A 30 1310 944 641 -9 -24 -22 C ATOM 688 O MET A 30 -17.852 6.212 65.486 1.00 9.05 O ANISOU 688 O MET A 30 1571 1151 718 84 98 231 O ATOM 689 CB MET A 30 -15.620 7.987 63.790 1.00 7.65 C ANISOU 689 CB MET A 30 1299 894 714 26 -120 -166 C ATOM 690 CG MET A 30 -14.229 7.965 63.231 1.00 8.62 C ANISOU 690 CG MET A 30 1464 1072 741 31 -163 -10 C ATOM 691 SD MET A 30 -13.130 6.745 64.006 1.00 9.04 S ANISOU 691 SD MET A 30 1555 961 919 105 -180 -94 S ATOM 692 CE MET A 30 -12.812 7.527 65.563 1.00 9.77 C ANISOU 692 CE MET A 30 1540 1284 889 150 -190 -62 C ATOM 693 H MET A 30 -16.395 7.062 61.653 0.21 8.12 H ***** ATOM 694 HA MET A 30 -15.872 5.965 63.962 1.00 9.19 H ATOM 695 HB2 MET A 30 -16.099 8.709 63.352 1.00 9.18 H ATOM 696 HB3 MET A 30 -15.550 8.173 64.739 1.00 9.18 H ATOM 697 HG2 MET A 30 -14.278 7.758 62.284 1.00 10.35 H ATOM 698 HG3 MET A 30 -13.831 8.840 63.354 1.00 10.35 H ATOM 699 HE1 MET A 30 -12.228 6.968 66.079 1.00 11.73 H ATOM 700 HE2 MET A 30 -12.397 8.378 65.406 1.00 11.73 H ATOM 701 HE3 MET A 30 -13.644 7.648 66.026 1.00 11.73 H

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Re: [phenixbb] Troublesome molecular replacement
by Yuri 29 Oct '12

29 Oct '12

Nat, Just a few simple thoughts: --1) Are you certain about the space group, and did you try letting --Phaser pick one for you? (It sounds like you did, but I can't tell --from your description.) I searched for a solution in all possible space groups in P 4. I thought I was certain of the space group, but maybe not... --2) How much refinement did you run to get an R-free of 42$, and did --you already try running AutoBuild with rebuild-in-place turned off? --Refinement alone may not have the radius of convergence you need. True, I only did a couple of rounds of rebuild/refine --3) What is the sequence identity? My model is a point-mutant of the crystal. --4) Are you using the latest version of Phenix? Phaser has had TNCS --support for almost a year now but I keep hearing from people who are --using ancient versions... I am using the latest official PHENIX built. --- -- Yuri Pompeu

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Troublesome molecular replacement
by Yuri 29 Oct '12

29 Oct '12

Dear community, I recently collected on a crystal that diffracted pretty well to 2.0 A. It indexes and scales fairly well in P 4 21 2 with cell dimensions 100, 100, 200. This would predict 4 molecules/ASU. I found a MR solution in P 41 21 2 but it does not refine very well Rfree =42%. Xtriage detects strong peaks at 0,0,0.25 for Translational NCS. Any suggestions on how to go about this one? Thanks -- Yuri Pompeu

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autobuilding homomers
by Ingemar Andre 29 Oct '12

29 Oct '12

I have a question about the proper procedure for building homomers. My test case is a trimeric coiled-coil with 3-fold symmetry (trimer in assymetric unit). My input model is a trimer with three chains (A,B,C) with identical sequence. If I run phenix autobuild (rebuild_in_place=False) with this model I get a structure with decent R/Rfree. However, there are some issues: 1) Helix 1 consists of chain A in the output structure. There is a jump in the sequence number for chain A at the end. However, disregarding this chain break the full sequence is correct for helix 1. 2) Helix 2 consists of chain B + C in the output structure. The chain B has the correct sequence for helix 2. Chain C has partly the right sequence for helix 2. 3) Helix 3 consists of chain C in the output structure. Chain C has partly the correct sequence for helix 3. Lots jumps in the sequence numbering. GIven that I know its has three subunits with identical sequences I gather it should be possible to have autobuild generate structures with three chains with identical sequences. I have tested a few things. With and without giving it the sequence file corresponding to the sequence of a monomer. With and without enforcing ncs based on the input model (find_ncs=False input_ncs_file=find_ncs.ncs_spec). I am never able to build sequence-symmetric structures with rebuild_in_place=False for any homomer I have tried to build. I have limited experience with phenix so it is likely I am missing something obvious. In any case, I would appreciate your input on this. Best regards, Ingemar

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Parallella
by Morten Groftehauge 27 Oct '12

27 Oct '12

Hi guys, So the Parallella project seems like it is going forward (with the smaller processor first off) http://www.kickstarter.com/projects/adapteva/parallella-a-supercomputer-for… I figure that phenix would have problems with low amount of RAM but are there other reasons that Phenix and Parallella might not play well together? Supposedly ships in May, btw. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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HYSS and Xtriage general questions
by Heather Condurso 26 Oct '12

26 Oct '12

Dear all, I am currently solving a structure using anomalous data from a Se-Met derivative. I collected a SAD set recently and am trying to use HYSS to find the sites. I am still not 100% sure which space group it is, but I am fairly confident that it is P43212/P41212. I have scaled the data with HKL and gave the resulting sca files to Xtriage. The recommended resolution cut off from Xtriage is 4.0 with the optimistic cut off at 3.6A. The anomalous signal is 0.15. I am hoping this data is good enough, but am also trying to get better data. In the meantime I am chugging along with the data I have. I have tried the fast version of HYSS with all of the higher P4 space groups varying the resolution and number of sites. I often find that for a given sca file the resolution given is important with 4.0A giving 1 site and 3.6A giving 24 out of 24 but with a cc of ~0.2. However, when I look at the sites and maps it seems a bit odd that all of sites lie in nearly a plane. So here are! a few questions: 1. My cell is rather large with dimensions of 132, 132, 195. Does expected CC for a good solution differ based on the size of the cell or the total number of expected sites? I expect 4 chains each with 6 sites. 2. Is it likely that I will find a solution with the anomalous signal only going to 4.0A? Are there other parameters that may clue me in as to whether or not it may be possible with this data? My data is also anisotropic. Does that play a role in finding a solution? I have other data sets, but in those the mosaicity varies outside the ideal range. In this set the mosaicity varies between 0.2 and 0.5 when I integrate the images without fixing the mosaicity. 3. I've also tried to use the full search, but I'm not sure if it is working or not. I am using the GUI with version 1.7.3-928 on a Mac running OS 10.6.8. I just realized now that this is not the latest version and I can try it on another machine that I know is running 1.8.1-1168. None the less, the run status window only shows that it is running, but the log display only shows the initial search parameters, not what it is currently doing. I also tried using different rescoring and the log display is blank. Does this mean it isn't doing anything? Or should I be more patient? Some of these have been running for days.... I appreciate any advice you may have to help me along! Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

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adding some user-defined graphical objects in a PDB file (and displaying them)
by Francois Berenger 25 Oct '12

25 Oct '12

Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.

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Re: [phenixbb] Table 1 stastics
by Kay Diederichs 25 Oct '12

25 Oct '12

Dear all, I just want to point out that one possible source of discrepancy between I/sigma reported by a data processing program, and I/sigma reported by a program that uses the relevant cctbx routine is the following: that cctbx routine calculates the variance of merged data as max("internal variance", "external variance") which is different from what the data processing programs do (they calculate the "internal variance" - I hope I didn't get it the wrong way round). SHELXC and SHELXL also calculate the variance of the merged data like the data processing programs do. I dislike this "feature" of cctbx but I do not know if phenix.table_one actually uses this routine for this purpose. thanks, Kay P.S. you can find the discussion over at the cctbx mailing list; see e.g. http://phenix-online.org/pipermail/cctbxbb/2012-September/000530.html and other posts. On 10/18/2012 09:08 PM, phenixbb-request(a)phenix-online.org wrote: > Date: Thu, 18 Oct 2012 08:07:44 -0700 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Table 1 stastics > Message-ID: > <CALeAa1NDDy7=ZCUqThgun+k-Si7-Gf920ROvuYwpPgsShAhHVQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Thu, Oct 18, 2012 at 7:53 AM, Andrew Waight<waight(a)msg.ucsf.edu> wrote: >> Thanks for Phenix! Anyway quick question, I tried out the "generate >> Table1" utility for fun and noticed that my I/SigI and completeness do not >> match what is found in my XSCALE file. >> ... >> How does Phenix compute these parameters? Obviously my I/sigI has gotten >> much better (1.59 versus 0.85) but the scaling statistics should be the >> correct ones. > > It computes these statistics directly from the reflection data you > provide, not the log file. (The reasoning being that since these are > the data that Phenix actually uses, the statistics calculated from > them are more accurate and relevant than whatever the scaling program > thinks.) My guess is that some of the internal processing accounts > for the difference - could you please send me the data file? > > FYI, the plan for the future is to recalculate all of these statistics > from unmerged data rather than rely on parsing data processing > logfiles, which obey no standard format and are subject to change > without notice. > > -Nat > -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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Problem with elbow
by Subhani Bandara 25 Oct '12

25 Oct '12

Dear all, I am using the PHENIX version 1.8.1-1168 and need to get the pdb file and the cif file for the metal-chelate complex Gd-DTPA for refinement of a structure. I got the pdb file and the cif file for a dimer of the complex. Then I edited those to contain only one metal chelator complex and used as inputs in elbow. I have attached the pdb file and the cif file I used as inputs. I gave cif file as chemical file type with pdb file as initial geometry and ran elbow. Then I used pdb file only or cif file only as inputs separately. Every time it ended with the error “Failed to determine the bonding of a fragment of the molecule” Also I tried using smile string C(CN(CC(=O)[O-])CC(=O)[O-])N(CCN(CC(=O)[O-])CC(=O)[O-])CC(=O)[O-].[Gd+3]and pdb file as inputs. Then it runs without an error, but it outputs cif and pdb files containing only Gd. How can I get the cif file for the metal-chelate complex? I want to use the metal-chelate complex as one entity in the refinement, so that it will have the correct geometry of the chelator. Thanks Subhani

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1.8.1 1168
by Colin Levy 25 Oct '12

25 Oct '12

Hi all, I have just updated to the latest version of Phenix 1.8.1 1168 but I now appear to have lost the ability to drag and drop files between different windows. Running on a mac 10.7.5 OSX. Thanks Colin Manchester Protein Structure Facility MIB 1.025 Tel 0161 306 5185 c.levy(a)manchester.ac.uk<mailto:[email protected]>

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question du jour: monomer libs where?
by Patrick Loll 24 Oct '12

24 Oct '12

Where does PHENIX find the monomer libraries? Here's why I ask: I submit a refinement job for a peptide containing a mix of D- and L-amino acids. The program seems to have no problem with D-versions of Glu, Asn, or Phe (DGL, DAS, or DPN), but it flags the atoms in a D-ornithine (ORD) residue as having unknown nonbonded energy type symbols. Curiously, when I look in the relevant directories in ...Contents/phenix-1.8.1-1168/chem_data/chemical_components I can find cif files corresponding to ALL of these D-amino acids, including ORD (...chemical_components/o/data_ORD.cif). Files are also present for DGL, DAS, and DPN. However, these files don't contain all of the information I'm accustomed to seeing in monomer libraries (e.g., explicit bond lengths & angles), so I'm not sure if the same information is somehow encoded differently (via the idealized coordinates, perhaps?), or if I'm barking up the wrong tree. So: Are these the actual monomer libraries that phenix.refine consults? And in this case why doesn't phenix.refine recognize ORD? Or are the true monomer libraries hiding elsewhere? As always, thanks, Pat ps the directory structure I'm describing is under OS X 10.7.5 --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjloll(a)gmail.com pat.loll(a)drexelmed.edu pat.loll(a)drexel.edu

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some basic questions about phenix autobuild and phenix.refine
by Niks 24 Oct '12

24 Oct '12

Dear All, I have recently started using PHENIX so I am a beginer in PHENIX field. I am getting better statistics (Rfactor/Rfree) as compared to REFMAC so having strong inclination to continue with PHENIX but there are some discripancies I found when comparing with CCP4 programs.Therefore i I have some basic questions which I request you to throw some light and wisdom. 1) I have solved my structure using AutoMR and got two files MR.1.mtz and MR.1.pdb as output with high LLG of 8236.889. When going for AutoBuild afterwards it uses output pdb (MR.1.pdb) which is fine but uses MR.1.mtz as map coefficient. Shouldnot it uses original mtz from scala? 2) Same in Phenix.refine when going after Autobuild finishes and it asks for refining the model it uses same AutoMR output mtz (MR.1.mtz). As I was suggested by many that we should use original mtz coming from scala for Refinement to reduce model bias. shouldnot phenix.refine use Original mtz file here too? 3) After going for AutoBuild after AutoMR, even when I unselect "Place Waters" options in parameters for Refinement, I see output pdb file with waters added to it. I do not want waters to be added till I refine my model to the best , but Autobuild option comes out with waters added. Is there anyway I can have autobuilt pdb without waters added? 4) Another question that troubling me most that in Phenix.refine even if I use original mtz which clearly specifies resoultion range from 127.488-2.5A my refined pdb files comes out with Resolution range used for refinement as 37.8-2.5A. I have tried to input low resolution range as 127.488 but deafult is always 37.8 selected. My data may be very poor in lower resolutions than 37.8A but my completeness is also going down (65.5% as opposed to 79.8% in REFMAC). Can I select my refinement using my specified values of Resolution from mtz file coming out from SCALA? Sorry for the lengthy mail and many questions. Thanks and regards Nishant PhD Student, C/O Dr. C. G. Suresh, National Chemical Laboratory, Pune, India -- "The most difficult phase of life is not when No one understands you;It is when you don't understand yourself"

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phenix GUI crash
by Sébastien Moniot 23 Oct '12

23 Oct '12

Hi, Little problem with the phenix GUI crashing ... we are running phenix via ssh login on a workstation and each time the REEL window or the graphical interface to make atom selection are called the whole GUI crashes. In the first case, only the following message is reported in the shell. --- segmentation fault ----- In the second case, --- (python2.7:29303) : Gtk-CRITICAL **: gtk_window_resize: assertion `width > 0' failed segmentation fault ---- Any idea how to fix this ? Best, Dr. Sebastien Moniot Department of Biochemistry University of Bayreuth Bayreuth, Germany

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