Search results for "look through"

Re: [phenixbb] where is brute rotation output

by Nathaniel Echols

On Wed, Jan 30, 2013 at 4:06 PM, Ursula Schulze-Gahmen <uschulze-gahmen(a)lbl.gov> wrote: > The message is > "No orientations to test for Set #1" > > I am quite sure I selected the previous solution. My guess would be either it's a bug, or (less likely) it didn't actually find any solutions but didn't make that obvious. I see very different output in the current code versus the log file you sent me, so it's not clear which is the likely explanation. However, if you can dig through the tracking data, you should find a file like this: $PROJECT/.phenix/project_data/phaser_mr_1.pkl with "1" replaced by the job ID for the brute rotation function search; if you can send me this file off-list I will take a look. (Fortunately it does appear to be possible to extract the keywords for specifying the solution, but you'll have to run Phaser in CCP4i to use it.) I'm hoping the problem is magically solved with the new code, although you'll have to wait at least another 20 hours to use it. -Nat

13 years

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

by Karthikeyan Subramanian

Thank you Phil, it worked.... With regards Karthik On 27-09-2016 08:44 PM, Phil Jeffrey wrote: > 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 >

9 years, 4 months

Re: [phenixbb] Random seeds?

by Ralf W. Grosse-Kunstleve

> Okay, a fairly mundane question concerning random seeds in > Phenix. Obviously they are random but any restrictions on how many > digits phenix will accept? It is determined by the random number generators we're using. Up to 9 digits should be fine. I'm not quite sure what the exact limit is. > Any other restrictions? Don't think so. Any integer up to a certain limit should work. > Are they (it) only used for coordinate > refinement Any time the weight calculation is involved random numbers enter through the assignment of random velocities for a short Cartesian dynamics calculation. This is used to "shake" the model before computing x-ray/neutron gradients and restraint gradients. The weight is determined as the ratio of the norms of these gradients (after outlier removal). > or do the random seeds get used for other things as well? The weight calculation and Cartesian or torsion-angle simulated annealing are the main uses. Beyond that it takes a closer look to know if random numbers enter into a particular procedure. Ralf

15 years, 6 months

Re: [cctbxbb] sparse matrix

by David Waterman

Hi Luc, That sounds great, thank you. Cheers -- David On 6 June 2014 15:06, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > > 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 > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

11 years, 8 months

Re: [phenixbb] R-free rules

by Nathaniel Echols

On Nov 13, 2009, at 1:08 PM, Ralf W. Grosse-Kunstleve wrote: >> [ phenix.refine v1.5 rel. tag 2 intel linux 2.6 ] >> >> if i provide the test set .mtz (flag = "1") in refinement >> separately from >> the data .mtz, it looks like reflection_file_converter.py does not >> flag >> the work set as "0", if the work set lacks such a flag -- is that >> right? > > I think that's true. > Nat wrote a more comprehensive tool for generating R-free flags, which > are included in recent nightly builds. I'm pretty sure Nat generates > the flags for all possible reflections. > >> i.e. when providing the test set, it looks like all observed data >> must be >> in the test set, however the work set has flag "0". > > Hm... not sure I understand, but try Nat's new tools first. It is > easiest through the GUI, but there's also a command-line version, > phenix.reflection_file_editor. I'm not sure I understand either - does this mean that the MTZ file with the test set only has Miller indices (i.e. h,k,l) for the reflections actually in the test set, and the work set is simply missing? If so, I'm almost certain that my program isn't going to do any better, since it assumes that the R-free flags are comprehensive, but if you send me (not the list!) the reflection files I can probably fix them quickly. ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

16 years, 2 months

Re: [phenixbb] Max_reasonble_bond_distance error in phene.resl.space.refine

by Rune Thomas Kidmose

Hi Pavel, Thx for getting back to me so soon. I have several examples, however if you are looking for PDB files you can fetch directly from the RCSB etc. then I dont know if I can help. But some of the files I have piped through my pipeline, always results in the before mentioned error. Both the starting model and map have been fetched directly from the RCSB and the EMDB respectively. I have included dropbox download links for one such example. The PDB file: https://www.dropbox.com/s/xi2qlqczmth69bv/last_frame.pdb?dl=0 The corresponding map: https://www.dropbox.com/s/igweq3avgf6o7uk/emd_3765.mrc?dl=0 The example PDB (and map) is a structure of the nucleosome containing both protein and DNA, and the stated resolution of the map is 4.8Å. I use default settings for the pehnix.real.space.refine run so my run command is: phenix.real_space_refine last_frame.pdb emd_3765.mrc resolution=4.8 I should mention that it seems we are running phenix version dev-2614 at our department, which I am guessing is not the newest official release? Anyway I will try and get our sys-admin to install the newest version and then run the same files through phenix.RSR and see what happens. Thx again for getting back to me Cheers /Ruki On 14 Nov 2017, at 16.20, Pavel Afonine <pafonine(a)lbl.gov> wrote: Hi Ruki, I have been playing around with phenix.real.space.refine as part of a small pipeline I am making for EM structures. Testing various deposited EM structures and their corresponding maps, within my pipeline, I sometimes run in to the below error: RuntimeError: Bond distance > max_reasonable_bond_distance: 79.8663 > 50: I'm trying to chase this down and eliminate. So if you come across a case that can be reproduced please send it to me and I will start from there. For now simply set "max_reasonable_bond_distance=999" for all your refinements that will mask but not fix the problem. However, this should not affect the refinement results. Make sure you are using the latest Phenix version. Followed by a list of distances between, what I am assuming is, atom numbers and the actual distance. I can get past it simply by changing the max_reasonable_bond_distance for the run to, in this case, 80. This happens because the procedure optimizes weights by trying a large sample of possible weight values. For some values restraints may be too weak and atoms run one onto another, thus creating a huge clash and strong repulsion that stretches the bond. This leads to the crash. But I tend to see, that the final results gets significantly worse when I use this bypass. This is based on very similar models going through the pipeline, where the ones which yields the error, scores much worse when using the above mentioned bypass, compared to the models that showed no max_reasonable_distance_error. Again, I'm very keep to investigate concrete reproducible cases. So if you have anything to share that would be most helpful! B: Any ide what I can do, to avoid running into this bond distance problem? I'd say help us to identify the issue so that we fix it and then you don't run into it any more. All the best, Pavel

8 years, 2 months

Re: [cctbxbb] First svn commit

by Nathaniel Echols

On Wed, Apr 17, 2013 at 10:19 PM, Richard Gildea <rgildea(a)gmail.com> wrote: > Also, I would prefer the function arguments to be spelled out explicitly > without using *args and **kwds, so that I can figure out what arguments it > takes without having to read through the function source code to figure out > that internally you are calling self.as_miller_arrays(), and then have to go > and look up the function arguments for that. My preference is actually the opposite (I do the same thing quite a bit in my code), because otherwise there is no guarantee that keyword arguments added to add_miller_arrays will also be usable with add_miller_arrays_map. Using *args, **kwds makes the APIs explicitly the same. (That said, I'm increasing favoring using **kwds alone in these circumstances.) > My IDE (WingIDE) shows me the > function signature in its source assistant and also provides code completion > for function arguments and keywords. However these won't be of much use when > functions only list *args and **kwds. <insert generic snarky vi advocacy here> -Nat

12 years, 9 months

[cctbxbb] Automated Travis CI for phenix

by Elliot Nelson

Hi I'm looking to run automated integration tests for software, which currently runs from CCTBX, but also calls phenix scripts. These are phenix.fmodel and phenix.maps. Currently I have a docker image which sources CCP4 to get access to CCTBX, but this will not allow me to test stuff reliant on the phenix scripts. As Phenix is not downloadable on command line (CCP4 build can be got through wget command), it is not obvious as the best way to setup up such a docker build on travis CI. I wouldn't want to source a local download of the software as i am unsure of the licesining implications of hosting a copy of the software. Any suggestions would be greatly appreciated? Software (with dockerfile): https://github.com/nelse003/exhaustive_search <https://github.com/nelse003/exhaustive_search>Current docker image: https://hub.docker.com/r/nelse003/ccp4_phenix_docker/ Thanks Elliot DPhil Student, Systems Approaches to Biomedical Science<http://www.sabsidc.ox.ac.uk/> Protein Crystallography<http://www.thesgc.org/groupprofile/9489>, Structural Genomics Consortium, NDM, University of Oxford Oxford Protein Informatics Group<http://opig.stats.ox.ac.uk/>, Department of Statistics, University of Oxford

7 years, 8 months

Re: [phenixbb] Refinement Strategy vs. R gap

by Nathaniel Echols

On Wed, Mar 16, 2011 at 1:19 PM, Yuri <yuri.pompeu(a)ufl.edu> wrote: > 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. That sounds like a bug. Can you send me the parameter files and log files? > 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. Definitely a bug - it is fixed in the nightly builds, but I will send you the patch for 1.7. However, the "Update and exit" button on the toolbar (green checkmark) closes the window. (So does the cancel button.) -Nat

14 years, 10 months

Re: [phenixbb] phenix automr

by Thomas C. Terwilliger

Hi Shya, It sounds to me as though phaser and automr are doing what they are supposed to do. The space group P41212 has the same point group as P43212 (and the same systematic absences) so from your raw data it is not possible to tell which (if either) is correct. Phaser evidently did not find a great solution as your LLG is negative and the map poor. Randy or others may give you some more detailed suggestions but here are some ideas: 1. Try a different search model (a different structure, a combination of models, trim off poorly-related parts) 2. Try changing the anticipated RMSD if you have set it instead of sequence identity. This could affect the calculation of the LLG. All the best, Tom T >> Hi all, >> >> I tried to use phenix automr by using the gui and also I am using the latest version of phenix (courtesy of the phenix development team). I asked it to search for two molecules in the asymmetric unit but it finds >> just one also I am getting negative (-29) LLG value for the final solution. The map also does not look good. I also asked it to search for >> all possible space group, although I processed the data with P43212 phenix >> automr finds a different one P41212.Will fixing the space group fix the problem? Does anyone know what is going on? I tried running phaser separately through ccp4 and phaser did find two molecules although the map >> did not look good in this either. >> Shya >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

16 years, 10 months

Search results for query "look through"