- phenixbb - phenix-online.org

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 31 Oct '11

31 Oct '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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