Search results for "look through"

Re: [phenixbb] phenix refinement question

by Katarina Moravcevic

Hi Pavel, after reading the paper you suggested I have to admit I am still confused with this discrepancy. In the section that describes specific reasons in R/Rfree discrepancies that could apply to my model, REFMAC and PHENIX supposedly use same principles. So, do these differences come from some slight variations in how for example bulk solvent and anisotropic scaling are treated in two programs? I am sorry for asking basic questions and please do not bother to reply if it is too silly. Thanks Katarina On Mon, Nov 15, 2010 at 4:50 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hello, > > > I have only started using PHENIX and have made an interesting observation. >>> If I run my model through PHENIX refine (individual sites, individual >>> ADPs, >>> occupancies, optimized X-ray/stereochemistry weight, optimized X-ray/ADP >>> weight options selected) I obtain R/Rfree 0.15/0.18 and very nice >>> geometry >>> values (data is to 1.7A). However, if I now take this refined model and >>> run >>> it through Refmac (without any refinement) I obtain R/Rfree of 0.19/0.21. >>> >> > sounds good to me, I would be worried otherwise. > > > Can anyone explain why is there such a big difference? Will this be an >>> issue >>> during PDB submission? >>> >> > Have a look at this: > > J. Appl. Cryst. (2010). 43, 669-676 > phenix.model_vs_data: a high-level tool for the calculation of > crystallographic model and data statistics > P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. > Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart and > P. D. Adams > > > Take a look at what phenix.refine reports for the number of >> reflections used for refinement in the logfile - I believe it will >> discard reflections that are flagged as suspicious (can't remember the >> reference, I think it's one of Randy Read's papers), >> > > It is typically from zero to a few dozens of reflections and unless they > are ~1.e+9 removing them rarely visible in terms of R-factor (if you just > re-compute it). > > Pavel. > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

15 years, 2 months

[phenixbb] phenix-online.org web server issues on Friday?

by Ben Eisenbraun

Howdy PHENIXians, One of my users reported a "Error attempting to get current version list: HTTP Error 500: Internal Server Error" on Friday morning last week. Looking through the source, I see: phenix/phenix/utilities/check_version.py which seems to do a version lookup against: http://www.phenix-online.org/download/get_versions.cgi It would be good to set an explicit timeout on the urlopen so the GUI doesn't hang on network errors, web server blow ups, etc. AFAICT, urllib2 uses the default global timeout for the socket module, but socket has no default timeout, so calls to a broken web server can hang your python program. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

15 years, 7 months

Re: [phenixbb] Refinement with optimize weights

by Pavel Afonine

Hello, have a look at "Improved target weight optimization in phenix.refine" article here: http://www.phenix-online.org/newsletter/ and, make sure you are using the latest version of PHENIX - this is essential: http://www.phenix-online.org/download/nightly_builds.cgi > I wanted to know what parameters should I use for subsequent refinement. Which parameters do you mean? Optimal weights are determined per refinement run. It is not given that in a next refinement run the optimal weights will be the same as in previous one. Since weights optimization takes a long time to run (if you have multiple cpu machine then it can be run in parallel), normally you run it towards the end of refinement and not all the way through. > I would like to know what Fix X-ray/stereochemistry weight and Fix > X-ray/ADP weights are for? In case you have your own weight values, you can specify them and then phenix.refine will use them as is. Pavel

14 years, 4 months

Re: [phenixbb] measuring the angle between two DNA duplexes

by Edward A. Berry

Pavel Afonine wrote: . . > The underlying procedure would do the following: > - extract two sets of coordinates of atoms corresponding to two provided atom selections; > - draw two optimal lines (LS fit) passing through the above sets of coordinates; > - compute and report angle between those two lines? > This could be innacurate for very short helices (admittedly not the case one usually would be looking for angles), or determining the axis of a short portion of a curved helix. A more accurate way to determine the axis- have a long canonical duplex constructed with its axis along Z (0,0,1). Superimpose as many residues of that as required on the duplex being tested, using only backbone atoms or even only phosphates. Operate on (0,0,1) with the resulting operator (i.e. take the third column of the rotation matrix) and use that as a vector parallel to the axis of the duplex being tested.

12 years

[phenixbb] autosol w/ "no merge original index"?

by Bryan W. Lepore

phenix 1.3b of 21-10-2007 confusion w/ "no merge original index" data file in phenix.autosol. this should work, right? caveat - the 'nmoi' hkl is actually from scala, but that usually is fine w/ e.g. solve-2.13. 'nmoi' requires declaration of cell='(numbers)' on command line. phenix.autosol seems to go through all the usual checks fine, then reports (in AutoSol_run_2_/LAST.LOG): ".... The error seems to be at line 0 Here is what the first few lines of this file look like: 1 -987 86.052 86.052 132.608 90.000 90.000 90.000 p41212 You have set the keywords readdenzo and unmerged Please check whether you should have set readformatted or readtrek or premerged ...." ... 'readdenzo' and 'unmerged' are just right for 'nmoi' files. etc. -bryan

18 years, 1 month

Re: [phenixbb] omit maps without density modification?

by Thomas C. Terwilliger

Hi Nathan, If you generate an omit map with two_fofc_in_rebuild=True then all your maps should come from phenix.refine and be the 2FOFCWT PH2FOFCWT maps which are not density modified. It may be slightly confusing because the names of the files will remain the same, and you'll want to look through the log file to confirm that these are indeed the maps from phenix.refine. It will say something like: Saving 2fofc information in cycle_best_2.mtz NOTE: 2fofc map to be used for model-building. It will be copied to overall_best_refine_map_coeffs.mtz and will also be copied to overall_best_denmod_map_coeffs.mtz All the best, Tom T Hi, Is there is a way to calculate simple omit maps and sa-omit maps in phenix without using density modification? The density modification seems to be flattening the weaker regions of my map - when compared to omit maps from cns for instance. Thanks! Nathan _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

16 years, 10 months

[phenixbb] questions about twinned structure and MR

by Christina Bourne

Hello bb, I am new to Phenix and am facing my first twinned structure. While I wait for my copy of Yeates Methods in Enzymology (albeit from 1997) to be delivered, perhaps this bb could answer a few questions? At what point do I detwin, or do I not do it at all? It seems Phenix does this itself, on the fly? Is it refining the twin fraction too? MR (Phaser) finds solutions with twinned or detwinned data. However, the solutions vary by 180degrees, so I suspect I'm finding solutions for both h,k,l and h,-k,-l. These come from two different runs, but one has refined LLgain of 1010.8 (matches soln found with detwinned data, both run through ccp4), and other has refined LLgain of 1073 (through Phenix; it's rotated 180degrees from the other). When performing AutoBuild after AutoMR, should I worry that I haven't assigned Rfree? Does Phenix account for twinning when it does this automatically, or what keyword(s) do I need to include? I see a section in the documentation about refining twinned structures, and am looking forward to getting to that point! I just want to be sure I'm following a "correct" procedure for the steps leading up to that. From the literature, it seems quite common to not account for twinning until refinement. My concern is the two MR solns...which should I use? If I know it's twinned, shouldn't I account for that from the beginning? More details: P41, data good to 2.2A, 2 molecules in the AU, twinning fraction ~0.4. Rmerge from scaling is reasonable at ~11% overall. MR model is 100% identical to this data, but from a different spacegroup (thus I'm running MR). Thanks for any tips or guidance! Christina Bourne ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

17 years, 9 months

Re: [phenixbb] Refining Anomalous Groups

by Brennan Bonnet

Ok. So I used the original mtz file created from my data to determine the heavy atom substructure using HySS which I then used as input for AutoSol. Next I carried the files through to AutoBuild these files are: exptl_fobs_phases_freeR_flags_1.mtz (experimental data) resolve_1.mtz (initial map) overall_best_placed.pdb (ligands, starting model) ha_1.pdb_formatted.pdb (heavy-atom sites) Finally I carried these through to phenix.refine and now is when it complains that my data is no longer anomalous and I can't find a file that phenix is happy with. Everything worked smoothly until this step. Any idea what file(s) I might be looking for? I have tried some data from earlier steps which are unmerged and it still complains. ~Brennan~ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] On Behalf Of Nathaniel Echols [nechols(a)lbl.gov] Sent: Monday, November 19, 2012 8:29 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Refining Anomalous Groups On Mon, Nov 19, 2012 at 6:11 PM, Brennan Bonnet <Brennan.Bonnet(a)lightsource.ca<mailto:[email protected]>> wrote: 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? No, the error message means exactly what it says: you need to supply anomalous data as input. This almost always means that the selected data labels should have "+" and "-" in them, and there will usually be 4 labels (e.g. "F(+),SIGF(+),F(-),SIGF(-)"). Data named "F,SIGF", on the other hand, is almost always merged/non-anomalous (although I think CNS files may break this assumption). -Nat

13 years, 2 months

Re: [phenixbb] Clashscore and average B

by Pavel Afonine

Hi Sam, > I am refining a structure with Phenix.refine and encounter an issue > which I appreciate your comments. The structure is in P1 and refined > to 36A-3A. Rw/Rf = 23.9%/29.1%, RMS bonds 0.002, RMS angles 0.544, > Ramachandran favoured 97.5%. The statistics is acceptable to me This look fine to me too! > but two numbers raised my concern. First is the clashscore of 7.7, > which is below minimum of other structures shown by Polygon. The lower, the better. So this is good! If it's lower than the others (as shown by Polygon) then you are doing better on this one! > Second is an average B of 37, with a minimum of 9.2. When I checked > again in Coot (Average Temp fact. analysis), none of the residues or > water look abnormal. I refined both individual and group B-factors and > applied 'Optimize X-ray/adp weight'. This looks fine too. > So my questions are: > (1) if a clashscore too high means a lot of bad contacts, how do you > comprehend a clashscore too low? How can I modify my strategy to get > around? It can't be "too low". Zero means you don't have any single steric clash, which is good. > (2) is there an acceptable low value of B? (I sort of went through a > similar thread in phenixbb appeared 9 years ago but seems the > discussion did not come to a conclusion). Any advice I should reliax > or tighten the adp restraints? Check out recent thread on ccp4bb: "acceptable difference between Average B-factor and Wilson B". Bottom line, I think what you have is just fine, unless you meaningfully and clearly define "low". Pavel

6 years, 10 months

Re: [phenixbb] Changing an amino acid to an unusual amino acid

by Schubert, Carsten [JRDUS]

Hi Nat, bonds in COOT do not mean much, as they do not translate into bonded interactions in the refinement programs. Phenix for instance tries to figure out the bonding by itself through some distance based heuristics. However in your case it looks as if the CRO residue may not be defined as a polymer, i.e. part of a protein chain in the monomer library you are using. In Windows the monomer library is located in C:\WinCoot\share\coot\lib\data\monomers. Look at the difference in the headers for CYS.cif and CRO.cif or PTR.cif (phosphotyrosine). The aminoacids or modified aminoacids considered part of the peptide chain have all 'peptide' in the header, CRO does not. That is probably the reason why coot does not make any bonds. This would probably cause problems later on with Phenix as well. You could pull out the CRO.cif into your directory, modify it to make it a peptide and read it into coot and phenix during refinement. I would also run it through REEL to make sure the definitions are kosher. HTH Carsten From: Natalia Ketaren [mailto:[email protected]] Sent: Tuesday, June 02, 2015 5:42 PM To: Schubert, Carsten [JRDUS] Subject: Re: Changing an amino acid to an unusual amino acid Hi Carsten, Th residue is a part of the correct chain. It just doesn't make an bonds with the residues on either side of it. Is this common for unusual amino acids when adding to the main chain? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/ On Jun 2, 2015, at 5:26 PM, Schubert, Carsten [JRDUS] <CSCHUBER(a)its.jnj.com<mailto:[email protected]>> wrote: Hi Natalia, if the missing/wrong chain IDs are really the problem you can change them in COOT under Calculate -> Change Chain IDs. The dialog is a bit tricky, since you probably have to use the correct residue range to change an individual residue into an existing chain. In your case I would write out the PDB file and use a text editor to change the chain ID and move the residue into its correct place in the file. HTH Carsten From: phenixbb-bounces(a)phenix-online.org<mailto:[email protected]> [mailto:[email protected]] On Behalf Of Natalia Ketaren Sent: Tuesday, June 02, 2015 5:17 PM To: phenixbb(a)phenix-online.org<mailto:[email protected]> Subject: [phenixbb] Changing an amino acid to an unusual amino acid Hello All, I'm working on a GFP structure and I'm trying to incorporate the CRO (chromophore) residue into the structure using coot. My process is to use Extension->Modelling->Replace residues, where it's suppose to replace a Tyr residue. I type the 3 letter code, CRO, the residue appears, I'm able to real space refine it, but it does not incorporate CRO into the desired chain. Would someone be able to help me figure out what I'm doing wrong? And possibly walk me through a solution? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

10 years, 8 months

Search results for query "look through"