Search results for "look through"

Re: [cctbxbb] some thoughts on cctbx and pip

by Aaron Brewster

(note, power at LBL is going down now, so save more thoughts on this until Sunday afternoon, in case the messages are lost :) On Fri, Aug 16, 2019 at 4:36 PM Aaron Brewster <asbrewster(a)lbl.gov> wrote: > Hi Luc, thanks. I did recall someone working on this a while back. > > For conda, there are a couple more things to finish and then we hope to > have cctbx available through conda. > > 1) There is work being done in a branch to make cctbx use boost in > standard locations (e.g. the system boost, or a conda boost). That will > allow us to use install boost by conda and not build it ourselves. ( > https://github.com/cctbx/cctbx_project/tree/conda_boost). Also, newer > versions of boost are being tested (up through 1.70). (This will also > enable python 3.7 support.) > 2) We need to work on getting a make install step in place so that we can > build the conda package and upload it. > 3) We want to split the dependencies up by builder (cctbx, cctbx-lite, > dials, phenix, etc.) into meta packages and their associated manifests. I > can talk more about this if there is interest. > > Thanks, > -Aaron > > > > On Fri, Aug 16, 2019 at 1:48 PM Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > >> Hi, >> >> I did look into that many years ago, and even toyed with building a pip >> installer. What stopped me is the exact conclusion you reached too: the >> user would not have the pip experience he expects. You are right that it is >> a lot of effort but is it worth it? Considering that remark, I don’t think >> so. Now, Conda was created specifically to go beyond pip pure-python-only >> support. Since cctbx has garnered support for Conda, the best avenue imho >> is to go the extra length to have a package on Anaconda.org, and then to >> advertise it hard to every potential user out there. >> >> Best wishes, >> >> Luc >> >> >> On 16 Aug 2019, at 21:45, Aaron Brewster <asbrewster(a)lbl.gov> wrote: >> >> Hi, to avoid clouding Dorothee's documentation email thread, which I >> think is a highly useful enterprise, here's some thoughts about putting >> cctbx into pip. Pip doesn't install non-python dependencies well. I don't >> think boost is available as a package on pip (at least the package version >> we use). wxPython4 isn't portable through pip ( >> https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). >> MPI libraries are system dependent. If cctbx were a pure python package, >> pip would be fine, but cctbx is not. >> >> All that said, we could build a manylinux1 version of cctbx and upload it >> to PyPi (I'm just learning about this). For a pip package to be portable >> (which is a requirement for cctbx), it needs to conform to PEP513, the >> manylinux1 standard (https://www.python.org/dev/peps/pep-0513/). For >> example, numpy is built according to this standard (see >> https://pypi.org/project/numpy/#files, where you'll see the manylinux1 >> wheel). Note, the manylinux1 standard is built with Centos 5.11 which we >> no longer support. >> >> There is also a manylinux2010 standard, which is based on Centos 6 ( >> https://www.python.org/dev/peps/pep-0571/). This is likely a more >> attainable target (note though by default C++11 is not supported on Centos >> 6). >> >> If we built a manylinuxX version of cctbx and uploaded it to PyPi, the >> user would need all the non-python dependencies. There's no way to specify >> these in pip. For example, cctbx requires boost 1.63 or better. The user >> will need to have it in a place their python can find it, or we could >> package it ourselves and supply it, similar to how the pip h5py package now >> comes with an hd5f library, or how the pip numpy package includes an >> openblas library. We'd have to do the same for any packages we depend on >> that aren't on pip using the manylinux standards, such as wxPython4. >> >> Further, we need to think about how dials and other cctbx-based packages >> interact. If pip install cctbx is set up, how does pip install dials work, >> such that any dials shared libraries can find the cctbx libraries? Can >> shared libraries from one pip package link against libraries in another pip >> package? Would each package need to supply its own boost? Possibly this >> is well understood in the pip field, but not by me :) >> >> Finally, there's the option of providing a source pip package. This >> would require the full compiler toolchain for any given platform (macOS, >> linux, windows). These are likely available for developers, but not for >> general users. >> >> Anyway, these are some of the obstacles. Not saying it isn't possible, >> it's just a lot of effort. >> >> Thanks, >> -Aaron >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >

5 years, 10 months

Re: [cctbxbb] Fwd: Re: indexing diffraction pattern

by Abbey Garant

So youre basically looking to do a search match? What inputs do you put into the software? Are these powder diffraction peaks? Laue? On Wed, Nov 14, 2018, 9:18 AM Pavel Afonine <pafonine(a)lbl.gov wrote: > Perhaps someone can reply Wen.. > > Pavel > > > -------- Forwarded Message -------- > Subject: Re: indexing diffraction pattern > Date: Sat, 10 Nov 2018 09:30:53 -0500 > From: Wen Jiang <jiang12(a)purdue.edu> <jiang12(a)purdue.edu> > To: Pavel Afonine <pafonine(a)lbl.gov> <pafonine(a)lbl.gov> > > Pavel, > Sorry for insufficient details. The scenario is that I have a numpy 2D > array of float values that represents an image of "diffraction pattern" > (generated by an image processing operation, not actual X-ray diffraction). > I need to determine the peak positions and then find a 2D lattice (two 2D > vectors) going through these peaks. I have my own simple functions that can > detect the peaks and find a 2-D lattice to cross the peaks but it often > fails when the "diffraction pattern" is not very clean. Thus, I want to > find a more robust method that works well when the peaks are relatively > weak, not very sharp, and when there are some spurious peaks off the > lattice. I think these tasks are exactly what cctbx has solved for indexing > X-ray diffraction images. > Hope that these explanations help clarify the problem. > Thanks, > > Wen > > Prof. Wen Jiang > Department of Biological Sciences > Department of Chemistry (Courtesy) > Scientific Director, Purdue Cryo-EM Facility > Purdue University > Hockmeyer Hall of Structural Biology > 240 S. Martin Jischke Drive > West Lafayette, IN 47907 > http://jiang.bio.purdue.edu > > > On Sat, Nov 10, 2018 at 8:03 AM Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Wen, >> >> I'm not sure I fully understand your question... You say a function that >> takes a numpy array.. Array of what? >> Then, "a list of diffraction spots" -- these are measured in diffraction >> experiment. >> >> If you could provide more details as to what you are trying to do as well >> as what exactly the inputs are then I will do my best to see how to do this >> in CCTBX or forward your questions to CCTBX mailing list so that others can >> comment. >> >> All the best, >> Pavel >> >> On 11/10/18 03:56, Wen Jiang wrote: >> >> Hi Pavel, >> I am looking for a function that takes a numpy array and returns a list >> of diffraction spots and lattice vectors. I think cctbx should have such a >> function but I am not familiar with it. Can you point me in the right >> direction? >> Thanks, >> >> Wen >> >> Prof. Wen Jiang >> Department of Biological Sciences >> Department of Chemistry (Courtesy) >> Scientific Director, Purdue Cryo-EM Facility >> Purdue University >> Hockmeyer Hall of Structural Biology >> 240 S. Martin Jischke Drive >> West Lafayette, IN 47907 >> http://jiang.bio.purdue.edu >> >> >> _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

6 years, 7 months

Re: [phenixbb] Completeness issue by phenix - revisited

by Pavel Afonine

Hi Jon, please run phenix.model_vs_data mode.pdb data.mtz and that will give the the numbers for data completeness. Please send me the output of the above command if it doesn't clarify this issue. Let me know if you have any questions. Pavel. On 2/3/10 7:48 PM, Mischa Machius wrote: > Could it be that you reserved 10% of your data for Rfree and are > looking at the completeness for the work set? Do you have an > I/sigma(I) cutoff that is high? If not, it might help to post the some > of the Phenix output, e.g., the table with the completeness data along > with the resolution limits, etc. Best - MM > > On Feb 3, 2010, at 10:42 PM, J. Fleming wrote: > >> Hi, >> >> I'm having a problem using phenix.refine with my x-ray data. My >> completeness is always 89% when it should be 99%. My data was >> originally processed with CCP4i. I found an old post (see below) >> with a potential fix that doesn't work for me. I've tried changing >> the 'Anomalous flag: True' to 'Anomalous flag: False' but my >> completeness is still 89%. I've clicked through a variety of other >> setting in the GUI that I thought would help but no luck. Does anyone >> have any ideas? >> >> Thanks in advance, >> Jon >> >> >> ----- Original Message ----- >> From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov <http://www.phenix-online.org/mailman/listinfo/phenixbb>> >> >> To: phenixbb at phenix-online.org <http://www.phenix-online.org/mailman/listinfo/phenixbb> >> Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern >> Subject: Re: [phenixbb] Completeness issue by phenix >> >> >> Hi YoungJin, >> >> I suspect phenix.refine decided your mtz file contains anomalous data >> when you actually have non-anomalous data. Could you look in the >> phenix.refine output for something like this: >> >> ================================== X-ray data ================================= >> >> >> F-obs: >> 1yjp.mtz:FOBS_X,SIGFOBS_X >> >> R-free flags: >> 1yjp.mtz:R-free-flags >> >> Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X >> Observation type: xray.amplitude >> Type of data: double, size=495 >> Type of sigmas: double, size=495 >> >> Number of Miller indices: 495 >> Anomalous flag: False >> ^^^^^ >> in particular here >> >> If you see "Anomalous flag: True" try adding this to the phenix.refine >> command line: >> >> >> xray_data.force_anomalous_flag_to_be_equal_to=False >> >> Let me know if this doesn't help. >> If it does help, I'd be interested to know how the .mtz file was >> generated. >> >> Ralf >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb > > ------------------------------------------------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

15 years, 4 months

Re: [phenixbb] Group ADP refinement restraints

by Pavel Afonine

Hi Taylor, you are correct, in group B factor refinement overall B factors of adjacent residues are restrained to be similar (or not too different). I will fix the documentation, thanks for pointing this out. There isn't much validation done to B factors, so dropping restraints can indeed lower R-factors but it isn't necessarily clear whether refined B factors are going to be meaningful. I guess you can try both and see what produces more meaningful B factors. Pavel On 11/25/19 16:34, Taylor Stevens wrote: > Hello, > > I am currently refining a low-ish resolution structure (through the > phenix.refine GUI) with phenix version 1.14 and had some questions > about the use of restraints in group ADP refinement. In the > phenix.refine documentation > (https://www.phenix-online.org/documentation/reference/refinement.html#refin…) > it is stated that “Group isotropic ADP or TLS refinement do not use > any restraints”, however, this does not seem to be the case. If I look > in the log file I can see the following lines of text which I believe > indicate that the restraints are being applied: > > |-group b-factor refinement (macro cycle = 0; iterations = 0)————————| > | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight > = None | > |——————————————————————————————————————| > |-group b-factor refinement (macro cycle = 1; iterations = 22)————————| > | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight > = 821.871| > |——————————————————————————————————————| > |-group b-factor refinement (macro cycle = 2; iterations = 22)————————| > | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight > = 821.871| > |——————————————————————————————————————| > |-group b-factor refinement (macro cycle = 3; iterations = 22)————————| > | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight > = 821.871| > |——————————————————————————————————————| > > If I manually set the wu parameter to 0 under “Refinement target > weights" nothing changes, however, if I navigate to "All parameters > > ADP settings > Group B-Factors" in the GUI there is a “Use restraints” > box that is checked by default. If I uncheck this box, there are no > longer any restraints being applied according to the log file, and in > the case of the structure I am refining, there is a substantial drop > in the rfree/rwork. Is this an issue with the program or > documentation? Or am I misunderstanding how the program is supposed to > work? Is it generally a good idea to use group ADP refinement without > restraints? > > Thanks, > > Taylor > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

5 years, 7 months

Re: [cctbxbb] flex index

by Monarin Uervirojnangkoorn

Thanks!. very useful. although doesn't really work with padded array (as in the case of real_map object). but found my way round. best mona On Oct 18, 2011, at 11:17 AM, Ralf Grosse-Kunstleve wrote: > Hi Mona, > > Try this: > > from scitbx.array_family import flex > a=flex.double([1,4,5,7,5,6,6,1]) > a.set_selected(a > 5, 5) > print list(a) > > Or in smaller steps: > > bool_selection = a > 5 > assert bool_selection.size() == a.size() > print list(bool_selection) > a.set_selected(bool_selection, 5) > print list(a) > > You can also call a.set_selected(bool_selection, b) > where b is an array with as many elements as you have True in the bool_selection. > > This kind of working with selections is very typical within cctbx/phenix. > If you look through our sources you'll find a lot of examples; in passing, we have two types of selections, bool selections as above, and integer selections. The latter are useful for permutations, e.g. to sort array elements, or if you know you select only a small number of elements from a large array. Let me know if you have more questions about selections and I'll be happy to explain. (I guess one day I should write a "Working with selections" tutorial.) > > Ralf > > On Tue, Oct 18, 2011 at 2:54 AM, Monarin Uervirojnangkoorn <monarin(a)biochem.uni-luebeck.de> wrote: > Hi, > > I'm using flex and 'd like to get an access to elements fall beyond/ below certain value. eg. > a=[1,4,5,7,5,6,6,1] > anything beyond 5 should be set to 5. (in matlab then a(a>5)=5;) > if you could tell me how to do this quickly for flex, that would be great. for now i use loop and that is... pretty slow. > > many thanks. > mona > > > > ^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^ > Institute of Biochemistry, > Institut für Neuro- und Bioinformatik, > Graduate School for Computing in Medicine and Life Sciences > University of Lübeck, > Ratzeburger Allee 160 > Lübeck 23538 > Germany > Tel: +49451-5004072 > Fax: +49451-5004068 > > > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb ^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^ Institute of Biochemistry, Institut für Neuro- und Bioinformatik, Graduate School for Computing in Medicine and Life Sciences University of Lübeck, Ratzeburger Allee 160 Lübeck 23538 Germany Tel: +49451-5004072 Fax: +49451-5004068

13 years, 8 months

Re: [cctbxbb] Module versioning (was Re: Debian Package)

by Radostan Riedel

On Sat, 01. Sep 03:33, Luc Bourhis wrote: > Now going back to patch 0007-adding-shlib-versioning, is it correct that we would just need to do: > env.Append(SHLINKFLAGS= [ "--version-info=c.r.a" ] > for the env that build a particular .so? Well, that would be for gcc and clang only of course. To be cross-platform I would suggest adding a pseudo-builder SetVersionInfo(vers) that does the right thing on Unix and nothing on Windows (for the time being, as perhaps there is a similar mechanism with msvc). That's a good idea. I'll try to rework by patch to ease everything up. > > But your well-written patch and that little sugar are the easy part as they are of the write once, reuse forever nature. We need a workflow here and the two extremes would be as follow. > > 1. Each and every cctbx developer becomes aware of so-versioning. Let's say a module is at 2.3.4, so we have > env.SetVersionInfo(vers="2.3.4") > and then a change is made to the C++ code. The developer responsible for that change should then figure out the new c.r.a and then add a comment > env.SetVersionInfo(vers="2.3.4", #next release# vers="c.r.a") > It would then be easy to automate an edit en-masse before release that would change that line and all its sisters to > env.SetVersionInfo(vers="c.r.a") > That's basically a formalised version of your proposition in your answer to Johan earlier. > > 2. Cctbx developers would not care about so-versioning and before a Debian release, the cctbx Debian maintainers would go through each call to SetVersionInfo to set the right c.r.a, based on a careful examination of the commits, complemented by asking questions to the core cctbx developers (or simply open questions on this forum). I'd of course like the first extreme better. For starters it would be great if everyone feels responsible for the "current" number. I'm not a c++ developer and I don't know if thats easy? > There are relatively very few shlibs compared to Python modules. Keeping track of the version of all of the latter by hand would be an enormous amount of work. I don't think we can get it done cheaply with some automatic keyword expansion if we want proper major.minor.patch or worse something as involved as so-versioning. Maybe it can be good to look on other projects how they are doing this. As a python developer I'm always expecting different API's when it comes to new upstream versions. I checked the policy for Debian and there seems to be nothing special in versioning extensions and modules. Maybe Justin can tell us something about Gentoo. I'd say we don't need to worry about it for now.

12 years, 10 months

[cctbxbb] Fwd: Re: indexing diffraction pattern

by Pavel Afonine

Perhaps someone can reply Wen.. Pavel -------- Forwarded Message -------- Subject: Re: indexing diffraction pattern Date: Sat, 10 Nov 2018 09:30:53 -0500 From: Wen Jiang <jiang12(a)purdue.edu> To: Pavel Afonine <pafonine(a)lbl.gov> Pavel, Sorry for insufficient details. The scenario is that I have a numpy 2D array of float values that represents an image of "diffraction pattern" (generated by an image processing operation, not actual X-ray diffraction). I need to determine the peak positions and then find a 2D lattice (two 2D vectors) going through these peaks. I have my own simple functions that can detect the peaks and find a 2-D lattice to cross the peaks but it often fails when the "diffraction pattern" is not very clean. Thus, I want to find a more robust method that works well when the peaks are relatively weak, not very sharp, and when there are some spurious peaks off the lattice. I think these tasks are exactly what cctbx has solved for indexing X-ray diffraction images. Hope that these explanations help clarify the problem. Thanks, Wen Prof. Wen Jiang Department of Biological Sciences Department of Chemistry (Courtesy) Scientific Director, Purdue Cryo-EM Facility Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 http://jiang.bio.purdue.edu On Sat, Nov 10, 2018 at 8:03 AM Pavel Afonine <pafonine(a)lbl.gov <mailto:[email protected]>> wrote: Hi Wen, I'm not sure I fully understand your question... You say a function that takes a numpy array.. Array of what? Then, "a list of diffraction spots" -- these are measured in diffraction experiment. If you could provide more details as to what you are trying to do as well as what exactly the inputs are then I will do my best to see how to do this in CCTBX or forward your questions to CCTBX mailing list so that others can comment. All the best, Pavel On 11/10/18 03:56, Wen Jiang wrote: > Hi Pavel, > I am looking for a function that takes a numpy array and returns a > list of diffraction spots and lattice vectors. I think > cctbx should have such a function but I am not familiar with it. > Can you point me in the right direction? > Thanks, > > Wen > > Prof. Wen Jiang > Department of Biological Sciences > Department of Chemistry (Courtesy) > Scientific Director, Purdue Cryo-EM Facility > Purdue University > Hockmeyer Hall of Structural Biology > 240 S. Martin Jischke Drive > West Lafayette, IN 47907 > http://jiang.bio.purdue.edu >

6 years, 7 months

Re: [phenixbb] Help with custom bond restraints syntax

by Andy Torelli

Thanks Pavel, that works well. Best, -Andy On 9/29/2009 12:21 PM, Pavel Afonine wrote: > Alternatively, you can do simply this: > > refinement.geometry_restraints.edits { > bond { > action = *add > atom_selection_1 = chain F and resid 1 and name FE1 > atom_selection_2 = chain A and resid 69 and name SG > distance_ideal = 2.35 > sigma = 0.1 > slack = None > } > } > > > Pavel. > > > On 9/29/09 8:54 AM, Andrew T. Torelli wrote: >> Hi all, >> >> I'm having what I believe is a simple problem defining custom bond >> restraints between a side chain in my protein model and a ligand >> (non-covalent bond). Here is a minimal form of my custom bond >> definition file that suffers from the error: >> >> refinement.geometry_restraints.edits { >> Atom1 = chain F and resid 1 and name FE1 >> Atom2 = chain A and resid 69 and name SG >> bond { >> action = *add >> atom_selection_1 = Atom1 >> atom_selection_2 = Atom2 >> distance_ideal = 2.35 >> sigma = 0.1 >> slack = None >> } >> } >> >> I'm using phenix 1.4-153 and I get the following error: >> ERROR: Unused parameter definitions: >> refinement.geometry_restraints.edits.Atom1 (file >> "/HOME/andrew/PHENIX_paramfiles/test.edits", line 5) >> refinement.geometry_restraints.edits.Atom2 (file >> "/HOME/andrew/PHENIX_paramfiles/test.edits", line 6) >> >> I've checked through the online manual and I believe my syntax is >> correct, but I'm not sure why my custom bond restraint is being >> ignored. >> >> A second question is: once I get the custom bond/angle restraints >> correctly implemented, is there a better or more convenient place to >> look and confirm that the restraints have been imposed other than the >> .geo file phenix.refine outputs? >> >> Thank you very much for your help, >> -Andy >> >> >> >> >> _______________________________________________ >> 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 >

15 years, 9 months

Re: [phenixbb] temp files

by James Holton

Thank you Tom! Ok. So, in order to change the default I need to go through the code looking for "temp_dir" and change things? On 4/24/2021 10:16 AM, Tom Terwilliger wrote: > Hi James, > > There is no overall Phenix temp directory specification, but most of > the temp_dir usage is from autosol/autobuild/ligandfit/map_to_model. > Each of these has the keyword "temp_dir=xxxx" which you should be > able to set to any directory you want (and local is better as you > note). Most programs using a temp_dir also have a keyword > clean_up=True as well. > > All the best, > Tom T > > On Sat, Apr 24, 2021 at 10:51 AM James Holton <jmholton(a)lbl.gov > <mailto:[email protected]>> wrote: > > Thank you Li-Wei > > Definitely not placing blame on one program. Phenix.autobuild is > another > big temp file producer. So is XDS. Clearly this ligand run was a > case > of a misconfigured, runaway task that never finished. However, the > files > lingered on disk, eating up inodes for 3 years! > > The reason I'm asking is I think there are significant performance > increases to be gained by using fast, local storage for scratch > files. > This is not just in speed but storage and overall system/cluster > performance. Very few things are more expensive than an NFS write! > > Does anyone know how to change the default temp file location across > phenix ? Is this a cctbx thing? > > Thanks > > -James > > > On 4/23/2021 9:38 PM, Li-Wei Hung wrote: > > Hi James, > > > > I'll leave the global Phenix temp aspect to Billy. > > For ligand identification specifically, the working directory is > where > > all the files are located. The program will purge most of the > > intermediate files upon completion. If the user interrupted the > runs > > or if the program crashed at certain spots, the purge mechanism > might > > not kick in. Even so, it'd take many runs to accumulate 20e6 (2e7?) > > files. In any case, you've got a point and I'll look into salvaging > > intermediate files of ligand identification as soon as they are not > > needed in the process. > > > > Thanks, > > > > Li-Wei > > > > On 4/23/2021 7:03 PM, James Holton wrote: > >> Hello all, > >> > >> Is there a way to configure phenix at install time (or perhaps > >> post-install) to put temporary files under /tmp ? I just had to > >> delete 20e6 temp files over NFS from a single user's phenix ligand > >> identification run. The delete took almost a month. > >> > >> Apologies if I am neglecting to look somewhere obvious in the > >> documentation, > >> > >> Happy Weekend! > >> > >> -James Holton > >> MAD Scientist > >> > >> _______________________________________________ > >> phenixbb mailing list > >> phenixbb(a)phenix-online.org <mailto:[email protected]> > >> http://phenix-online.org/mailman/listinfo/phenixbb > <http://phenix-online.org/mailman/listinfo/phenixbb> > >> Unsubscribe: phenixbb-leave(a)phenix-online.org > <mailto:[email protected]> > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org <mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/phenixbb > <http://phenix-online.org/mailman/listinfo/phenixbb> > Unsubscribe: phenixbb-leave(a)phenix-online.org > <mailto:[email protected]> > > > > -- > 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 > <mailto:[email protected]> > Tel: 505-431-0010 >

4 years, 2 months

Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel

by James Holton

I'm no expert, but it looks to me like the test is getting something from the phenix regression repository. Maybe it is this dependency that's making it bonk? -James On 9/22/2017 8:58 AM, richard.gildea(a)diamond.ac.uk wrote: > I was unaware that the code was actually used by anyone. > > So does anyone know enough about the code to fix the failing test that Oleg and Graeme both complained about? > > Cheers, > > Richard > > Dr Richard Gildea > Data Analysis Scientist > Tel: +441235 77 8078 > > Diamond Light Source Ltd. > Diamond House > Harwell Science & Innovation Campus > Didcot > Oxfordshire > OX11 0DE > ________________________________ > From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of Aaron Brewster [asbrewster(a)lbl.gov] > Sent: 22 September 2017 15:56 > To: cctbx mailing list > Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel > > FWIW I have used it on several occasions to understand how diffraction looks for different settings. For example, when I was working on amyloids on the cspad detector I would run it like this: > > rstbx.simage.wx_display unit_cell=24.1460,4.8614,22.2291,90.000,107.319,90.000 wavelength=1.452514 detector.distance=111 detector.size=194.15,194.15 detector.pixels=1765,1765 ewald_proximity=0.042500 point_spread=20 > > Twiddle the rotx, roty and rotz. It's nifty. > > I don't see any reason to kill this code. > > -Aaron > > > On Fri, Sep 22, 2017 at 4:22 AM, <markus.gerstel(a)diamond.ac.uk<mailto:[email protected]>> wrote: > This appears to be true: looking through cctbx_project, dials, labelit, phenix, phenix_regression I found no references apart from the tests that sparked this thread. > I would just remove it for retirement - it will be preserved in the history. > > -Markus > ________________________________________ > From: cctbxbb-bounces(a)phenix-online.org<mailto:[email protected]> [cctbxbb-bounces(a)phenix-online.org<mailto:[email protected]>] on behalf of richard.gildea(a)diamond.ac.uk<mailto:[email protected]> [richard.gildea(a)diamond.ac.uk<mailto:[email protected]>] > Sent: Friday, September 22, 2017 12:08 > To: cctbxbb(a)phenix-online.org<mailto:[email protected]> > Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel > > As far as I recall rstbx/simage was a research project by Ralf that hasn't been touched for over 5 years, and isn't used by any code outside of rstbx/simage. Could this code be potentially "retired" somewhere outside of cctbx? > > Dr Richard Gildea > Data Analysis Scientist > Tel: +441235 77 8078<tel:%2B441235%2077%208078> > > Diamond Light Source Ltd. > Diamond House > Harwell Science & Innovation Campus > Didcot > Oxfordshire > OX11 0DE > ________________________________ > From: cctbxbb-bounces(a)phenix-online.org<mailto:[email protected]> [cctbxbb-bounces(a)phenix-online.org<mailto:[email protected]>] on behalf of Oleg Sobolev [osobolev(a)lbl.gov<mailto:[email protected]>] > Sent: 20 September 2017 19:33 > To: cctbx mailing list > Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel > > Dear colleagues, > > Accidentally I found out that this command: > > rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True > finishes with traceback. > > It is run as part of > phenix_regression/misc/tst_rstbx.csh > > The second problem is that test_all_parallel script fails to detect an actual failure. > > It would be great if somebody who is in charge of rstbx and testing could look at this. > > Best regards, > Oleg Sobolev. > > -- > This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. 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Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/cctbxbb > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/cctbxbb > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb

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