- phenixbb - phenix-online.org

Re: [phenixbb] AutoBuild runtime
by Nathaniel Echols 05 Nov '11

05 Nov '11

On Sat, Nov 5, 2011 at 12:02 PM, Shya Biswas <shyabiswas(a)gmail.com> wrote: > I was running autobuild using my protein sequence and the best MR model that > I got out of phaser, however it is taking really long to finish the job. Is > there a way to reduce the time period? Several options: - turn on quick mode (quick=True, or equivalent button in GUI) - use multiple processors if you have them (nproc=X, or equivalent control in GUI) - cut back resolution: if you have really good and/or high-resolution data*, you may be able to get nearly as good a model with fewer reflections, and it will be much faster (mostly due to refinement time, I think). However, this can also significantly degrade your model if the data aren't that great. - instead of AutoBuild, use phenix.phase_and_build (also in the GUI), which is basically the building procedure from AutoSol. It will usually not produce as complete a model (or R-factors as low) as AutoBuild, but it's much faster. -Nat (* the p9-sad tutorial is a good example of this - when we run workshops, we usually tell attendees to set the resolution limit for AutoSol to 3.0 instead of using all data to 1.7. The resulting model is nearly complete, and it finishes in less than half the time. Of course these data are unusually good...)

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Call for submissions to Computational Crystallography Newsletter (corrected)
by Nigel Moriarty 05 Nov '11

05 Nov '11

Calling for articles and short communications of interest tostructural biologists. The deadline for publication in the January2012 issue is 1st Dec, 2011. The Computational Crystallography Newsletter (CCN) is an electronicnewsletter for structural biologists, and is published online every 6months. Feature articles, meeting announcements and reports can besubmitted to me at any time for consideration. Submission of text byemail or word-processing files using the CCN templates is requested.Past newsletters and the template are available atwww.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Call for subscriptions to Computational Crystallography Newsletter
by Nigel Moriarty 04 Nov '11

04 Nov '11

Calling for articles and short communications of interest to structural biologists. The deadline for publication in the January 2012 issue is 1st Dec, 2011. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and the template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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metal coordination restraints
by Laurie Betts 04 Nov '11

04 Nov '11

How does PHENIX know where to look for proper bond lengths and angles for a metal ion I add to a protein structure - do I just add the metal into difference density and any waters, and then run ready set and it knows where to look for that particular metal and the atoms to which is is coordinated? And shouldn't there be a 'cif file that it outputs, or is that something that I need to get myself? Sorry it's still not obvious to me from the documentation. Thanks Laurie Betts

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Postdoctoral Position at King's College London, UK
by Steiner, Roberto 04 Nov '11

04 Nov '11

A three-year postdoctoral position in the field of mechanistic enzymology is immediately available in the Steiner Laboratory of King’s College London. The salary is £33,193 per annum inclusive of London allowance. The project aims at studying the intriguing biological process of cofactor-independent oxygenation catalysis (1). To understand how dioxygen chemistry takes place in a cofactor-less manner we will use enzymes for which we have recently obtained structural information in various catalytically relevant states (2). The ideal candidate has a strong biochemistry/chemistry background, extensive experience in structural biology focused on enzyme mechanisms and an interest in molecular dynamics (MD). The MD work will be carried out in collaboration with Prof. Ceccarelli of the University of Cagliari, Italy, where the postdoc will be able to spend some time to improve his/her skills in MD techniques. The postdoc will also be in close contact with the Manchester group of Prof. Scrutton where complementary spectroscopic and kinetic studies will be carried out. This project will equip the post-holder with a rare and sought-after skill-set as well as a comprehensive overview of an inter-disciplinary study. To apply for this position go to http://www.kcl.ac.uk/depsta/pertra/vacancy/external/pers_detail.php?jobinde…. Please make sure you quote the reference number G6/JKA/772/11-JT. Informal enquiries are welcome at roberto.steiner(a)kcl.ac.uk<mailto:[email protected]>. The closing date for this application is 24 Nov. 2011. (1) Fetzner S. and Steiner RA (2010). Cofactor-independent oxidases and oxygenases. Appl. Microbiol. Biotechnol. 86, 791-804. (2) Steiner RA, Janssen HJ, Roversi P, Oakley OJ, Fetzner S (2010). Structural basis for cofactor independent dioxygenation of N-heteroaromatic compounds at the •/•-hydrolase fold. Proc. Natl. Acad. Sci. USA, 107, 657-662. Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.steiner(a)kcl.ac.uk<mailto:[email protected]>

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Re: [phenixbb] Molecule and maps will not load into coot from Phenix 1.7.1-743
by Jobichen Chacko 03 Nov '11

03 Nov '11

Dear Nat, Any progress in this matter. To add, do you have any version of Phenix which is working perfectly (the communication of Phenix with pymol and coot) in ubuntu system in you lab? Jobi On Tue, Nov 1, 2011 at 5:08 PM, Jobichen Chacko <jobichenc(a)gmail.com> wrote: > Dear Nat, > Just to add when I try open the files in pymol, it doesnot open up and > show this output. > > /usr/local/phenix-1.7.1-743/build/intel-linux-2.6-x86_64/base/bin/python2.7: > No module named pymol > > Jobi > > > On Tue, Nov 1, 2011 at 10:58 AM, Jobichen Chacko <jobichenc(a)gmail.com> wrote: >> Dear Nat, >> I installed the the coot version you sent to me. Still not working. >> jobi >> >> On Tue, Nov 1, 2011 at 10:43 AM, Nathaniel Echols <nechols(a)lbl.gov> wrote: >>> On Mon, Oct 31, 2011 at 7:34 PM, Jobichen Chacko <jobichenc(a)gmail.com> wrote: >>>> Dear Nat, >>>> Thank you for your help. >>>> Please see the attached output after running coot_test.py >>>> I will also try to install the coot version you send to me. >>>> Jobi >>>> ... >>>> 'import site' failed; use -v for traceback >>> >>> Wow, that's way more broken than I was expecting. I think this means >>> a library conflict, but I've only come across this error on Mac. Can >>> you try one more thing? >>> >>> export PYTHONVERBOSE=1 >>> coot --script coot_test.py >>> >>> (If you're using csh or tcsh as your shell, the first line should be >>> "setenv PYTHONVERBOSE 1" instead.) >>> >>> -Nat >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >

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Ligands at special positions
by Subhani Bandara 02 Nov '11

02 Nov '11

Hi everyone, There are some ligands in my protein structure, that are very close to a special position. But they are not exactly at a special position, so when I apply symmetry in coot it generates another ligand away from the original one. How can I move them exactly on to a special position. Is there any script I can use for this? Thanks Subhani

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NMR vs Xtal structures
by Yuri 02 Nov '11

02 Nov '11

Could someone point me to a good paper on comparing of structures of the same protein determined by X-ray vs. NMR Best, -- Yuri Pompeu

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Autosol
by Kiran Kulkarni 01 Nov '11

01 Nov '11

Hi, I am getting following error message while running Autosol. *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoSol_guess_setup_for_scaling: 'nat_der_list' ******************************************************************************** *************ERROR ENDING ******************* Please help me to fix this. Details: PHENIX VERSION: 1.7.2 of 23-09-2011 PHENIX RELEASE_TAG : 869 PHENIX MTYPE : mac-intel-osx-x86_64 PHENIX MVERSION : osx-10.6.8 Space group: P41 EXPT_TYPE = SIR Native data Resolution= 3.8A Derivative data Resolution= 6.5A Program runs smoothly for derivative data alone (i.e. for SAD mode). Many thanks, -Kiran

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Molecule and maps will not load into coot from Phenix 1.7.1-743
by Jobichen Chacko 01 Nov '11

01 Nov '11

The same old problem, I tried to add the coot path using preferences. Coot version result: COOT_PREFIX is /usr/local /usr/local/bin/coot-real --version 0.6.1 (revision 2740) [with guile 1.8.7 embedded] [with python 2.6.0 embedded] The coot opens just after phenix-refine job starts and after the job finishes. But no maps and models are loaded. Thanks. Jobi

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"ATP" monomer in phenix_refine
by Zhang yu 28 Oct '11

28 Oct '11

Hi, I had a trouble of refining "ATP" in Phenix. I appreciate any help. ATP with tri-phosphate is in the 5' end of RNA chain. It is added to the RNA chain in coot as a monomer "ATP", and it could be connected to the downstream base after I changed the "_chem_comp.group" option to "RNA" in the cif file. But when I refine the model in Phenix, Phenix treated the "ATP' as a monomer and didn't connect it to the downstream base. I tried two ways to solve it 1. Add the the modified (chang the "_chem_comp.group" option to "RNA") cif file in phenix_refine, but Phenix doesn't recognize it. 2. In REEL, I found phenix has its own cif file for ATP, but the its header couldn't be edited. Any suggestions? Thanks. Yu

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Problem avoiding real space refinement
by Jerome Nwachukwu 27 Oct '11

27 Oct '11

Hi: We noticed that in some of our refinements, real space refinement was performed even though we chose not to do this. I tried to opt out of real space refinement as follows: " refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies group_anomalous ..." however, the R-free is identical whether we select real space refinement or not, and the logfile shows " Validate: |--------START--------| |--------FINAL--------| residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc "LYS A 18 " 0.9359 16.78 0.00 0.9107 17.60 0.00 "ARG A 19 " 0.9513 21.82 0.00 0.9470 20.97 -6.52 <<< "ARG A 26 " 0.9440 26.72 0.00 0.9474 27.33 -2.43 "ARG A 69 " 0.9685 31.36 0.00 0.9659 32.58 0.00 "GLN A 86 " 0.9681 23.57 -5.81 0.8850 19.29 -18.27 <<< "GLU A 89 " 0.9689 26.30 -4.43 0.8977 23.67 -11.59 <<< "LYS A 93 " 0.9746 25.19 0.00 0.9682 26.47 2.90 ... " and suggesting that real space refinement was performed. Is there a way to correct this, or to ensure that real space refinement is not performed during refinement? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida

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problem to add D atom on carbonyl group (enol) as alternate conformation
by Maxime Cuypers 27 Oct '11

27 Oct '11

Dear all, i have a problem that i block on for quite a while. i need to add a D atom on carbonyl group (enol) as alternate conformation to a main chain protein amide group to refine with phenix.refine. It is not something that the program phenix.reduce can perdeuterate as it is an unusual position. it actually perdeuterates all the rest of the protein successfully. Does anyone have an idea how to proceed? i tried so far to rename the residue and give .cif restraints generated with readyset for the new tautomer. phenix seemed to recognised it but it failed due to the fact it does not recognise the residue as being a residue to link to the other residues and bounds bounce off. A friend told me a cif_link was the problem. Then i tried to apply cif_modification in a parameter file with the corresponding .cif file as explained briefly on: http://www.phenix-online.org/documentation/refinement.htm#anch88 it does not solve the problem. the link between the new tautomer residue and the rest of the residues does not occur in refinement. Thanks for your help in advance. i am getting deseperate. Maxime

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exploring the conformational space of sidechains
by Francois Berenger 27 Oct '11

27 Oct '11

Hello, Is there a way to do this with Phenix? I.e., from a given model, obtain models with different but also reasonable sidechains conformations. N.b.: I don't have X-ray data so I am looking for a geometric thing, and I'm OK if the model's backbone undergoes some small movement because of the sidechains having moved. Thanks a lot, F.

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Molecule and maps will not load into coot from Phenix 1.7.1-743
by Yuri 27 Oct '11

27 Oct '11

Read the thread I waas just a part of maybe it is related -- Yuri Pompeu

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Re: [phenixbb] COOT not "connected" to PHENIX
by Yuri 25 Oct '11

25 Oct '11

I installed the version with python embedded in coot And it works!! Thanks a lot!! On Tue, 25 Oct 2011 11:41:38 -0700, Nathaniel Echols wrote: > On Tue, Oct 25, 2011 at 11:40 AM, Yuri <yuri.pompeu(a)ufl.edu> wrote: >> Now here comes the stupid question... >> How do I fix it? >> Install a different coot version or is it something in my >> architecture? > > Install a different Coot. If you're downloading from Paul Emsley's > page, you need a package with "python" in the file name. I have no > idea whether the Linux binaries distributed by CCP4 have Python or > not > (the Mac version definitely does). > > -Nat -- Yuri Pompeu

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COOT not "connected" to PHENIX
by Yuri 25 Oct '11

25 Oct '11

Hello everyone, I am running 1.7.2-869 and coot 0.6.2 By telling phenix where hte path is, I can get it to launch from any phenix job tab. However in one of my machines, even though COOT launches through phenix it is not connected to it which does not allow me to look at clashes when building in coot- a very useful feature may I add!!! In one of my RHEL5 machines it is working nicely, and I dont see any obvious differences between the working and the non-working one. Any ideas? Thank you much -- Yuri Pompeu

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phenix.phaser generate .sol file
by G Y 25 Oct '11

25 Oct '11

Dear Experts, I run phaser in phenix with GUI and script using params.eff. For both case, I can not find .sol file in the outputs. What option or command I should used in GUI and params.eff to generate the .sol file in the outputs? Thanks for your kind help! GY

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phenix.pdbtools --show-adp-statistics
by Krzysztof Bzymek 24 Oct '11

24 Oct '11

Hi, I noticed that this option is longer supported in phenix 1.7.2-869. Is there an equivalent command that would print out the statistics? Thanks, Chris

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coot from phenix
by Andreas Förster 24 Oct '11

24 Oct '11

Dear all, I'm running phenix 1.7.2-869 on RHEL 6.1 64-bit. When I click on "Open in Coot" after refinement, coot doesn't open and I get the following error in the shell from which I started phenix: /csb/soft/Linux64/share/phenix-1.7.2-869/phenix-1.7.2-869/phenix/phenix/command_line/start_coot.sh: line 33: /csb/soft/Linux/src/coot-0.6/bin/coot: No such file or directory In the script that launches coot, $PHENIX_COOT is defined as /csb/soft/Linux/src/coot-0.6/bin/coot, which doesn't exist (and is a path that we used in the old days of 32-bit). Typing phenix.find_coot_command in the shell from which phenix was started returns /csb/soft/Linux64/src/coot-0.7-rev3689/bin/coot, which is the right coot. To me it seems the phenix script to launch coot is falling back on an internally defined $PHENIX_COOT variable (that's not defined from the shell). That's shouldn't be, should it? How do I fix this short of hardwiring $PHENIX_COOT as /csb/soft/Linux64/src/coot-0.7-rev3689/bin/coot? Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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Unusual CCP4 to Phenix data conversion result
by R.M. Garavito 24 Oct '11

24 Oct '11

In upgrading to CCP4 6.2.0 and Phenix-1.7.2-869 (from CCP4 6.1.13 and Phenix-1.7.1-743, respectively) a bug has crept into reading of the MTZ files. We tend to scale and merge XDS processed data with Scala in CCP4, then use the resulting data in CCP4 and Phenix (with great success I might add). However, I just noticed that in testing the upgraded CCP4 and Phenix on OSX 7.2 (Lion) that the MTZ file is no longer read correctly. An example is below where after the output from scaling and merging of nonanomalous data from the CCP4i GUI gives, at the end of FREERFLAG, some 47,000 reflections. Putting this into xtriage or the reflection file editor in the Phenix GUI, one finds that the data for the F and the DANO columns are used; just selecting Fs alone is impossible. The end result is a doubling of the reflection number and the switching of the anomalous flag on. Processing with earlier versions did not do this except when actually using anomalous data. Why this has happened is not clear to me, but the column order in the MTZ file changed slightly between CCP4 6.1.13 and CCP4 6.2.0. Any ideas, am I missing something, or is this a push to only refine with intensities? Regards, Michael ***************** From Scala (3.3.20) Total number unique : 46813 From FREERFLAG Number of Reflections = 47044 (including non-observed NaN reflections) MTZ column labels H K L FreeR_flag F_S13E_X2 SIGF_S13E_X2 DANO_S13E_X2 SIGDANO_S13E_X2 F_S13E_X2(+) SIGF_S13E_X2(+) F_S13E_X2(-) SIGF_S13E_X2(-) ISYM_S13E_X2 IMEAN_S13E_X2 SIGIMEAN_S13E_X2 I_S13E_X2(+) SIGI_S13E_X2(+) I_S13E_X2(-) SIGI_S13E_X2(-) ****************** In Phenix: Xtriage output choosing "Imean" Miller array info: /Users/garavito/ccp4_projects/sus1_S13/reflections_tmp.mtz:IMEAN_S13E_X2,SIGIMEAN_S13E_X2 Observation type: xray.amplitude Type of data: double, size=46772 Type of sigmas: double, size=46772 Number of Miller indices: 46772 Anomalous flag: False Xtriage output choosing "Fs" Miller array info: /Users/garavito/ccp4_projects/sus1_S13/reflections_tmp.mtz:F_S13E_X2,SIGF_S13E_X2,DANO_S13E_X2,SIGDANO_S13E_X2 Observation type: xray.amplitude Type of data: double, size=88486 Type of sigmas: double, size=88486 Number of Miller indices: 88486 Anomalous flag: True **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: garavito(a)msu.edu ****************************************************************

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phenix.pdbtools
by Abhinav Kumar 21 Oct '11

21 Oct '11

Hi, I had been using the pdbtools to obtain the rmsd on various geometry parameters using the command: phenix.pdbtools my.pdb --show-geometry-statistics Now pdbtools does not recognize the option "--show-geometry-statistics" What is the option now? I am using phenix-1.7.2-869. -- Thanks, Abhinav JCSG@SSRL, SLAC Phone: (650) 926-2992 Fax: (650) 926-3292

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ligands at a special position
by Subhani Bandara 19 Oct '11

19 Oct '11

Hi, I am trying to solve a structure of a protein that is cocrystallized with a chelator complex using phenix (GUI). The complex is Tb(DPA)3 and DPA stands for dipicolinic acid. In the structure (C222) there are few Tb complexes on the two fold axis with symmetry coordinates 1/4X, 1/4Y, Z. In those, Tb and the center C (C4) and N (N1) of one DPA are sitting directly on the 2 fold axis. So I left only half of that DPA ligand structure on PDB file and changed the occupancy of N1 and C4 to 1/2 while keeping the occupancy of all other atoms of the half ligand structure at 1.00. Then I refined it while keeping above occupancies and xyz coordinated of the ligand fixed. After doing this the other half of the ligand could be built by symmetry, but it left a space between two halves(so it was not as one ligand). Can you please let me know what I can do to fix this structure. Also is there a way to keep only x and y coordinates fixed while varying z during refinement. Thanks Subhani

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Re: [phenixbb] Phenix building residues not found in input sequence file
by Thomas C. Terwilliger 18 Oct '11

18 Oct '11

Hi Allan, I assume that there is density showing protein in the region where autobuild is building these extra residues...is that right? If so...then is the remainder of the model matched very well to sequence (i.e., is more or less what you expected to see found, plus there is extra density?) It could be that there is really something in the crystal that you didn't expect. It could also be that part of the structure is not (or not correctly) assigned to sequence, so that this part of the structure really does go with part of your sequence. Does that help? It would be interesting to hear more details of this. All the best, Tom T >> Hi everyone, >> >> Apparently my Phenix (1.6.3-473) is building in extra residues in the >> C-terminal region, which is not found in my input sequence file. >> >> It's trying to build a model which is longer than I expected. Phenix >> building 87 extra amino acids. Any clue what's wrong? >> >> I made sure that these amino acids are not residues found in the >> N-terminal region or anywhere else in the protein. >> >> Allan >> >> -- >> Allan Pang >> >> PhD Student >> >> G35 Joseph Priestley Building >> Queen Mary University of London >> London >> E1 4NS >> >> Phone number: 02078828480 >>

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post-doc position at SSRL
by van den Bedem, Henry 18 Oct '11

18 Oct '11

Modeling Conformational Ensembles of Proteins and Complexes A post-doctoral position with a focus on modeling conformational ensembles of proteins and complexes is available immediately in the Structural Genomics Division of Stanford Synchrotron Radiation Lightsource at the SLAC National Accelerator Laboratory (http://ssrl.slac.stanford.edu). Macromolecules and assemblies are studied by a variety of experimental techniques, including protein crystallography and Small Angle X-ray Scattering. Nano-crystallography and single particle imaging data from the Linac Coherent Light Source (LCLS), a first-of-its-kind free electron laser, are also being targeted at these systems. Accurately modeling the conformational variability of macromolecules is essential to understanding their cellular function. This position at the forefront of computational structural biology aims to develop advanced algorithms to fit domains or proteins to experimental data from multiple sources while allowing for significant conformational changes. The goal is to automatically compute 3-D models, and to provide structural insights into functionally relevant dynamics, especially for time-resolved experiments or a series of static structures. The position offers the opportunity to closely collaborate with the Stanford Computer Science Department and work with X-ray, SAXS and LCLS nanocrystallography data. SLAC houses ample computational resources. Funding is available for up to 3 years. The starting date is as soon as possible. Candidates should have a recent PhD in computer science, applied mathematics, computational biology/crystallography or a related field with strong programming skills. Please send a CV, a short summary of your research experience and two letters of recommendation to Henry van den Bedem (vdbedem(a)slac.stanford.edu). Further details are available upon request. Relevant publications: Yao et al. Sampling-based exploration of folded state of a protein under kinematic and geometric constraints. Proteins: Structure, Function, and Bioinformatics (in press). Fraser et al. (2011) Accessing protein conformational ensembles using room-temperature X-ray crystallography. PNAS 108:16247-16252 van den Bedem et al. (2009) Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers. Acta Cryst. D65:1107-1117

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