Search results for "look through"

[phenixbb] Re: red blobs (Andrea Smith)

by Dr. Kevin M Jude

Jumping on an old thread… I have a similar situation to Andrea’s; optimize_mask converged to the default values of rsolve and rshrink, but running phenix.mosaic produced quite improved maps. I’m trying, using version 1.21.2-5419, to run phenix.refine with main.mosaic=True and can’t find the setting in the gui, nor is it recognized when I run from the command line. Is it implemented in this version, or in some other version I can download? Best wishes Kevin -- Kevin M. Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 From: phenixbb-bounces(a)phenix-online.org <phenixbb-bounces(a)phenix-online.org> on behalf of Pavel Afonine <pafonine(a)lbl.gov> Date: Thursday, March 28, 2024 at 7:49 AM To: Andrea Smith <andrea.smith(a)uochb.cas.cz> Cc: phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org>, Kay Diederichs <Kay.Diederichs(a)uni-konstanz.de> Subject: Re: [phenixbb] red blobs (Andrea Smith) Hi Andrea, here is what you can do today.. phenix.mosaic model.pdb data.mtz (yes, command line only, so far). This will take a minute or less (or more if the model is very large) and create model_mosaic.mtz file that contains the following Fourier map coefficients for mFo-DFc and 2mFo-DFc kind of maps: mFo-DFc_whole mFo-DFc_main mFo-DFc_mosaic 2mFo-DFc_whole 2mFo-DFc_main 2mFo-DFc_mosaic (you can see the MTZ file content by using this command: phenix.mtz.dump model_mosaic.mtz) The suffixes 'whole', 'main' and 'mosaic' refer to the types of masks used in calculation of each map and are explained in the paper: https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909 To reiterate: 'whole' refers to the standard default bulk-solvent mask; 'main' refers to the largest part of the standard default bulk-solvent mask (small mask droplets inside protein region are removed); 'mosaic' refers to the mosaic mask, which is essentially the 'main' mask plus only those smaller masks that contain measurable amounts of the bulk-solvent (the rest, empty ones, that are responsible for 'red blobs' are removed). Next, you load these maps and your atomic model into Coot and inspect. Artifacts such as 'red blobs' you reported earlier should be absent in 'mFo-DFc_mosaic' map. This may lead to improvement of corresponding '2mFo-DFc_mosaic' map. Now, as you can see, this is separate from refinement. Here is what you should be able to do tomorrow.. Today I will add a parameter to phenix.refine (main.mosaic=True/False), which means if you get and install tomorrow's nightly build of Phenix (dev-5285 and up) the mosaic maps, both mFo-DFc_main and 2mFo-DFc_mosaic, will be present in the MTZ file created by phenix.refine (which is available in both CL and GUI). Let me know if you have any questions! Good luck! Pavel On 3/28/24 06:24, Andrea Smith wrote: > Hi all, > > can anyone please tell me how to use the mosaic model? I went through > the phenix documentation and didn't find anything about how to use it. > > Thank you, > Andrea > > > > On Friday, March 15, 2024 22:14 CET, "Andrea Smith" > <andrea.smith(a)uochb.cas.cz> wrote: >> Hi, >> >> I went through the paper quickly during the day thinking I will have >> a thorough look at home only to realize I don't have acces to it. >> >> From the quick look it seemed that my biological background will not >> be enough to understand all of it, but I remember that it said at the >> end that the mosaic model is implemented in phenix. However, I don't >> know where. I went through the parameters in GUI and didn't find >> anything that seemed to fit the description. >> >> Could you please explain what setting I need to use in the refinement? >> >> Thank you, best, >> Andrea >> >> On Friday, March 15, 2024 16:16 CET, Pavel Afonine <pafonine(a)lbl.gov> >> wrote: >>> Hi All, >>> >>> The explanation of the reason for these blobs and the solution is both >>> detailed in depth in this paper: >>> >>> https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909 >>> >>> Quick facts are: >>> >>> - These blobs are artifacts of bulk-solvent modeling. >>> - You can efficiently deal with them in Phenix. >>> - In some cases (which I witnessed myself), it is important to deal with >>> them for map improvements elsewhere (for example, in regions of >>> interest, such as ligands). >>> >>> Let me know if you have any questions! >>> >>> All the best, >>> Pavel >>> >>> >>> On 3/15/24 07:39, Mitchell D. Miller wrote: >>> > Hi Andrea, >>> > >>> > You can also put a few zero occupancy atoms in the negative >>> > density to force phenix.refine to exclude the region >>> > from the bulk solvent mask. >>> > >>> > (You may also need to set >>> > refinement.mask.ignore_zero_occupancy_atoms = False >>> > so that the zero occupancy atoms are included in the mask) >>> > >>> > Regards, >>> > Mitch >>> > >>> > >>> > >>> > Quoting Kay Diederichs <kay.diederichs(a)uni-konstanz.de>: >>> > >>> >> Hi Andrea, >>> >> >>> >> hmm, did phenix.refine actually use optimize_mask=true ? >>> >> >>> >> If you compare the logfiles of phenix.refine (for the default run >>> >> with opimize_mask=false, and the new run with optimize_mask=true) >>> >> side-by-side with xxdiff or vimdiff (yes this needs to be run from a >>> >> command-line) then there should be a difference. >>> >> >>> >> Making peace with the red blobs is somewhat unsatisfactory from a >>> >> technical viewpoint, but probably not relevant from a biological one. >>> >> >>> >> I'd guess that the authors of >>> >> https://journals.iucr.org/a/issues/2024/02/00/pl5035/index.html would >>> >> be interested to look at your case ... >>> >> >>> >> Best wishes, >>> >> Kay >>> >> >>> >> >>> >> Am 15.03.24 um 08:27 schrieb Andrea Smith: >>> >>> Hi Kay, >>> >>> >>> >>> I tried the mask optimization and there is no change in how the >>> >>> final map looks like. >>> >>> >>> >>> Should I just make peace with it? >>> >>> >>> >>> Best, >>> >>> Andrea >>> >>> >>> >>> On Thursday, March 14, 2024 23:11 CET, Kay Diederichs >>> >>> <kay.diederichs(a)uni-konstanz.de> wrote: >>> >>>> Hi Andrea, >>> >>>> >>> >>>> in your case, phenix.refine seems to fill bulk solvent into volumes >>> >>>> that >>> >>>> are not actually filled by solvent. >>> >>>> It might help to optimize the mask, see >>> >>>> >>> https://phenix-online.org/documentation/reference/refinement.html#bulk-solv… >>> >>>> >>> >>>> "6. Mask parameters". >>> >>>> >>> >>>> Best, >>> >>>> Kay >>> >>>> -- >>> >>>> Kay Diederichs http://strucbio.biologie.uni-konstanz.de >>> >>>> email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 >>> >>>> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 >>> Konstanz >>> >>>> >>> >>>> This e-mail is digitally signed. If your e-mail client does not >>> >>>> have the >>> >>>> necessary capabilities, just ignore the attached signature >>> >>>> "smime.p7s". >>> >>>> _______________________________________________ >>> >>>> phenixbb mailing list >>> >>>> phenixbb(a)phenix-online.org >>> >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>>> Unsubscribe: phenixbb-leave(a)phenix-online.org >>> >> >>> >> -- >>> >> Kay Diederichs http://strucbio.biologie.uni-konstanz.de >>> >> email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 >>> 4049 >>> >> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 >>> Konstanz >>> >> >>> >> This e-mail is digitally signed. If your e-mail client does not >>> have the >>> >> necessary capabilities, just ignore the attached signature >>> "smime.p7s". >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > phenixbb mailing list >>> > phenixbb(a)phenix-online.org >>> > http://phenix-online.org/mailman/listinfo/phenixbb >>> > Unsubscribe: phenixbb-leave(a)phenix-online.org _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

1 year, 3 months

Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR

by Xavier Brazzolotto

For information Apple M2 running Ventura 13.4.1 with 64 Go memory Phenix 1.20.1-4487 (Intel one). I’ve run MR of the same dataset (2.15A - I422) with the same model both with the command line and through the GUI. Command line (phenix.phaser) : 48 secs. GUI (Phaser-MR simple one component interface): 18 mins ! In copy the two log files if this helps > Le 4 juil. 2023 à 12:54, Luca Jovine <luca.jovine(a)ki.se> a écrit : > > Hi Xavier and Randy, I'm also experiencing the same on a M2 Mac! > -Luca > > -----Original Message----- > From: <phenixbb-bounces(a)phenix-online.org <mailto:[email protected]>> on behalf of Xavier Brazzolotto <xbrazzolotto(a)gmail.com <mailto:[email protected]>> > Date: Tuesday, 4 July 2023 at 12:38 > To: Randy John Read <rjr27(a)cam.ac.uk <mailto:[email protected]>> > Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org <mailto:[email protected]>> > Subject: Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR > > > Hi Randy, > > > Indeed I’m running Phenix on a brand new M2 Mac. > I will benchmark the two processes (GUI vs command line) and post them here. > > >> Le 4 juil. 2023 à 12:32, Randy John Read <rjr27(a)cam.ac.uk <mailto:[email protected]>> a écrit : >> >> Hi Xavier, >> >> We haven’t noticed that, or at least any effect is small enough not to stand out. There shouldn’t be a lot of overhead in communicating with the GUI (i.e. updating the terse log output and the graphs) but if there is we should look into it and see if we can do something about it. >> >> Could you tell me how much longer (say, in percentage terms) a job takes when you run it through the GUI compared to running the same job outside the GUI on the same computer? Also, it’s possible the architecture matters so could you say which type of computer and operating system you’re using? If it’s a Mac, is it one with an Intel processor or an ARM (M1 or M2) processor? (By the way, we finally managed to track down and fix an issue that cause Phaser to run really slowly on an M1 or M2 Mac when using the version compiled for Intel, once I got my hands on a new Mac.) >> >> Best wishes, >> >> Randy >> >>> On 4 Jul 2023, at 10:44, Xavier Brazzolotto <xbrazzolotto(a)gmail.com <mailto:[email protected]>> wrote: >>> >>> Dear Phenix users >>> >>> I’ve noticed that molecular replacement was clearly slower while running from the GUI compared to using the command line (phenix.phaser). >>> >>> Did you also observe such behavior? >>> >>> Best >>> Xavier >>> _______________________________________________ >>> 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]> >> >> >> ----- >> Randy J. Read >> Department of Haematology, University of Cambridge >> Cambridge Institute for Medical Research Tel: +44 1223 336500 >> The Keith Peters Building >> Hills Road E-mail: rjr27(a)cam.ac.uk <mailto:[email protected]> >> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk >> > > > > > _______________________________________________ > 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]> > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. > > > Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

2 years, 7 months

[phenixbb] Postdoctoral Position at the University of Illinois at Chicago | POLIKANOV Lab

by Yury Polikanov

*Postdoctoral Position Available in the Polikanov Lab <https://sites.google.com/view/polikanovlab>Department of Biological Sciences, University of Illinois at Chicago* *The Polikanov Laboratory <https://sites.google.com/view/polikanovlab> in the Department of Biological Sciences at the University of Illinois at Chicago is looking for a talented, skillful, and highly motivated researcher to fill the Postdoctoral Fellow position to study the structure and function of the bacterial ribosome.* For full consideration, please submit your application and cover letter describing your scientific interests and how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group at: https://uic.csod.com/ux/ats/careersite/1/home/requisition/14663?c=uic *Position Summary:* The research in the Polikanov Laboratory at UIC is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. Postdoctoral Fellow will conduct research in the Polikanov lab and be involved in the determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography and potentially cryo-EM techniques. *Duties & Responsibilities:* - Perform research relevant to the assigned projects; - Act independently in planning, executing, and troubleshooting the experiments; - Purify bacterial ribosomes and additional components necessary for the crystallization experiments; - Collect X-ray diffraction data from the ribosome crystals at the APS Synchrotron and/or collect cryo-EM data at the UChicago cryo-EM facility; - Perform structural data analysis; - Directly participate in writing manuscripts and grants based on the obtained experimental data; - Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry; - Attend weekly group meetings and journal clubs. *Minimum Qualifications:* - PhD in biology, chemistry, biochemistry, biophysics, or a related field; completed within the past 5 years *Preferred Qualifications:* - Strong background in molecular biology and biochemistry; - Practical skills with the most standard methods currently used in molecular biology and biochemistry (such as protein expression and purification); - Experience in structural biology (cryo-EM or X-ray crystallography); - Experience in RNA biology is desired. About the University of Illinois Chicago: UIC is among the nation’s preeminent urban public research universities, a Carnegie RU/VH research institution, and the largest university in Chicago. UIC serves over 34,000 students, comprising one of the most diverse student bodies in the nation and is designated as a Minority Serving Institution (MSI), an Asian American and Native American Pacific Islander Serving Institution (AANAPSI) and a Hispanic Serving Institution (HSI). Through its 16 colleges, UIC produces nationally and internationally recognized multidisciplinary academic programs in concert with civic, corporate and community partners worldwide, including a full complement of health sciences colleges. By emphasizing cutting-edge and transformational research along with a commitment to the success of all students, UIC embodies the dynamic, vibrant and engaged urban university. Recent “Best Colleges” rankings published by U.S. News & World Report, found UIC climbed up in its rankings among top public schools in the nation and among all national universities. UIC has over 300,000 alumni, and is one of the largest employers in the city of Chicago.

9 months, 2 weeks

Re: [phenixbb] alternatives to RMSD

by Pavel Afonine

Hi Patrick, supposing models are superposed appropriately (see previous comments on phenixbb), step-by-step I see it as following: - compute density map for model A (or its Fourier synthesis of resolution 1A or higher), - compute density map for model B (or its Fourier synthesis of resolution 1A or higher), - compute map CC per residue or per atom between maps corresponding to A and B. I would think that "superposed appropriately" is a key here. Pavel On 7/5/14, 7:22 AM, PC wrote: > Hi Pavel, > > Thank you very much, this sounds very interesting. > > I have used ccp4, coot and phenix but I am no expert but I am > definitely interested in trying this method if you could give more > information. > > Thank you, > Patrick. > > > -----Original Message----- > *From:* pafonine(a)lbl.gov > *Sent:* Fri, 04 Jul 2014 20:34:33 -0700 > *To:* patrick.cossins(a)inbox.com, phenixbb(a)phenix-online.org > *Subject:* Re: [phenixbb] alternatives to RMSD > > Hi Patrick, > > RMSD is a poor measure in this case as it does not account for > B-factors, occupancies, alternative conformations and so on > information a crystal structure model may make available. > Macromolecules are not a bunch of points in space. > > While I'm sure more thorough methods exist, I would vote for the > simplest, most direct and obvious one. You can calculate electron > density map using a Gaussian approximation from model A and B > (yes, electron density map - not a Fourier image of it!). That > will naturally account for all: B-factors, occupancies, other > disorder. Then you can calculate a map similarity measure, such as > map correlation, for instance. After all, why use a cannon to kill > a fly?! > > If you are interested to follow this route I can explain the details. > > All the best, > Pavel > >> Hi Phenix users, >> >> I am not a crystallographer but I though you guys might be a good >> place to ask this question. >> >> I have 2 super secondary structures, A and B and they consist of >> Helix-turn-Strand >> >> Due to the turn the two structures have a poor RMSD because the >> two flanking fragments of Helix and Strand are far from each >> other but when I superimpose the two fragments >> individually(helixA with helix B and standA with strandB in Pymol >> they align very well). >> >> Now, is there a way to express this instead of using the RMSD? >> When the two structures align well the RMSD is very good but a >> slight movement and the RMSD is awful. >> But looking at the two structures I can see they follow the same >> path through space. >> >> Thank you, >> Patrick > > ------------------------------------------------------------------------ > Protect your computer files with professional cloud backup. Get PCRx > Backup and upload unlimited files automatically. > <http://backup.pcrx.com/mail>

11 years, 7 months

Re: [phenixbb] alternatives to RMSD

by Pavel Afonine

Hi Tim, consider two atoms located at say 1A distance apart. In one case their B-factors are 1A**2 and in the second case their B-factors are 100A**2. In the first case these are two individual atoms and measuring distance between them makes sense, while in the second case atoms virtually coincide (within the cloud of their possible locations, given their B-factor) and therefore measuring distance between them isn't very meaningful. Using the map would differentiate these two scenarios, while usual way of computing RMSD would not. I guess this is what I was trying to say in my previous post. Whether the values of a metric of choice are intuitive or not is a separate question. After all you can always calibrate your expectations using examples with known answer. Pavel On 7/7/14, 3:47 AM, Tim Gruene wrote: > Hi Patrick, > > why don't you superimpose only the matching segments and report their > RMSD? It is the common procedure for RMSD's from superpositions to > report the aligned residues together with the RMSD. > > The advantage compared to a map CC is similar to that of R_sym over > R_meas: readers have a better concept (from experience) of what the > numbers mean. > > Best, > Tim > > On 07/02/2014 05:15 PM, Patrick. C wrote: >> Hi Phenix users, >> >> I am not a crystallographer but I though you guys might be a good place to ask >> this question. >> >> I have 2 super secondary structures, A and B and they consist of Helix-turn-Strand >> >> Due to the turn the two structures have a poor RMSD because the two flanking >> fragments of Helix and Strand are far from each other but when I superimpose the >> two fragments individually(helixA with helix B and standA with strandB in Pymol >> they align very well). >> >> Now, is there a way to express this instead of using the RMSD? >> When the two structures align well the RMSD is very good but a slight movement >> and the RMSD is awful. >> But looking at the two structures I can see they follow the same path through space. >> >> Thank you, >> Patrick >> >> >> -------------------------------------------------------------------------------- >> 3D Earth Screensaver Preview <http://www.inbox.com/earth> >> *Free 3D Earth Screensaver* >> Watch the Earth right on your desktop! Check it out at www.inbox.com/earth >> <http://www.inbox.com/earth> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

11 years, 7 months

Re: [phenixbb] alternatives to RMSD

by MARTYN SYMMONS

That's a reasonable approach and I think that it is similar to the one used by FATCAT - which I notice is the basis for structural comparison at the RCSB site. Motivation and some results in the paper ( http://www.ncbi.nlm.nih.gov/pubmed/14534198) It's not clear to me, though, how to fairly compare the resulting RMSD of fragments with twists between. If I introduce an arbitrary number of twists then I can improve the rmsd artificially. In sequence matching there is a penalty for introducing a gap and that is scaled compared with the amino acid substitution scoring to split the match into a 'reasonable' number of sub-alignments. Obviously in 3D case there should also be a penalty for introducing a split in the structure to do a twist re-orientation - but how to quantify it compared with RMSD and get a global score? Seems to me better would be to express the whole problem in torsional space - so the twists would be large displacements while the matched sections should have close fit in torsional angles. And a global score could be calculated. Someone must have tried this? All the best Martyn Cambridge ----Original message---- >From : tg(a)shelx.uni-ac.gwdg.de Date : 07/07/2014 - 11:47 (GMTDT) To : phenixbb(a)phenix-online.org Subject : Re: [phenixbb] alternatives to RMSD Hi Patrick, why don't you superimpose only the matching segments and report their RMSD? It is the common procedure for RMSD's from superpositions to report the aligned residues together with the RMSD. The advantage compared to a map CC is similar to that of R_sym over R_meas: readers have a better concept (from experience) of what the numbers mean. Best, Tim On 07/02/2014 05:15 PM, Patrick. C wrote: > Hi Phenix users, > > I am not a crystallographer but I though you guys might be a good place to ask > this question. > > I have 2 super secondary structures, A and B and they consist of Helix-turn-Strand > > Due to the turn the two structures have a poor RMSD because the two flanking > fragments of Helix and Strand are far from each other but when I superimpose the > two fragments individually(helixA with helix B and standA with strandB in Pymol > they align very well). > > Now, is there a way to express this instead of using the RMSD? > When the two structures align well the RMSD is very good but a slight movement > and the RMSD is awful. > But looking at the two structures I can see they follow the same path through space. > > Thank you, > Patrick > > > -------------------------------------------------------------------------------- > 3D Earth Screensaver Preview <http://www.inbox.com/earth> > *Free 3D Earth Screensaver* > Watch the Earth right on your desktop! Check it out at www.inbox.com/earth > <http://www.inbox.com/earth> > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

11 years, 7 months

Re: [cctbxbb] some thoughts on cctbx and pip

by Dr Robert Oeffner

Agree. I talked with a small molecules software developer here at the ECM32 yesterday. He would love to be able to do “pip install cctbx” when he develops his program, provided it doesn’t take up much file space. Rob Sent from my Windows 10 phone -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234 From: Derek Mendez Sent: 20 August 2019 18:06 To: cctbx mailing list Subject: Re: [cctbxbb] some thoughts on cctbx and pip I think its worth getting a cctbx-light pip build.. I think modules like cctbx miller, sgtbx are extremely useful. Also simtbx.nanoBragg. -Derek On Sun, Aug 18, 2019 at 10:48 PM Graeme.Winter(a)Diamond.ac.uk <Graeme.Winter(a)diamond.ac.uk> wrote: Hi Aaron Re: talk about if interest I think it would be very useful to have a roadmap of where this is going, the intentions and how we expect it to play with other cctbx-dependent projects - have I missed this? Having it somewhere e.g. on the wiki would be a big help Thanks Graeme On 17 Aug 2019, at 00:36, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> 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<mailto:[email protected]>> 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<http://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<mailto:[email protected]>> 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<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<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). 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 http://phenix-online.org/mailman/listinfo/cctbxbb

6 years, 5 months

Re: [cctbxbb] coordinates -> space group + matrices

by Kris Andersen

Ralf, thanks for your reply as well. Let me see if I understand. Since I can get the lattice symmetry easily, I assume cctbx can give me the point group symmetry operations for the lattice. Then I "just" need to cycle through at most 48 matrices to see which are compatible with my coordinates. Assuming I can find that subset, cctbx can easily tell me the final space group, right? (The answer may be along the lines of correlation coefficients, but that's alright.) The problems then are, 1. What basis are the point group symmetry matrices for the lattice in? 2. What about translations? Am I right in thinking that the P1 map solves the second problem? If I find all the space groups, down to P1, that contain a subset of my point group symmetry operations and try all the space group operations in them again my coordinates, that solves the problem right?. Can cctbx help me with that? I'm still not sure about the first issue. I guess one of the crystallography tomes must define a unique way to represent my coordinates for a given space group such that the group operations are also in that basis? How about cctbx helping me with that? Thanks again for all the help. I am happy to do some coding work on this myself, but first I need to understand things better. Best regards. On Sep 17, 2007, at 11:53 PM, Ralf W. Grosse-Kunstleve wrote: > Hi Kris, > your questions isn't simple and the solution isn't straightforward. > The functionality you are looking for isn't implemented in the cctbx. > You are right in your assumption that most of what you need > is already available, but there are missing pieces. > Given a unit cell (your primitive vectors), the cctbx can give you > the corresponding highest point-group symmetry (lattice symmetry) > in a very robust way, but there is nothing to loop over the > compatible space groups and to check if the symmetry operations > are compatible with the coordinates. > There are some programs out there which do this. I think Ton Spek's > PLATON for example. The Superflip program (google) determines the > symmetry > from a P1 map. There is also J. Appl. Cryst. (2005). 38, 237-238 and > J. Appl. Cryst. (1998). 31, 922-928. There may be more. I haven't > followed the developments very closely. > An idea that has been floating around in my mind for a long time is > to use the fast translation function. Make a map given your > coordinates, > loop over all space group, use the fast translation function to find > the origin. This is implemented in phenix.hyss. It should be > relatively > easy to adapt this implementation for your purpose. You'd get > scores (correlation coefficients) instead of yes/no answers. This > could be useful to uncover approximate symmetry, but I'm just > guessing. > If you want to try implementations yourself, I'd be happy to > answer specific questions. > Ralf > > > Tonight's top picks. What will you watch tonight? Preview the > hottest shows on Yahoo! TV. > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/cctbxbb

18 years, 4 months

Re: [cctbxbb] Automated Travis CI for phenix

by Billy Poon

Hi Elliot, Also, to run those files from the command-line, you would have something like, libtbx.python <CCTBX directory>/mmtbx/command_line/fmodel.py <your command-line arguments> The libtbx.python will call python with the proper environment to be cctbx-aware. -- 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 Thu, May 24, 2018 at 10:39 AM Oleg Sobolev <osobolev(a)lbl.gov> wrote: > Hi Elliot, > > phenix.fmodel and phenix.maps scripts are fully available in cctbx: > > cctbx_project/mmtbx/command_line/fmodel.py > cctbx_project/mmtbx/command_line/maps.py > > and have zero dependencies from Phenix closed-source repository. > You can just call them with cctbx-aware python in your software. > > Best regards, > Oleg Sobolev. > > On Thu, May 24, 2018 at 3:37 AM, Elliot Nelson <elliot.nelson(a)dtc.ox.ac.uk > > wrote: > >> 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 >> >> >> _______________________________________________ >> 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 >

7 years, 8 months

Re: [phenixbb] phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups

by Pavel Afonine

Hi Mark, tomorrow I will a post a link to some detailed description of underlying algorithms and examples. Pavel. On 12/14/10 7:34 PM, Mayer, Mark (NIH/NICHD) [E] wrote: > Great; look forwards to using, > A question for those of us who have been using TLSMD for a few years > is how the groups differ. You give timing comparisons for GroEL but > do not report if the TLS groups differ, and if they do, how much the > groups differ: e.g. is it a residue or two at the group ends, or larger > differences. > > Mark > > ________________________________________ > From: Pavel Afonine [pafonine(a)lbl.gov] > Sent: Tuesday, December 14, 2010 9:45 PM > To: PHENIX user mailing list > Subject: [phenixbb] phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups > > PHENIX users: > > starting dev-610 (development version of PHENIX) there is a new tool > available for completely automated partitioning a model into TLS groups: > > http://www.phenix-online.org/download/nightly_builds.cgi > > To run: > > phenix.find_tls_groups model.pdb > > or if you have a multiple CPU machine: > > phenix.find_tls_groups model.pdb nproc=N > > where N is the number of CPUs available (thanks Nat for > parallelization!). There is no parameters that a user is supposed to > tweak (except defining the number of CPUs, if desired). > > The result of running the above command are atom selections that define > TLS groups. These atom selections are ready to use in phenix.refine. > > This is available from PHENIX GUI too, where automatically defined TLS > groups can be readily visualized and checked on the graphics (thanks Nat!). > > The algorithm is fast. > For example, for a GroEL structure (3668 residues, 26957 atoms, 7 > chains) it takes only 135 seconds using 1 CPU, and 44 seconds using 10 > CPUs. Analogous job takes 3630 seconds using TLSMD server. > For a lysozime structure it takes 9.5 seconds with one CPU, and 2.5 > seconds using 10 CPUs. The timing results may vary depending on the > performance of your computer. > > There is ongoing work that will slightly improve phenix.find_tls_groups > within the next few weeks / a month; however the current version is > functional and can be tried now. An example of such improvements are > analyzing (scoring) user-defined TLS groups (for example, TLS groups > from PDB file header), automated combining cross-chain TLS groups > (non-contiguous segments) that will be obtained through connectivity > analysis, better handling non-protein chains, and more. Integration with > phenix.refine is also planned. > > Any feedback is very much appreciated! > > Thanks, > Pavel. > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

15 years, 1 month

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