Search results for "look through"

[phenixbb] Difficult MR with TNCS

by Ian Slaymaker

Dear Phenix Community, I am having difficulties solving a protein-DNA complex structure and was hoping for some ideas or strategies. My data diffracts to 3A and depending on how I index my data fits well into I4 or P4. I have also been exploring everything in lower space groups. My MR model has 64% identity to my unsolved protein. The crystal protein is 24kD and runs as a monomer or sometimes a dimer. Xtriage strongly suggests that there is tNCS due to a strong patterson peak at 0.5, 0.5. 0.5. Using the phaser GUI, when I search around P4, I get very promising statistics (TFZ = 20's and LLG ~2000), and oddly, in these cases phaser places two subunits on top of each other (despite default packing limitations) with the protein beta sheet cores overlapping, and rotated 180 degrees of each other. The density looks believable, but obviously something is very wrong. The crystal packing would be feasible if another subunit were placed, but I have been able to coax phaser to find a complete solution. It would rather place it overlapping than in available spaces. My questions: 1) does this suggest that there is some form of twinning going on? 2) sometimes phaser (phenix GUI) tells me it is adjusting for tNCS and sometimes it says its NOT (even when there is an even number of subunits being searched for), is this a bug or deliberate? 3) I have tried using phaser from the command line in MR_AUTO mode with the keywords TNCS_USE ON TNCS PATT PERCENT 88 TNCS_NMOL 2 or 4 but dont see any indication that the TNCS adjustments are being made and I have not been able to repeat my phaser GUI results this way. 4) What is a good strategy for tackling this particular problem? Right now I am just chugging through my list of possible space groups, compositions and resolution ranges, but need to look through each possible solution individually because of the misleading statistics and so is very inefficient and time consuming. Thank you for any help or comments. Ian

12 years, 7 months

Re: [phenixbb] Phenix-RSR model fit issue in CS-Map

by pramod kumar

Dear Pavel, Thank you so much for the consideration, I have shared the file with you. Best regards, Pramod On Tue, Oct 22, 2019 at 7:26 PM Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Pramod, > > I need to see the map and models before and after refinement to diagnose > the issue. Can you share the files? I will have a look once I have the > files. > > Pavel > > On 10/22/19 10:34, pramod kumar wrote: > > Dear Experts, > > I have a map generated through cryosparc (ab initio-reconstr and > homo-refine at 3.7A* FSC and sharpened in Scipion and separately in EMAN2). > I have build the initial pdb through BALBES which has perfect validation > parameters and nice fitting in the map (with the mtz output) but the > co-ordinates are shifted from the true origin of CS-map. I used phenix-RSR > to fit and refine, but validation results remained too far to accept the > model as good solution and also a small region entered in wrong nearyby > densities. > > So far following independent and downstream approaches I have taken:- > > In phenix; dock in map, map to model, rigid body refine followed by real > space refine (with both .map and converted .mtz), using only chain A-map > boxing and model generation through NCS. > > I have tried chimera fit for entire assembly and also only one chain in > boxed map and full map but still the validation remained far from > acceptable values and a small region in wrong neighboring density. > > Please help. > > > -- > Best regards, > Promod > > >

5 years, 8 months

Re: [phenixbb] phenix.refine & twinning

by Pavel Afonine

Hi Nick, I looked through the files you sent and it looks like a bug in phenix.refine (someone reported the same problem before). Sorry about this. I fixed this bug yesterday so please use the latest PHENIX version from nightly builds available after January 17: http://www.phenix-online.org/download/nightly_builds.cgi Meanwhile a quick work-around is to remove a PDB file header (all REMARK 3 records) from input PDB file. Also, to make sure using twinning in refinement will make any difference (at least R-factor wise), run this command: phenix.model_vs_data model.pdb data.mtz and see it it tells the data is twinned. Please let me know if you have any questions. Pavel. On 1/17/11 11:53 AM, Nicholas Cody Sennett wrote: > > Can phenix detwin data? I have tried to input the twinning law > (l,-k,h) but phenix.refine does not create the appropriate maps and > there is no appreciable change in R-factor. I have attached my xtriage > and refinement logs. >

14 years, 5 months

[phenixbb] High B-factors after Phenix restrained refinement

by Da Duan

Hi all I am rather new to the crystallography so please bear with me, :-). I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of rigidbody refinement with Phenix Refine I proceeded to restrained refinement. The R/Rfree from the refinement decreased nicely as expected but the B average is at ~100 (using Group B factor refinement option). I took the same model and mtz through Refmac and the B average is about ~40. Has anyone experienced this before? I am almost positive it maybe a setting issue in Phenix Refine that i should be looking at to get the B factors to refine correctly. Thanks in advance for your help! Da Duan

13 years, 6 months

[phenixbb] error when running REEL

by Sabine Schneider

Hi everyone, I would like to use REEL, but get the following error message and only parts of the gui are displayed. (python:7745): Gtk-Warning **: GModule initialization check failed: Gtk+ version too old (micro mismatch) I looked through repositories, but am not entirely sure what I need to update. I am using Suse10.3 (x86_64) Thanks a lot for your help in advance! Sabine ------------------------------------------ Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/

16 years, 11 months

Re: [cctbxbb] Inserting F000 into reflection (mtg) file

by Pavel Afonine

Hi Nick, > I’ve been looking through the cctbx/phenix scripts and although there’s a script for estimating F000 (phenix.f000), I can’t find any way of inserting it into an mtz file to make it accessible for easy map generation. Is this implemented anywhere/what do people use as the best way of doing this? > > If the insertion of F000 into an mtz file has been purposefully avoided, I presume it's done because we don't want the possibility of someone refining a model where F000 is used in refinement. Unless there’s another reason? have a look at fft_map method of miller class (cctbx/miller/__init__.py) - it takes f_000 as an optional parameter. If you just want to add it to existing miller_array then it is something like this: f_obs_new = f_obs_old.customized_copy( indices = f_obs_old.indices().append((0,0,0)), data = f_obs_old.data().append(VALUE)) then you can dump into MTZ file: mtz_dataset = f_obs_new.as_mtz_dataset(column_root_label="F-obs") mtz_object = mtz_dataset.mtz_object() mtz_object.write(file_name = "data.mtz") You need to have an estimate of F000 (which includes contributions from macromolecule and bulk-solvent). Pavel

8 years, 10 months

Re: [phenixbb] phenix refinement question

by Steiner, Roberto

Dear Katarina I would suggest you post the same question to the CCP4bb and hopefully Refmac users/experts will comment on this. It is always very difficult to understand what's going on without having a look at input/output files. Best wishes Roberto From my iPhone On 15 Nov 2010, at 23:25, "Katarina Moravcevic" <katarinm(a)mail.med.upenn.edu<mailto:[email protected]>> wrote: 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 <<mailto:[email protected]>pafonine(a)lbl.gov<mailto:[email protected]>> 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 <mailto:[email protected]>phenixbb(a)phenix-online.org<mailto:[email protected]> <http://phenix-online.org/mailman/listinfo/phenixbb>http://phenix-online.org/mailman/listinfo/phenixbb <ATT00001..c>

14 years, 7 months

Re: [phenixbb] Submitting SLURM jobs through PHENIX GUI

by Billy Poon

Hi Tom, Can you provide your submission script to your cluster? I think we only call sbatch with no other parameters. We do not have access to a slurm cluster, so we do not do any real testing. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Fri, Oct 26, 2018 at 10:54 AM Thomas Cleveland < thomas.cleveland(a)gmail.com> wrote: > Hi all, > > Has anyone gotten SLURM job submission to work through the PHENIX GUI? > > Under Preferences/Processes, I set Queueing system to SLURM with queue > submit comand "sbatch." The job does indeed submit to the queue, and I can > see it in the listing using the "squeue" command. However, there is quickly > an error, "OSError : [Errno 2] No such file or directory: > '/home/clevelandt/data/MX/181016_P1_merge/phenix/.phenix/tmp/10.libtbx_info.LOCK'". > > I've attached the full error log. Basically the program is looking for a > lock file that isn't there. I'm not sure why it's not there. All compute > nodes should have access to this directory, and there is no caching of any > kind, so any files placed there should immediately be accessible. > > I can manually submit e.g. phenix.refine jobs to the queue using the > command line and everything works fine. It would be really nice to have it > through the GUI though. > > Thanks for any help, > Tom > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

6 years, 8 months

Re: [phenixbb] How to define Fobs labels for phenix.refine in command line mode

by Phil Jeffrey

Try something in the form of: refinement.input.xray_data.labels="Fobs,SigFobs" usually if you make a guess and do: phenix.refine labels="Fobs" it'll return the list of possibilities: Best matches: refinement.input.neutron_data.labels refinement.input.xray_data.labels refinement.input.experimental_phases.labels although looking through the .eff/.def files will often make it clear. Cheers Phil Jeffrey Princeton On 9/27/16 11:00 AM, Karthikeyan Subramanian wrote: > Dear All, > > Is it possible to define the Fobs (or) Iobs labels for phenix.refine in > command line mode? > > Thanks > > Karthikeyan S. > > IMTECH, Chandigarh > > India

8 years, 9 months

Re: [phenixbb] High B-factors after Phenix restrained refinement

by Pavel Afonine

Hi, > I used Phenix AutoMR to solved a structure to 3.3A and after 1 round > of rigidbody refinement with Phenix Refine I proceeded to restrained > refinement. The R/Rfree from the refinement decreased nicely as > expected but the B average is at ~100 (using Group B factor refinement > option). I took the same model and mtz through Refmac and the B > average is about ~40. Has anyone experienced this before? I am almost > positive it maybe a setting issue in Phenix Refine that i should be > looking at to get the B factors to refine correctly. do restrained individual ADP (B-factor) refinement. With the type of restraints that phenix.refine is using it is totally ok at 3.3A resolution. Pavel

13 years, 6 months

Search results for query "look through"