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Small issue with residue PTR
by Terry Lang 14 Nov '11

14 Nov '11

Hey Everyone, I have found a small issue with atom naming for residue PTR. When phenix.ready_set adds hydrogens to the residue, it names the hydrogens connected to the CB atom to be HB3 and HB2. However, the hydrogens in the cif file located in chem_data/mon_lib are labeled HB1 and HB2. Manually changing either the cif file or the atom name in the pdb file solves the problem. Terry -- P. Therese Lang Post Doc Alber Lab, UC Berkeley

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How can I add another chain to my PDB by Coot
by Dialing Pretty 14 Nov '11

14 Nov '11

Dear All, By Phenix refine I got a PDB (Only one chain) and mtz output files. After analysis by Coot I find I need to add a protein fragment so that a large blob will disappear. I know I use Baton to construct the protein fragment. Will you please tell me how can I input the sequence file of the protein fragment so that I can refine the protein fragment by Coot? I am looking forward to getting your reply. Regards. Dialing

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twin/pseudo-symmetry question
by Green, Todd 11 Nov '11

11 Nov '11

Hello all- I have a question regarding the possibility of twinning and or psuedo-symmetry. I have a crystal that processes well in R32, ie. less than 6% r-merge at 2.2 angstrom. We collected multiple potential derivatives and were able to get some phasing from one that was good enough to model in the helices. The strange thing is that when looking at the harker sections there were a lot of unexplained strong peaks. And there is a very narrow range of parameters that we could get the sites with Shelx and end up with interpretable maps(i know that this part might not be unusual). My first thought was that there could be twinning. Since there is no twin law for this space group, I thought that it might suggest that there was twinning in a lower symmetry space group and/or that we have a pseudo-R32 crystal. Processing works well in C2 and R3, as expected. In those cases Xtriage suggests that the real symmetry is likely to be R32. In the case of C-2, xtriage suggetss if it is twinned then it is about 45% twinned. That's the background. Fast forward with the help of phenix Autobuild and some manual correction, we have been able to refine the structure with the R32 processed data(with tls) to r_work = 0.1894, r_free = 0.2287, bonds = 0.007, angles = 0.908 at 2.2 angstrom with almost everything accounted for. I think I should be quite comfortable with this. BUT, I'm still wondering about those Harker sections. I've been reading the manuscripts of Dauter regarding twinning and I think I am at this point more curious than anything. But not leaving well enough alone, I went back to the data processed in C2. I can easily do molecular replacement, following refinement at 2.3 angstrom(I need a lot more frames for this sg so the cutoffs are a bit lower but r-merge is ~ the same as R32) with TLS I get r_work = 0.1850, r_free = 0.2249, bonds = 0.007, angles = 0.946. this doesn't seem significant to me. However if I refine with the two possible twin operations, the values drop with one being better than the other. both have the same starting model: r_work = 0.1639 r_free = 0.1880 bonds = 0.006 angles = 0.902 r_work = 0.1582 r_free = 0.1866 bonds = 0.006 angles = 0.891 The twin fraction from the refined pdb header is 0.544 for the better statistical model and the r-values seem too low for 2.3 angstrom data. Is the high twin fraction suggestive of the higher symmetry space group or inconclusive towards that. of interest is that the maps look better to me than the r32 maps. by that i mean that the maps don't have what i would call minor dots of negative density for some(not a lot) of the side chains as we see for some side chains in the R32 case. also some side chains look better in the C2 twin refined case. Lastly for some of the monomers(there are now 6 copies versus 2 in the R32 case), I can add an additional residue or two on the termini which are not seen before. I wonder if this also suggests that the true space group is C2. Are these r-values too low? does the difference in values according to each twin law mean something? In the end, the models are essentially the same in either space group (with the exception of a couple of residues at the termini). So, I don't think I learn much one way or the other. But the curiocity keeps coming back. So is it likely to be R32 or C2 or C2 with a hefty twin fraction? Anyone have an explanation? Thanks in advance- Todd

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peptide link problem solved LINKR in pdb is not recognized but LINK is
by Christian Roth 10 Nov '11

10 Nov '11

Hi, In my pdb from Refmac the keyword LINKR is used but only LINK is interpreted by phenix. I changed this and now it works as it should. Sorry, a careful analysis sometimes help. Regards Christian

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peptide link
by Christian Roth 10 Nov '11

10 Nov '11

Hi, I have an modified aminoacid in my peptide chain (backbone modified). I have a cif file and I refined it previously in Refmac. I put the Link definition in the pdb and Refmac has interpreted the peptide link as I wanted. Now I did a run in phenix to compare the results and the chain is broken I created the SNN cif file with ReadySet Reel and I tried to incorporate the link definition via GUI in the following way apply_cif_link: data_link: TRANS residue_selection_1: chain A and resseq 366 residue_selection_2: chain A and resseq 367 apply_cif_link: data_link: TRANS residue_selection_1: chain A and resseq 367 residue_selection_2: chain A and resseq 368 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7983 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 496, 7926 Unusual residues: {'SNN': 1} Classifications: {'undetermined': 1, 'peptide': 495} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 37, 'TRANS': 456, None: 2} Not linked: pdbres="ASP A 366 " pdbres="SNN A 367 " Not linked: pdbres="SNN A 367 " pdbres="GLY A 368 " Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 This fails with an error message that it cannot interpret the links. In my previous pdbs I have also defined the atoms which I wanted to link. Maybe I have to do this also somhow in Phenix. I have tried to extract the Link definition using phenix.link_edits but the resulting .edits file is empty. How can I resolve issue? Thanks Christian

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Rebetta fragment library
by Wei Shi 10 Nov '11

10 Nov '11

Hi everyone, I am trying to generate a fragment library in Rebetta server for my sequence of interest to use with mr_rosetta. I can open the 9-mer and 3-mer fragment results: aat000_09_05.200_v1_3 and aat000_03_05.200_v1_3, but didn't see link to download these two files. Does anyone know how to download these two files? If I do copy and paste, what file type or format is compatible with mr_rosetta? Thank you so much! Best, Wei

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define angle between groups of atom 'planes' for refinement restraint?
by Francis E Reyes 10 Nov '11

10 Nov '11

Hi all I was wondering if there was language in the monomer restraint libraries (.cif) or a custom phenix.refine geometry restraint a that defines an angle between two planes, where each plane is a group of coplanar atoms. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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nproc for autobuild
by Michael Thompson 09 Nov '11

09 Nov '11

Hello, I apologize if this question seems very basic, but I am new to phenix.autobuild. I would like to set up a series of phenix.autobuild runs on our cluster, and would like to maximize the speed. I am trying to make single rebuilt models using the command below: phenix.autobuild data=data.mtz model=coords.pdb map_file=map_coeffs.mtz multiple_models_number=1 n_cycle_rebuild_max=5 ncycle_refine=5 s_annealing=true refine_with_ncs=True place_waters=True nproc=?? run_command=/home/qsub.sh The AutoBuild documentation says "if you are using rebuild_in_place=False, then use nproc=4" and "if you are using rebuild_in_place=True, then use nproc=5. (Any more will not make any difference)." My interpretation of the documentation is that for the above AutoBuild run with multiple_models_number=1, I should set nproc=5 (or 4?). Is this correct? Also, if I were to change the command so that multiple_models_number=10, should I then use nproc=50 (i.e. 5 processors per model), or is it still the case that setting nproc>5 doesn't make a difference? Thanks in advance for your help! 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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phenix.phaser output .param file
by G Y 08 Nov '11

08 Nov '11

Dear Experts, I run my script for phenix.phaser in bash shell and one of the output file is filename.param (please note there is no "s" at the end of param) There are only two lines inside this file: # [no title set] TNCS IGNORE ON I do not really know what this file doing for. And, if I run the phaser from GUI, I will not find any .param file. What is this file doing for? Is it some kind of redundant information which is not useful at all? What should I edit in input params.eff file to avoid this output file? I would appreciate to any help from you. Thanks. Best, G

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Constrained group refinement
by Christian Roth 08 Nov '11

08 Nov '11

Dear all, I defined the following contrained groups which should a ligand in two alternative forms and an ion at the same position refine to an summed occupancy of 1. constrained_group { selection = chain Z and resname 2CL and altloc A selection = chain Z and resname 2CL and altloc B selection = chain r and resname Cl } constrained_group { selection = chain c and resname 2CL and altloc A selection = chain c and resname 2CL and altloc B selection = chain m and resname Cl } constrained_group { selection = chain N and resseq 69 and altloc A selection = chain N and resseq 69 and altloc B selection = chain o and resname 2Cl } } At the end I get an error because of the very small nonbonded interactions. it seems that my definition are not correct, but I am at the moment unsure why. Could someone point me to the mistake. Thanks in advace for your help Best Regards Christian

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Constrained group refinement Addendum
by Christian Roth 08 Nov '11

08 Nov '11

Do the ions have to be altlocC for the group definition? Best Regards Christian

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Cross Validation Reflection Set question
by Yuri 07 Nov '11

07 Nov '11

Thanks for the replies. >I just tried doing this, and it looks like the R-free flags will cover >the full resolution range, at least with the current code. By current code, you mean 1.7.2-869 and newer, right? >Is this really necessary in this case (refine against lower res data, >then continue with the whole data set I think I have a backbone shift in this structure (relative to native protein used for MR) so I wanted to do it this way befor trying to go all the way down to 2A. One last question does phnix do NCS averaging to improve maps? -- Yuri Pompeu

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Re: [phenixbb] AutoBuild runtime
by Nathaniel Echols 07 Nov '11

07 Nov '11

On Mon, Nov 7, 2011 at 9:14 AM, Shya Biswas <shyabiswas(a)gmail.com> wrote: > Thanks for the suggestions. Unfortunately my MR solution is not good enough > to get a good map. Autobuild does give me a solution when i put in my > sequence but the map does not look good. I was wondering if the final model > that Autobuild gives has undergone density modification. Strictly speaking, it's the map that undergoes density modification - but yes, this will be done unless you explicitly disable it. -Nat

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Cross Validation Reflection Set question
by Yuri 06 Nov '11

06 Nov '11

Dear All, Here is the situation, I have data to 2 A. I refined the model to 3 A first with S.A. Now I want to use higher res data for the rest of refinement. My Rfree created in the first round when I only used data to 3A. Was Rfree set created using all the data or just up to 3A shell? or do I have to extend into higher res shells? one caviot is I had twin law h,-k,-h-l enabled when they were created. Thanks, -- Yuri Pompeu

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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 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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