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Re: [phenixbb] phenix.find_ncs and DANO
by Tom Terwilliger 24 Jan '08

24 Jan '08

Hi Bryan, >in principle, phenix.find_ncs should be fine with FP=DANO, right? I'm not quite clear on this, but yes, find_ncs wants a map, and you can give it any map coefficients with labin="labin FP=FP PHIB=PHIB FOM=FOM " >and - do i understand correctly that phenix only correlates the map with >the .pdb sites, and does not rotate the map about itself (like in getax, i >think)? Correct, find_ncs is looking for NCS in the heavy-atom sites as presented in a PDB file, or in a model as given in a PDB file, without rotating the map. Any crystallographic symmetry is automatically applied. >-bryan > >p.s: > >i can run phenix.find_ncs with FP=DANO, but seems that resolve wants it to >be FP as usual. It might be helpful if you could send me this example! I hope that helps! -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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high resolution refinement with phenix.refine
by Pavel Afonine 22 Jan '08

22 Jan '08

Dear phenix.refine users: responding to Vijayalakshmi Janakiraman's questions about refinement at high resolution with phenix.refine, I finally documented this functionality of phenix.refine and supplied it with a small example. This paragraph (see attached HTML file) will be available as part of phenix.refine documentation in the next release of PHENIX and CCI Apps. *Important:* writing this text I assumed that the latest version of phenix.refine is used (currently, it is one from CCI Apps: /2008_01_09_2058/ , http://www.phenix-online.org/download/). Cheers, Pavel. >> I have a high resolution structure with NADP as ligand bound to it. >> I was using CNS to start with. Somehow the Rfree was always very >> high. But when I tried with default options of data= and model=, >> in phenix.refine with the whole data and the intial rigid body >> refined coordinates from CNS, the Rfactors came down to 31%. I have >> now decided to do refinements with phenix.refine. >> Do you suggest any protocol for refinement of structure at this high >> resolution starting from initial rigid body refinements? >> Since I would like to handle alternate conformations in the final >> steps. I am wondering if the 2007 July version could handle >> refinements of alternate conformations. >> Thanks, >> Viji

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Re: [phenixbb] Autosol Feedback and questions
by Tom Terwilliger 22 Jan '08

22 Jan '08

Hi Partha, At 03:53 AM 1/2/2008, you wrote: >Happy new year everybody, > >I had quite a bit of difficulty with a SAD dataset which also showed >Sulphur. Previously I had tried SHELEX to find sites, MLPHARE to >refine, AddSOLVE to find more , and both SOLVE and PHASER to solve >but it did not get to a point where I could do manual building. >Autosol worked beautifully, the input files were scalepack merged >data, ha.pdb (from addsolve step), and the sequence. PHASER to solve >and TEXTAL & RESOLVE with through build option. > >This actually leave me with some confusions / questions: > >1. When I compare the other "solutions", they look like the right >one, just not good enough. Where exactly is the autosol making a >difference? Is it the ability of of TEXTAL to build something more >meaningful when the solution is not good or number of iterations? Autosol uses the quality of the model built as a score, if any model is built (R-factor if < 0.40; number of residues built less 2 * number of chains otherwise).. If no model is built, it uses the standard 4 or 5 criteria that are printed out on the AutoSol wizard screen (CC and R-factor for density modification; skew of electron density histograms, FOM, CC of NCS). >2. How does PHASER know the different anomalous atoms? Does is use a >different scaling factor for SE and S? It can tell by the ratio of anomalous to real scattering corresponding to each atom. >3. I see that phenix.refine has been used in the internal runs, I >have used phenix.refine earlier. But after playing with the side >chains in Coot, when I tried to use the modified pdb file and >resolve.mtz, it complained about the good old Free_R flag. However, >it ran directly in Refmac. Is it a known problem or maybe I did >something stupid? I could do a dry run and change the read mtz and >not cns if that would solve the problem. As Pavel and Ralf have mentioned, this is because AutoSol has tossed a few (usually blank) reflections from your reflection file when it created the refinement file exptl_fobs_phases_freeR_flags_15.mtz # or something similar. Without the "_15" if from AutoBuild The solution is to either (1) use the refinement file from AutoSol (exptl_fobs_phases_freeR_flags_15.mtz), or to delete the MD5 remark record from the AutoSol/AutoBuild PDB file. >4. Lastly, is it possible to use multiple processors to run the job? As Pavel mentioned...we are thinking about this but do not have anything yet. -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Re: [phenixbb] Continue from an AutoBuild job abruptly killed
by Tom Terwilliger 22 Jan '08

22 Jan '08

Hi Miguel, I'm sorry for the slow response...you can continue AutoBuild by typing: phenix.autobuild run=1 if you were previously on run #1 and you want to continue it. All the best, Tom T At 02:24 AM 1/16/2008, you wrote: >Dear all, > >We had a problem with a machine running >AutoBuild, which resulting in the computer going >down and the AutoBuild job consequently killed. >I've tried to find out if there is a way to >continue the job (it had been running for four >days and still had a few hours to go I guess: a >pretty big unit cell) but I failed. I would >appreciate if someone could point to the >relevant pages in the manual/tutorials or give >me advice about how to do such a thing. If that's possible, of course. > >We're using the latest phenix (1.3b-rc6) and cci apps. > >Thank you! > > >Miguel >-- ><http://www.pangea.org/mol/spip.php?rubrique2>http://www.pangea.org/mol/spip.php?rubrique2 > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Je suis de la mauvaise herbe, >Braves gens, braves gens, >Je pousse en liberté >Dans les jardins mal fréquentés! > >Georges Brassens >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Re: [phenixbb] picking Rfree set
by Peter Zwart 22 Jan '08

22 Jan '08

yes, it will. This is useful for when the data is twinned. P 2008/1/22, David Garboczi <dgarboczi(a)niaid.nih.gov>: > So, for instance, when addition of a ligand to a P212121 cell (1 mol) > changes the symmetry to P21 (almost same cell, but 2 mol), the > selection of the Rfree set from the P21 data by phenix.refine will > take the higher almost symmetry into account? > > Dave > > >btw3: the lattice symmetry is taken into account when choosing an free > >set in phenix.refine (unless specified otherwise). If all NCS > >rotational operators are approximately parallel to twin laws, you > >should be fine. > > > >P > > > > > > > > > > > >2008/1/22, Ralf W. Grosse-Kunstleve <rwgk(a)cci.lbl.gov>: > >> > Does phenix.refine take NCS into account when picking the Rfree set? > >> > Thin shells, or other strategy... > >> > >> The short answer is no. > >> We had long internal discussions about this without reaching a final > >> conclusion. In the long run we may integrate alternative R-free set > >> distributions in phenix.refine; in the meantime you have to use > >> an external program (e.g. dataman or sftools). > >> BTW 1: just to prove that we have thought about this subject, we have a > >> simple tool for "visualizing" distributions of R-free flags: > >> iotbx.r_free_flags_accumulation your.mtz > >> It writes a file with x,y pairs which you can plot with e.g. Excel > >> or any other 2D plotting program. > >> BTW 2: The free reflections aren't as free as one may think. When > >> using a maximum likelihood target (any program), the free reflections > >> are used in the estimatation of the error model. This estimation > >> becomes more tricky if the reflections are distributed in thin > >> shells. I.e. if you go to thin shells you may in fact account to some > >> degree for the NCS, but at the same time you compromise the error > >> model estimation. > >> Ralf > >> _______________________________________________ > >> phenixbb mailing list > >> phenixbb(a)phenix-online.org > >> http://www.phenix-online.org/mailman/listinfo/phenixbb > >> > >_______________________________________________ > >phenixbb mailing list > >phenixbb(a)phenix-online.org > >http://www.phenix-online.org/mailman/listinfo/phenixbb > > > -- > David N. Garboczi, PhD > Phone: 301-496-4773 > Investigator, Structural Biology Section (SBS) > Laboratory of Immunogenetics (LIG) > National Institute of Allergy and Infectious Diseases (NIAID) > National Institutes of Health (NIH) > Twinbrook 2/Room 110 > 12441 Parklawn Drive > Rockville, Maryland 20852-1742 > Fax: 301-402-0284 > Email: dgarboczi(a)niaid.nih.gov > > > > > The information in this e-mail and any of its attachments is > confidential and may contain sensitive information. It should not be > used by anyone who is not the original intended recipient. If you have > received this e-mail in error please inform the sender and delete it > from your mailbox or any other storage devices. The National Institute > of Allergy and Infectious Diseases (NIAID) shall not accept liability > for any statement made that are the sender's own and not expressly made > on behalf of the NIAID by one of its representatives. > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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picking Rfree set
by David Garboczi 22 Jan '08

22 Jan '08

Does phenix.refine take NCS into account when picking the Rfree set? Thin shells, or other strategy... Dave --

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Re: [phenixbb] autosol : input_ncs_file
by Tom Terwilliger 22 Jan '08

22 Jan '08

Hi Bryan, No, autosol does not let you tell it what the NCS is with input_ncs_file. This is a good idea, however... -Tom T At 06:45 PM 1/15/2008, you wrote: >using PHENIX VERSION: 1.3b of 20-11-2007. > >does phenix.autosol use "input_ncs_file"? > >the documentation implies that phenix.autosol will take `input_ncs_file` >(at the 'find_ncs' entry, "input_ncs_file" is mentioned but no where >else), yet, i get a 'Sorry, unknown file or keyword:' message with no such >command line option listed. > >-bryan >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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modify_start_model.adp.set_b_iso doesn't seem to work on PDB files with ANISOU cards
by Stephen Graham 21 Jan '08

21 Jan '08

Hi all, I just tried to reset my B values to the wilson B before TLS refinement (in an attampt to shake some model bias that I am sure is hiding somewhere in my temperature factors...). My start model was a TLS-refined PDB file from phenix.refine (hence with ANISOU cards). I issued the following command: > phenix.refine my_model.pdb my_data.mtz modify_start_model.adp.set_b_iso=60 output.prefix=my_model_resetB main.number_of_macro_cycles=0 As far as I can tell, this should reset my B values to 60 and then exit. However, when I look at the resultant PDB file the Bs for all the solvent molecules 60 but for the protein they are not; rather the protein Bs are almost identical to the starting PDB file. If I try to remove the TLS-derived ANISOU cards by adding the command line option "adp.convert_to_isotropic=true" the result is the same (except the output PDB file no longer has ANISOU cards). However, if I strip out the ANISOU cards from my starting pdb file and _then_ run the above command the resultant PDB file _does_ have the correct values for both protein and solvent. It seems like modify_start_model.adp.set_b_iso=60 does not work when atom has an ANISOU card. The behaviour I would *expect* would be for the adp be reset to an 'isotropic' 60 (i.e. set the diagonal elements to 1 and the off-diagonals to 0). Is this a bug, or am I doing something silly? Cheers, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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d_min_textal=
by Bryan W. Lepore 19 Jan '08

19 Jan '08

the documentation says : "Textal has an optimal high-resolution limit of 2.8 A" is that to say that resolutions != 2.8 are not optimal? -bryan

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Re: [phenixbb] disulfide bonds in phenix.refine
by Ralf W. Grosse-Kunstleve 18 Jan '08

18 Jan '08

Hi Allister, > 1) How do I specifically prevent a disulfide bond from being defined > between two sulfurs that are close together (I tried manipulating the > "disulfide_distance_cutoff" variable but this doesn't seem to stop a > disulfide being formed). If you set, e.g. disulfide_distance_cutoff=0.1 you shouldn't get any disulfide bonds anymore. I just tried it on a small structure and it worked as expected. > 2) How can I soften the restraint on the disulfide bond length for > specific cysteine residues. With the current phenix.refine you cannot edit the automatically determined disulfide bonds (sorry). However, you can use disulfide_distance_cutoff=0.1 to turn off the automatic bonds. Then use geometry_restraints.edits (see documentation at http://phenix-online.org/documentation/refinement.htm) to define the disulfides manually one by one, with the ideal distances and sigmas you want to use. Use a log file from a previous phenix.refine run to obtain the list of all disulfides. Ralf

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