- phenixbb - phenix-online.org

Refining Anomalous Groups
by Brennan Bonnet 20 Nov '12

20 Nov '12

Hi All, I am trying to use phenix.refine to refine partially occupied xenon sites using the Anomalous Groups selection under "Refinement settings". My list of anomalous scatters initially consisted of 22 peaks as located by HySS. Some of these were removed as they originated from S atoms from Met and Cys residues and a few others were removed after previous refinement steps due to having zero occupancy. My remaining sites consist of my xenons (hopefully) and other metals such as Mg or Zn which are mixed in and look like partially occupied xenon sites. My problem is that when I try to define the 11 remaining sites for the "refine anomalous groups" selection the software complains: Invalid combination: F-obs not anomalous, but refinement of 11 f_double_prime values requested (11 scatterers): Please provide anomalous reflection data or fix all f_double_prime values (see refinement.refine.anomalous_scatterer.group input blocks) I can't figure out exactly what I need to change to make it work and can't find a guide anywhere. Do I need to provide additional data or is the syntax for the sites incorrect maybe? Please help! ~Brennan~

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Phaser
by Morten Groftehauge 19 Nov '12

19 Nov '12

Hi guys, I was trying out the new Parallel Phaser (dev-1214) and using a model prepared by Rosetta covering 25% of the total structure (32% identity to the homology model), NCS = 2. 5 models actually but not really relevant since the program spontaneously stopped running after a couple of hours (I love what it's supposed to do though!). My question is about the log however. In the Parallel Phaser log it says: Expected LLG and Resolution Limits ---------------------------------- Expected LLG target: 120.00 Expected LLG achieved: 120.0 Resolution of All Data: 2.38 Resolution limited by eLLG target: 4.83 This resolution WILL NOT be used as the default The expected LLG achieved is greater than 120 (eLLG target) but when I tried to recreate that run in the regular Phaser-MR I get this message in the log Expected LLG and Resolution Limits ---------------------------------- Expected LLG target: 120.00 Expected LLG achieved: 49.7 Resolution of All Data: 2.38 Resolution limited by eLLG target: 2.38 This resolution WILL NOT be used as the default The expected LLG achieved is less than 60 (half eLLG target) FTF rescoring WILL be performed due to low expected LLG signal Deep search will be performed from the start I think the second result looks more realistic (unfortunately) but I still don't understand why the difference? Cheers, Morten PS Seems like there's a memory leak in 1214 and 1207 when I run the Phaser step of MR_Rosetta. Does this sound right? Definitely in 1207 but it seems like it's still there in 1214. -- Morten K Grøftehauge, PhD Pohl Group Durham University

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SASTBX server
by Tanner, John J. 19 Nov '12

19 Nov '12

I apologize if this is an inappropriate post for phenixbb… Has anyone had trouble with the SASTBX server lately? I have been getting this error since Friday when calculating shapes and P(r). Server error! The server encountered an internal error and was unable to complete your request. Error message: Premature end of script headers: cctbx_web.cgi If you think this is a server error, please contact the webmaster<mailto:[email protected]>. Error 500 sastbx.als.lbl.gov<http://sastbx.als.lbl.gov/> Fri Nov 16 07:56:37 2012 Apache/2.2.17 (Unix) PHP/5.3.4

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fwd: West Coast Protein Crystallography Workshop
by Nathaniel Echols 18 Nov '12

18 Nov '12

(There will probably be several people from our group attending this year.) ---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Date: Sun, 18 Nov 2012 08:15:19 -0800 Subject: West Coast Protein Crystallography Workshop All, Wayne Hendrickson will be the keynote speaker for the West Coast Protein Crystallography Workshop, scheduled for March 17th - March 20th at the Monterey Plaza and Spa. Registration will open up Dec 1st. Hope to see you there! Best, John Williams WCPCW Organizer

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v1.8.1 installation hangs
by Alex Theodossis 18 Nov '12

18 Nov '12

Hi, I'm attempting to install the latest version of phenix on mac 10.5.8, using the command line installer. Installation proceeds well until towards the end, where it hangs on: precompiling .py files I can leave it for up to an hour without any further progress, but upon typing: ctrl+c The installation comes back to life and proceeds to completion. Can anyone advise as to what might be causing this and on how reliable this installation is going to be? Thanks in advance.

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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 14 Nov '12

14 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 14 Nov '12

14 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 13 Nov '12

13 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 02 Nov '12

02 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 01 Nov '12

01 Nov '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 26 Oct '12

26 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

2 1

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]>

2 1

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"

4 3

phenix GUI crash
by Sébastien Moniot 24 Oct '12

24 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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hydrogen nomenclature
by Patrick Loll 23 Oct '12

23 Oct '12

Hi, I'm trying to sort out some monomer libraries for a high-resolution refinement involving non-canonical amino acids, but now I've become side-tracked with a hydrogen nomenclature issue that seems to affect even canonical amino acids. I will use the example of L-leucine to illustrate: In the CCP4 monomer library LEU.cif, the two hydrogens on CB are named HB1 and HB2. However, if I look at the LEU entry on the RCSB PDB site, these two hydrogens are named HB2 and HB3. Looking at pdbe.org is not too helpful, since it lists those two hydrogens as HB2 and HB3, but includes alternate "PDB names" of HB1 and HB2. Similar situations pertain for other atoms and other residues. Presumably I need to stick with the nomenclature found in the monomer library in order for refinement to work properly; but will this come back to bite me later when I submit coordinates to the PDB? Any insights welcome. Thanks, Pat

4 3

Durandal clustering applied to homology models
by Quentin Delettre 23 Oct '12

23 Oct '12

Dear Phenix users, I am new to phenix and the Durandal tool, i would like to know if Durandal is an appropriate way to cluster many homology models of a protein. And if so, what is the syntax of the output ? The man page does not provide any information beside inputs commands. Thanks.

2 1

problem installing Phenix 1.8.1 on Fedora16
by Marianna Biadene 22 Oct '12

22 Oct '12

Dear all, I am trying to install Phenix 1.8.1-1168 on my Linux 64bit, Fedora 16. If I try to install it in the default directory (/usr/local) I have no problem, but when I try to install it in /usr/local/bin using the command written in the documentation (http://www.phenix-online.org/documentation/install.htm) ./install --prefix=</usr/local/bin> I got the following error message: -bash: syntax error near unexpected token `newline' I am not a super expert in Linux and I have tried to search in Internet for a solution but I am lost. Any idea of how could I solve this problem? Thanks a lot, Marianna -- Dr. Marianna Biadene Division of Biological Chemistry - Group Prof. Scheffzek Biocenter Medical University Innsbruck Innrain 80 / 4 6020 Innsbruck Austria Phone: +43 512 9003 70336

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xyz and adp weight optimisation
by Alex Theodossis 19 Oct '12

19 Oct '12

Dear bb, I have made use of the target weight optimisation feature with great results. The question is, having optimised these weighting terms, how can I use the optimised values in subsequent runs without having to keep the optimisation option switched on? In the last round of refinement I get: Best XYZ weight: 9.000 Best ADP weight: 0.695 But the output .eff file does not seem to have saved these values for use in subsequent refinements: target_weights { optimize_xyz_weight = True optimize_adp_weight = True wxc_scale = 0.5 wxu_scale = 1 wc = 1 wu = 1 fix_wxc = None fix_wxu = None Is it appropriate to enter the optimised values in the fix_wxc and fix_wxu fields? Thanks in advance

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Re: [phenixbb] Metal Coordination and symmetry operation
by Pavel Afonine 19 Oct '12

19 Oct '12

Hi Alex, thanks for the file - I will have a closer look. Did you mean the restraint did not work or it worked but you wanted something else? (I'm just trying to understand if this is a Phenix problem that we need to fix). Pavel On 10/18/12 10:30 PM, Alex Theodossis wrote: > Hi Pavel, > > thanks for the info. With it I was able to correctly define the > symmetry-related links as per this example: > > refinement.geometry_restraints.edits { > bond { > action = *add > atom_selection_1 = name ZN and chain C and resname ZN and resseq > 1 > atom_selection_2 = name NE2 and chain A and resname HIS and altid > A and resseq 39 > symmetry_operation = -x+1,y+1/2,-z+1/2 > distance_ideal = 2.030000 > sigma = 0.050 > } > > Unfortunately, this didn't have the desired result. Instead, the > addition of riding hydrogens fixed the problem. > I've also attached the relevant fragment of the refined model as > requested. > > Cheers, > > Alex > > > > On 17 October 2012 13:04, Pavel Afonine <pafonine(a)lbl.gov > <mailto:[email protected]>> wrote: > > Hi Alex, > > Nigel is the best person to reply, so he may provide more > comments. My understanding is that phenix.metal_coordination > command (or whatever the equivalent click in the GUI is) should > account for symmetry related atoms. If not you can fix it > manually. First create edits file using phenix.metal_coordination > and then add symmetry related bonds as described here: > > http://www.phenix-online.org/documentation/refinement.htm#anch353 > > Also, could you please send me the PDB file or its portion > containing relevant to your question atoms and I will have a > closer look? > > Pavel > > > On 10/16/12 6:33 PM, Alex Theodossis wrote: >> >> Dear bb, >> >> I am trying to refine a Zn ion coordinated by symmetry >> related residues. To avoid groups being pushed away. I have >> use phenix.metal_coordination to >> generate the necessary link edits. However only non-symmetry >> related interactions are accounted for. Is there a relevant >> option I can switch on? >> Alternatively, does anyone have an example of the syntax >> required to define the necessary symmetry operations in the >> elbow.edits file? >> >> Thanks in advance. >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb > >

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Re: [phenixbb] Metal Coordination and symmetry operation
by Alex Theodossis 19 Oct '12

19 Oct '12

> > Dear bb, > > I am trying to refine a Zn ion coordinated by symmetry related residues. > To avoid groups being pushed away. I have use phenix.metal_coordination to > generate the necessary link edits. However only non-symmetry related > interactions are accounted for. Is there a relevant option I can switch on? > Alternatively, does anyone have an example of the syntax required to > define the necessary symmetry operations in the elbow.edits file? > > Thanks in advance. >

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Re: [phenixbb] Table 1 stastics
by Nathaniel Echols 18 Oct '12

18 Oct '12

On Thu, Oct 18, 2012 at 8:45 AM, Katherine Sippel <katherine.sippel(a)gmail.com> wrote: > Part of the problem could lie in whether he input the original mtz as > intensities or not. In older versions of phenix some intensities were > dropped if they were below the cutoff and particularly for high res data the > completeness would go down significantly. I know you have implemented the > French and Wilson conversion in the newer versions but if he comes from a > lab like my old one and is refining off of intensities that could be the > culprit. This is a good point, but it depends on the version of Phenix, the type of input data, and how the data file was processed. I checked my code for Table 1 and if the input data are intensities, the negative observations should *not* be discarded. The same goes for phenix.refine, among other programs. However, if amplitudes were used as input for Table 1, and had previously been filtered through a program that does not perform the French & Wilson treatment, they may be missing some data (most of which will probably be at high resolution). One caveat: the reflection file editor in Phenix has an option to convert intensities to amplitudes, but this will not run F&W, which is perhaps a bug... -Nat

1 0

Table 1 stastics
by Andrew Waight 18 Oct '12

18 Oct '12

Hi All, 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. From Table 1 Completeness (%) 98.62 (90.57) Mean I/sigma(I) 7.39 (1.59) Wilson B-factor 59.78 R-sym R-factor 0.2006 (0.3275) R-free 0.2241 (0.3739) From XSCALE SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 20.00 313 69 72 95.8% 3.6% 4.6% 313 30.88 4.3% 99.9* 8 0.725 54 10.00 2174 471 471 100.0% 3.9% 4.8% 2174 28.71 4.4% 99.8* 34* 0.972 382 6.00 8195 1983 1992 99.5% 4.7% 5.3% 8160 20.70 5.4% 99.8* 12* 0.913 1299 5.00 8055 1818 1820 99.9% 7.0% 6.9% 8051 17.73 7.9% 99.5* 7 0.892 1337 4.50 7207 1634 1636 99.9% 6.0% 6.2% 7207 20.06 6.8% 99.6* -1 0.824 1163 4.00 9603 2479 2521 98.3% 6.8% 6.7% 9536 17.05 7.9% 99.4* -2 0.819 1369 3.60 13641 3141 3156 99.5% 9.6% 9.5% 13621 13.71 11.0% 99.1* -2 0.799 2073 3.20 22112 4948 4951 99.9% 16.5% 16.6% 22083 8.82 18.8% 98.1* 4 0.810 3383 3.00 14155 3550 3579 99.2% 27.8% 27.7% 14058 5.45 32.1% 94.6* -1 0.742 1875 2.80 19676 4584 4611 99.4% 44.9% 46.2% 19604 3.71 51.2% 88.5* 3 0.740 2750 2.60 26749 6192 6202 99.8% 76.3% 78.4% 26686 2.20 87.2% 71.8* 1 0.717 3598 2.40 33999 8339 8388 99.4% 130.9% 132.7% 33810 1.26 150.6% 48.5* 1 0.671 4170 2.30 22347 5332 5348 99.7% 198.4% 206.4% 22276 0.85 227.7% 31.5* 0 0.623 2685 total 188226 44540 44747 99.5% 9.0% 9.4% 187579 7.09 10.3% 99.8* 2 0.755 26138 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. Thanks, Drew

2 2

close contact and torsion angle
by hchxia＠ujs.edu.cn 12 Oct '12

12 Oct '12

Hi, There are some close contacts (hydrogen bonds) in my refined model. Can I just ignore it, delete it or what? I added hydrogen for refinement since the resolution is 1.47 A. Should I remove all these added hydrogens and refine again? Second question is there are several outilers of torsion angles (6 from Ramachandran plot in coot ). But 16 are outside expected Ramachandran regions from the validation report from PDB bank(ADIT) . What is the cause? And should I re-refine to correct them? Or just go ahead to deposit it? Thanks! chuan

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how to continue an aborted phenix.refine
by hchxia＠ujs.edu.cn 11 Oct '12

11 Oct '12

Hi! I aborted a run of phenix.refine due to linux problem. Is there a way to continue from the aborted point to finish the run? or I have to start from 0 to rerun it ? Thanks a lot! chuan

2 1

OS X 10.8 Mountain Lion
by Alexander Batyuk 10 Oct '12

10 Oct '12

Dear all, Could anybody confirm that Phenix does or does not run on OS X 10.8 Mountain Lion, please? Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

3 5

labelit and latest mosflm
by "Weiergräber, Oliver H." 04 Oct '12

04 Oct '12

Hello, the labelit.index executable provided with phenix 1.8.1 has a problem with the latest mosflm (7.0.9, as included in ccp4 6.3.0): "MosflmVersionError: mosflm versions after 7.0.8 not supported" Is there any reason to believe that mosflm 7.0.9 has really become incompatible with labelit? If not, can the version check be overridden as a temporary fix? Best, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unsere app? http://www.fz-juelich.de/app

2 1

automr
by Shya Biswas 02 Oct '12

02 Oct '12

Hi all, I was wondering if anyone knows how to change the packing clash distance in Automr gui. Thanks, Shya

2 1

changes from 1.8.1-1161 to official 1.8.1?
by Eric Williams 02 Oct '12

02 Oct '12

Where any major bugs fixed between the 1161 nightly build and the official 1.8.1 release? I have a large batch job running that uses 1161. If the squashed bugs are big enough, it might be worth stopping the job to install the new release. Otherwise, I'll just let it run to completion. Thanks. :) Eric

2 1

Phenix version 1.8.1 released
by Paul Adams 01 Oct '12

01 Oct '12

The Phenix developers are pleased to announce that version 1.8.1 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: ==================== - New GUIs: phenix.find_alt_orig_sym_mate General: ======== - Multiple bug fixes - New commands: phenix.erraser, phenix.merging_statistics - Added geometry restraints for over 400 non-standard amino acid entries Refinement: =========== - Overall B-cart now applied to individual atomic B-factors (restores pre-1.8 behavior) - Improvements to torsion NCS rotamer correction - Real-space refinement (including rotamer fitting) for twinned data New command: ============ - phenix.erraser: - New method from Fang-Chieh Chou and Rhiju Das (Stanford) combining Rosetta nucleic acid rebuilding with phenix.refine (requires separate installation of Rosetta 3.4 or more recent) Molecular Replacement: ====================== - Phaser updated to version 2.5.2: - Scattering from HETATM records that represent modified amino acids (e.g. MSE/SeMet) included so that maps no longer show holes for these HETATM records in the model; occupancies will not be reset. - Packing test was incorrectly applied to reoriented molecules where there was PTNCS Experimental Phasing and Model Building: ======================================== - AutoSol: - Scale of derivative in SIR (for RIP phasing) can be set with keyword "derscale" - AutoBuild: - Unassigned chains are now given the segid of "UNK" and are normally given chain ID="U" Ligands: ======== - eLBOW: - New option, --multiple-planes, to generate planes around double bonds - Saturated rings now have dihedral restraints to maintain chair conformation - REEL: - View relationships between ligands using PubChem fingerprint and tanimoto score. Miscellaneous: ============== - phenix.real_space_correlation: - Simplified command-line behavior - phenix.merging_statistics (new command): - Calculate statistics for unmerged data in a variety of formats, including <I/sigmaI>, R-merge, R-meas, R-pim, CC1/2 - References: Diederichs K & Karplus PA (1997) Nature Structural Biology 4:269-275 Weiss MS (2001) J Appl Cryst 34:130-135. - phenix.kinemage: - Improvements to handling of alternate conformations. - phenix.combine_models: - Combine two models, taking the best parts of each to create a new model For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area 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: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

1 0

point-n-click installer is bjorking OS X Dock
by Scott Classen 27 Sep '12

27 Sep '12

Hello, After running the OS X point-n-click installer for the 1.8.1-1160 nightly build, the dock becomes unresponsive and I can no longer command+tab to switch between applications. I've reproduced this on 2 Macs. One running 10.8.2 and the other running 10.7.5 Relaunching Finder does not fix the proton dock/app switching Logging out and then logging back in fixes the problem. Scott

2 5

den refinement with multiple reference files
by Andreas Förster 26 Sep '12

26 Sep '12

Dear all, I've started DEN refinement on a structure obtained by MR from data optimistically going to 3.8A. There are several chains of two kinds in the structure. High-resolution structures exist for both. How do I use two reference files for DEN refinement, and how do I assign which chain corresponds to which reference? (Currently, I'm using reference_file = None.) Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

2 2

Phenix cut out density labels choice
by Mikalai Lapkouski 21 Sep '12

21 Sep '12

Hello, I have a following issue with running Phenix.cutout density either on command line or in GUI. I have multiple columns in the mtz.file and I want to choose map coefficients FOFCWT_d1-8,PHFOFCWT_d1-8 for the difference map to be cut around pdb selection. I run a command: phenix.cut_out_density model.pdb my.mtz cutout_fix_position=True cutout_model_radius=10 cutout_type=model \ map_coeff_labels=FOFCWT_d1-8,PHFOFCWT_d1-8 Problem: The output cutout.mtz has FWT and PHWT (which I did not have at all in the input) and not my difference map coefficients, and obviously the map is not my difference map. In GUI is the same problem, I choose columns I need but it outputs FWT and PHWT again. Please, let me know what I am doing wrong. Thank you very much! Mikalai

3 2

Combine map labels
by Mikalai Lapkouski 21 Sep '12

21 Sep '12

Hello, I have a following question. I have generated several Fo-Fc sa omit maps (FOFCWT, PHFOFCWT) for different portions of a DNA molecule. Now that I have each omit map as a separate file to display the whole DNA omit map I have to load them in coot one by one. Is there a way of how to combine all this maps into one file and have a single name for label columns so that the whole map will open at once? I managed to put them all in one file but column labels are separate: FOFCWT_1, PHFOFCWT_1 FOFCWT_2, PHFOFCWT_2...... Can they all go under FOFCWT, PHFOFCWT? Thank you very much for any suggestion Mikalai

5 5

Specifying union of two chains in pdb_atom_selection
by Francis E Reyes 21 Sep '12

21 Sep '12

Hi all, I issue the following command to pdb_atom_selection but I get 0 atoms selected at the end? $ phenix.pdb_atom_selection refine_to_submit.pdb "chain X and chain B" refine_to_submit.pdb Monomer Library directory: "/usr/local/phenix-1.8-1069/chem_data/mon_lib" Total number of atoms: 3817 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1800 Classifications: {'RNA': 84} Modifications used: {'rna3p_pyr': 26, 'rna2p_pur': 5, 'rna3p_pur': 44, 'rna2p_pyr': 9} Link IDs: {'rna3p': 70, 'rna2p': 13} Chain: "X" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1800 Classifications: {'RNA': 84} Modifications used: {'rna3p_pyr': 26, 'rna2p_pur': 5, 'rna3p_pur': 44, 'rna2p_pyr': 9} Link IDs: {'rna3p': 70, 'rna2p': 13} chain X and chain B 0 atoms selected Thanks! F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

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