Search results for "look through"

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

14 years, 1 month

Re: [phenixbb] Refinement Strategy vs. R gap

by Yuri

Nat, I checked the log file and it looks like it picked residues to be anisotropic, but when I re-ran it with the automatic selection it did not. Sometimes I have to exit out and re open the GUI so it picks up on changes. On a different note, I am having trouble running TLS. After I find the optimal number of groups (either through phenix or TLSMD server) my selection shows up on the GUI but there is no button that lets me close that window to move on with the refinement. The only way to close that window is by hitting Cancel, clearly not what we want... If I dont close the window, phenix.refine says I am still editing TLS params and will not start obviously. any light? -- Yuri Pompeu

14 years, 10 months

Re: [phenixbb] Where is phenix.refine finding starting r values?

by Pavel Afonine

Hi Aaron, this is because Refmac reports residual B-factors in ATOM records and the TLS component is stored in PDB file header that is ignored when you run phenix.refine (slides #30-36): http://www.phenix-online.org/presentations/neutron_japan_2009/phenix_japan_… It is not a problem if you run an equivalent refinement in phenix.refine, since within a macro-cycle or two it will be equilibrated. Pavel. On 1/18/10 6:47 PM, Bart, Aaron G wrote: > Greetings, > > I am fairly new to crystallography, and have just started to use Phenix for structural refinement. I am currently working on a 2.8A structure that was run through multiple rounds of rigid body refinement via Refmac and manual revision using Coot. I eventually got stuck where large portions of my molecule had very poor density and the rwork and rfree stayed around 0.3. I then performed a TLS refinement which resulted in better density, and tried running it through phenix.refine with default ADP settings, as well as simulated annealing. It worked beautifully, however when I looked at the log file for the refinement, phenix was reporting a starting rwork and rfree that represented my first stage of refinement in refmac, 0.38/0.44. My question is, is phenix somehow neglecting the refinement that was done in refmac? > > Regards > -Aaron > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

16 years

Re: [cctbxbb] sparse matrix

by Luc Bourhis

On 6 Jun 2014, at 15:40, David Waterman <dgwaterman(a)gmail.com> wrote: > I don't intend to assign any particular index in the matrix_column > more than once. I'm not sure if that perhaps gives me the upper hand > wrt the trade-offs you mention? That's the other way around actually: I designed the sparse columns so as to make operations like x(i) += 1.0 or x(i) = 2.0 (a) basically O(1), at the price of wasting some memory, and the necessity of calling x.compact() when the construction of the vector is finished. On the contrary, reading x(i) is O(log n) where n is the number of non-zero elements in x. I chose that because operations (a) are repeated many times to build a Jacobian by pieces and composition (the aim was constraints for small molecule crystallography). On the contrary, all sparse algorithms can be written so as to avoid indexing (by iterating through the known non-zero elements). Actually, looking at my code, I realise that I designed it so that compact() is called as needed! You don't need to do it explicitly. In any case, it looks like the right structure if you want to deal with sparse Jacobian indeed. Ok, no problem, I'll add selection then. Best wishes, Luc

11 years, 8 months

Re: [phenixbb] (no subject)

by Terwilliger, Thomas Charles

Hi Ashok, Here is one approach you could try: A. Make each helix be a separate chain (chains A and B). Probably this is already the case B. Run phenix.find_ncs to find the operators and any point-group symmetry present: phenix.find_ncs force_ncs=true chainsAB.pdb map_coeffs.mtz C. Now look at the file: temp_dir/NCS_correlation.log Near the end of the file it will either say, Did not find any NC operator combination consistent with a point group or else it will give information related to what you are looking for: Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 0.009 29.305 0.005 xyz (fractional)= 0.000 1.172 0.000 in the direction of xyz (orthogonal A) = 0.903 0.430 0.002 No additional SG symmetry found to be part of point group All the best, Tom T On Jul 9, 2015, at 11:20 PM, Ashok Nayak wrote: > > Dear Phenixites, > > I have a helical bundle structure, where in I wish to understand by what rotation and about which axis the dimers are inter-related. What I get from the superposition with Superpose is the transformation matrix and not the axis, and the angles are also elusive. > > > Ashok Nayak > CSIR-CDRI > Lucknow, India > > > -- > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

10 years, 7 months

[phenixbb] Call for abstracts: IUCR session on SARS-CoV-2 structural biology

by Gianluca SANTONI

Dear all, Andrea Thorn and I are co-chairing a session at IUCr meeting 2021 entitled "Structural biology of coronaviruses" on the 16th of August. The subject of the session are structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. Abstract deadline has been extended to the 15th of may. We will select 4 abstracts for a 20 minutes talk. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Please feel free to forward this to scientists who may want to contribute an abstract, including junior researchers! We are looking forward to the meeting and the abstracts, best wishes, Gian and Andrea

4 years, 9 months

[phenixbb] Odd behaviour of real-space refinement

by Tristan Croll

Hi all, I'm just finalising the re-refinement of a 3.6 Angstrom structure. The stats in general are excellent (Rwork/Rfree = 0.219/0.260; Ramachandran outliers 0.12%; Clashscore < 2) and I've gone through the whole structure to check and double-check fit to the density. The only stat that bugs me a little is the rotamer outliers (2.3%). When I run through a fairly standard refinement protocol (XYZ coords, Individual B-factors, optimizing weights, secondary structure restraints), all seems fine - the Rfree rattles around within 0.2% or so. But when I include the real-space option, very strange things start to happen. Each rsrl step causes a 3-4% jump in both Rwork and Rfree, and jumps the Clashscore up to 40 or so. Rotamer outliers briefly go to zero but then increase substantially in subsequent steps, and the number of Ramachandran outliers increases. I thought I'd missed some dreadful error in my structure until I looked more closely at the results. The attached image is an example of what's happened: an exposed arginine in the middle of a beta-sheet (admittedly with no observable density associated with its sidechain, but register is well fixed by surrounding residues) has been flipped from its original orientation (yellow) to point directly into the hydrophobic core of the domain. Somewhat surprising, to say the least. Is this a bug in the algorithm, or is it simply that 3.6A is too low resolution for it to work reliably? My version of Phenix is a nightly build from about 2 weeks ago. Thanks, Tristan

10 years, 11 months

[phenixbb] Understanding Biology through Structure, March 16-20, 2020 in Santa Fe, NM

by Tom Terwilliger

Hi Structural biologists, particularly students and postdocs! I hope that you can come to our second "Understanding Biology through Structure” conference, to be held in Santa Fe, NM March 16-20, 2020. The purpose of the conference is to provide a forum for students and postdocs to meet established researchers as well as some rising stars, and to see and discuss presentations on the latest methods and results. The last conference was a huge success (see https://bit.ly/2Gfkm4t and https://bit.ly/2Gg39rm) and this one is looking great (see https://cvent.me/4kq9P) We have a super group of speakers (keynote speakers are Ilme Schlichting, David Stuart, Erica Ollmann Saphire, Robert Stroud, Suzanne Scarlata, David Eisenberg, Wayne Hendrickson, Yvonne Jones, Eva Nogales, and Tom Blundell), and all the talks will be followed by 10-15 minutes of discussion with participation by students and postdocs especially encouraged. There are a number of fellowships covering hotel and registration available for students and postdocs. Successful applicants will be notified on a rolling basis about a month after they register for the conference. After the main conference there will be an optional Phenix workshop with lectures and hands-on sessions on using Phenix for crystallography and cryo-EM. You can register now at https://cvent.me/4kq9P ! Best regards, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

6 years, 6 months

Re: [phenixbb] Clashes problem

by Simon Kolstoe

Are there not restraints to prevent steric clashes? In cns I seem to recall that the energy terms went through the roof if atoms got too close together. Secondly, if I remove the clashes through model building and then run phenix.refine both my R and Rfree go up, and phenix actually puts some of the clashes back again - does the community accept deposited pdb's with such obviously poor chemistry? Simon On 11 Feb 2008, at 14:51, Peter Zwart wrote: >> I am slightly concerned that a refinement program seems happy to >> allow >> such clashes. Is this a problem with the version of phenix.refine I >> am >> running, or is there a more obvious explanation that I have missed? > > Clash scores are not really used directly in refinement, so the > refinement program doesn't really care about this. Adding hydrogens > could improve the situation a bit, as would some model building do. > > How does your starting model look? > > HTH > > Peter > > > >> >> Thanks, >> >> Simon >> _______________________________________________ >> 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

18 years

Re: [phenixbb] Refinement Problem

by Pavel Afonine

Hi Chris, hm... ok, let's start somewhere: - check for twinning: phenix.xtriage data.mtz - are you sure about space group? I guess you can ask PHASER to try all possible SGs; - run through Autobuild if get stuck, send me the data, model and sequence files and I will have a look. Pavel. On 1/12/11 2:12 PM, Christopher W Davies wrote: > > I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me? > > > Thanks. > > Chris

15 years

Search results for query "look through"