Search results for "look through"

Re: [cctbxbb] sparse matrix

by David Waterman

Hi Luc, I suspect my application may be very similar to your original use case. I am preparing a Jacobian matrix to pass into the add_equations method of an lstbx non_linear_ls object. By the way, I am sure this is your code as well - so I thank you for this. My gradient calculations mostly involve vector calculus and are neatly done in a "vectorised" fashion from the Python side using operations on flex.vec3_double, mat3_double and so on. I naturally end up with some values in a flex.double array for some subset of the problem that I'd like to put into a sparse matrix column. The code you pasted looks ideal for this. 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? Additionally most of the problems I deal with are not sparse, so I intend to keep the existing code for most cases and only use this alternative when I know the problem will be sparse. If this all sounds reasonable, and you don't mind doing so, then I would indeed appreciate it if you could make that code work. Cheers -- David On 6 June 2014 14:18, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > Hi David, > > > Without having tried this, I sense it might be a burden. I have a lot > of values to set and don't really want to convert from flex.double via > a dictionary. Are there any philosophical/technical/other reasons for > not writing a set_selected method for sparse.vector? If not, I might > try to do this. > > > First I am the author of that sparse matrix code. > > Then could you tell me what application you have in mind? My sparse matrix > code has very specific memory and time trade-offs, that may not be suitable > for your problem. > > But I can already answer your question: it would be slow as well as > cumbersome to go through an intermediate dictionary. Initialising a sparse > vector with a dictionary, I only implemented it to make testing easier. It > is not designed to be used in heavy-duty production code. Moreover it would > be perfectly legitimate for the sparse columns to support assignment through > selections. I could easily make the following work: > > x = sparse.vector(10) # vector with 10 elements > x.set_selected(index_selection, another_vector) > x.compact() # part of the trade-offs I was talking about > > Best wishes, > > Luc > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

11 years, 8 months

Re: [phenixbb] Clashes problem

by Schubert, Carsten [PRDUS]

Simon, I saw you fixed your wxc_scale to 0.1. What happens to the clashes if you let the program refine this parameter? Carsten > -----Original Message----- > From: phenixbb-bounces(a)phenix-online.org > [mailto:[email protected]]On Behalf Of Simon Kolstoe > Sent: Monday, February 11, 2008 10:01 AM > To: PHENIX user mailing list > Subject: Re: [phenixbb] Clashes problem > > > 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 > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > >

18 years

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

by Da Duan

Hi Nat I was just looking at the average B in the refinement log files from Refmac and Phenix Refine. Thanks for the clarification on how Refmac and Phenix calculate the average B. My next question is when depositing the structure, is it more common to deposit structures with the "residual" B-factors or B-factors generated by Phenix that includes the TLS and Ucryst contribution? I also performed sfcheck and the average B generated by the Wilson plot is ~100 which seems to suggest that the Phenix average B is probably "more" correct? Thanks again Da On Fri, Dec 16, 2011 at 12:31 AM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13(a)queensu.ca> wrote: > > 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. > > How are you calculating the average B? Refmac prints "residual" > B-factors in the B column of ATOM records - these do not include the > contribution from TLS and Ucryst (an overall B-factor for the entire > crystal). In Phenix, the ATOM records always have the total isotropic > B-factor, and this will always be higher than the equivalent in > Refmac. So it's quite likely that both programs are correct, they're > just reporting very different things. (And for what it's worth, a > mean B-factor of 100 is totally normal at 3.3A resolution.) > > -Nat > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

14 years, 1 month

Re: [phenixbb] Occupancy refinement of anomalous scatters

by Pavel Afonine

Hi Chen, my apologies for the late reply, somehow I managed to overlook your email.. Ok, here it is (better late than never!): > I have a question about the occupancy refinement of the anomalous > scatters. This is because when I went through all the HA sites, I > found that some of them has too high B factor and too high occ. I > manually adjusted the occ and fed the model into refinement, but the B > factor and occ came back to around their original level again. It > seems that those have a stronger peak in the anomalous difference > Fourier map has a higher occupancy after refinement, but this does not > necessarily equals to a strong density peak in 2Fo-Fc map (some of > them even disappear after refinement), and this might be related to > their high B factor. Am I doing something wrong in the refinement? I > am basically using phenix.refine default setting, but with > TLS+isotropic B factor refinement and occupancy refinement of a small > region (5-8 residues). The resolution is 3 A, and the refinement is > already at the final stage. I am still at the learning stage and your > input will be greatly appreciated. HA sites may be partially occupied. Try this for HA with high B: set occupancy of HA to some number less than 1 and reset B to mean B, then run phenix.refine (make sure occupancy refinement is enables, which is the default). If this does not help then please send me files and I will have a closer look. Pavel

11 years, 5 months

[phenixbb] fwd: Application deadline approaching: CCP4 summer school at APS, in USA

by Nathaniel Echols

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "'phenixbb(a)phenix-online.org'" <phenixbb(a)phenix-online.org> Cc: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> Date: Tue, 3 Apr 2012 17:19:36 -0500 Subject: Application deadline approaching: CCP4 summer school at APS, in USA Dear Colleagues, We would like to point out that the application deadline for the 5th annual CCP4 Summer School “From data collection to structure refinement and beyond” is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will cover all aspects of macromolecular structure determination and validation. Some of the world’s leading experts will be providing instruction and hand-on help. We are looking forward to another productive school this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

13 years, 10 months

Re: [phenixbb] sigma cutoff

by Joe Krahn

Kay Diederichs wrote: >> >> Hi, >> >> According to the Phenix manual, phenix.refine uses no sigma cutoff by >> default. Since I haven't changed this manually, why do I see in my pdb >> file MIN(FOBS/SIGMA_FOBS) 1.340? >> >> Thanks for help, >> Karolina >> >> > > This one I can answer because I asked myself the same question recently. > > The answer is that Phenix does not impose any sigma cutoff, but rather > your data are such that the minimum value of Fobs/Sigma_Fobs is 1.34 . > > You can verify this for yourself by going through your reflection file, > line by line, and calculating Fobs/Sigma_Fobs for each reflection. You > will find that all your reflections have a Fobs/Sigma_Fobs larger or > equal to 1.34 . So it has nothing to with phenix; phenix just reports a > property of your data. > > An easier way than doing it "manually" is using CCP4 sftools for > calculating a new column "ratio", writing out the resulting MTZ file, > and looking at this with mtzdmp. > > HTH, > > Kay > We were initially puzzled by Fobs/Sigma_Fobs of about 1.9, for data processed with XDS. It turns out that the data was culled at processing time, by software applying a 2-sigma cutoff. Joe Krahn

16 years, 2 months

Re: [phenixbb] ncs restraints

by Ralf W. Grosse-Kunstleve

Hi Tim, If you start from nearly identical copies (due to previous refinement), in the absence of a strong signal from the data, it is expected that the copies remain fairly similar even if you increase the sigma / lower the weight. We just added a new feature to phenix.refine that could be useful to introduce differences between the NCS copies, guided by the model density through a new real-space refinement protocol: strategy=individual_sites_real_space plus real_space_refinement.mode=lockit. At your resolution it is turned on by default. I.e. to try it out all you need to do is get dev-602 or higher and run phenix.refine again. Only trouble, those installers aren't generally visible since there were some minor problems, but watch out for a new one soon. Ralf > >From: Timothy Springer <springer(a)idi.harvard.edu> >To: phenixbb(a)phenix-online.org >Sent: Tue, December 7, 2010 7:31:44 PM >Subject: [phenixbb] ncs restraints > >Hi, I am using NCS restraints for 4 copies of a molecule at 3.05 Å. We are using >the standard weights: > coordinate_sigma = 0.05 > b_factor_weight = 10 >and the 4 molecules look identical. What are suggested values for looser >restraints? One of my colleagues said that varying them did not make a >difference- ncs was still very strict. Is there a way to make them less strict? >Thanks, >Timothy A. Springer, Ph.D. > > > > >

15 years, 2 months

[phenixbb] Re: Simulate map from model

by James Holton

Ostensibly, all you need to do is run phenix.fmodel with scattering_table=electron . And perhaps try to come up with what k_sol should be for the bulk solvent density. There are caveats, of course, not the least of which is that, last I checked, the modified scattering from formal charges like ions vs neutral groups is not implemented. I don't actually know of a program that handles things like charges. I've heard rumors that someone was working on full QM calculations of electrons moving through matter to try and get this "right", but I have not heard about any progress for some time. Sorry can't be more helpful, -James On 4/2/2025 4:52 AM, Ricardo Righetto wrote: > Hi, > > Apologies if I'm missing something obvious, but I was not able to find > this in the documentation: is there a PHENIX tool for simulating > Coulomb potential maps (aka "cryo-EM maps") from atomic models? > > I'm looking for something like the molmap > <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html> > command in ChimeraX, but more accurate. One such alternative is the > simulate program from cisTEM, but I figured PHENIX might also have > something? > > Thank you! > > -- > Ricardo Diogo Righetto > > _______________________________________________ > phenixbb mailing list --phenixbb(a)phenix-online.org > To unsubscribe send an email tophenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s

10 months, 1 week

Re: [phenixbb] Phenix "hangs" on a Mac?

by Nathaniel Echols

On Mon, Jul 22, 2013 at 2:13 PM, Joseph Noel <noel(a)salk.edu> wrote: > Has anyone had a problem when using Phenix refine through the GUI on a Mac > wherein the program after hitting Run locally starts but then hangs without > proceeding? Seems to happen to me about one out of five times I run refine > and always hangs when I experiment with ramachandran restraints for only a > portion of the polypeptide chain. I've tried letting things alone for > several hours and nothing happens. I can abort and then often resubmit and > it then runs fine (except for rama restraints). I've found this happens with > both nightly builds and stable releases. I am currently running the latest > nightly build 1439. I guess the moral here is "never use Ramachandran restraints", which is good advice under nearly any circumstances, but this sounds like a bug we need to address. A few follow-up questions: 1) Can you please send me all inputs off-list? The .eff file would be helpful too - you can get to this from the job history tab by clicking "Show details". 2) Open the console (in /Applications/Utilities) and look for suspicious error messages. In particular, I get occasional mysterious crashes which output a mention of "malloc", and the phrase "set breakpoint to debug". (Totally unrelated to Ramachandran restraints, as far as I know.) thanks, Nat

12 years, 6 months

Re: [phenixbb] Difference in water molecules count

by Nathaniel Echols

On Tue, Feb 7, 2012 at 6:29 AM, <bsubedi(a)btk.fi> wrote: > The average B-factors for the protein and solvents are: > Main chain > [snip] > Yes, the water molecules were identified automatically by phenix.refine > programme. Okay, so the 1.6A structure with significantly fewer waters has slightly higher B-factors overall. Since many of the waters will be defined largely (entirely?) by high-resolution data, and the cutoffs used by phenix.refine are relatively conservative, it wouldn't surprise me if it's just missing a lot of weaker sites - and there probably really are fewer to find anyway. At the end of refinement I don't think you should rely on phenix.refine to find all of the waters anyway; try using the water-picking in Coot, filter out the obviously wrong ones, and refine a final time without solvent update. (This applies to the other datasets as well, at least the two at 1.6A - it wouldn't surprise me if there are more waters to be found.) For the obsessive-compulsive or just curious, there is now a standalone tool in the nightly builds for looking at difference maps: mmtbx.find_peaks_holes model.pdb data.mtz write_pdb=True This is basically recycled from phenix.refine but since the idea wasn't to add waters, but to make it possible to cycle through the map peaks in Coot, it's slightly more aggressive and thorough. (The novel features are incorporation of the anomalous difference map if available, and identification of "waters" with suspicious mFo-DFc peaks.) We'll probably merge this with phenix.refine at some point. -Nat

14 years

Search results for query "look through"