Search results for "look through"

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

10 years, 11 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

10 years, 11 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.

2 months, 1 week

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

5 years, 10 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

17 years, 9 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, 1 month

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

14 years, 6 months

Re: [phenixbb] phenix.automr high zscore but too many clashes

by Andreas Förster

Hey Zach, remove the loops from your search model and rerun the MR. Alternatively, increase the maximum number of clashes allowed until you get a solution written out. See where your solutions clash. Again, if it's in a loop region, cut the loop and rerun. Your z-scores look great. (Notice that you have zed-scores when you run phaser through ccp4i and zee-scores when you run phaser through phenix.) Andreas zach powers wrote: > Hi, > > > I have a problem and i wonder if someone has had a similar experience. I > have been using phenix.automr program to find an MR solution for a > protein. When I ask Phaser to use copies=2 I find a number of solutions > with poor z-scores (3-4). When I ask it to use copies=3, I get great > Z-scores (see below) but no solution due to the high number of clashes > (>100!). > > As an x-ray newbie I am a bit perplexed of what to make of this: the > solution is not good because there is not enough space in the unit cell > to comfortably accommodate all three molecules yet the Z-score indicates > the structure is good. > > My structure does have several loops and these may be contributing to > the clashing residues. As a newbie I have a newbie question - what does > this mean (great z-score but no solutions)? Is this non-solution a > possible solution if I play with it, or is the packing simply too tight > and the Z-scores are not valid? > > In the meantime I am chopping my protein into sub-domains as recommended > in the Phaser documentation, but if anyone has seen something like this > before, any suggestions are welcome. > > thanks > zach charlop-powers > > > > > Packing Table: Space Group P 3 > ------------------------------ > Solutions accepted if number of clashes = 135 (lowest number of > clashes in list) > provided this number of clashes <= 10 (maximum number of allowed clashes) > # #Clashes # Accepted Annotation > 1 188 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=10.4 > 2 156 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=10.2 > 3 151 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=9.8 > 4 146 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=9.7 > 5 187 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 > TFZ=10.5 > 6 202 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=9.2 > 7 170 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=9.1 > 8 144 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 > TFZ=10.2 > 9 177 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=9.1 > 10 153 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.9 > 11 150 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.8 > 12 217 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.6 > 13 182 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.6 > 14 135 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.5 > 15 175 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.3 > 16 159 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.3 > 17 192 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.3 > 18 165 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 > TFZ=9.2 > 19 169 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 > TFZ=9.1 > 20 158 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.0 > 21 173 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.0 > 22 154 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 > TFZ=8.9 > 23 206 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=7.8 > > 0 accepted of 23 solutions > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

16 years, 2 months

Re: [cctbxbb] Niggli-reduced cell C++ implementation

by Ralf Grosse-Kunstleve

Hi Martin, Let me know if you need svn write access to check in your changes. All I need is your sourceforge user id. Ralf On Fri, Mar 23, 2012 at 3:35 AM, Martin Uhrin <martin.uhrin.10(a)ucl.ac.uk>wrote: > Dear David and Rolf, > > thank you for your encouragement. > > David: I'm more than happy to port your implementation to cctbx if you're > happy with this. Of course I don't want to step on your toes so if you'd > rather do it yourself (or not at all) that's cool. > > There may be some licensing issues to sort out as it looks like cctbx has > a custom (non viral) license but the BSD license is likely compatible. > > On first impression I think a new class would be the way to go but I'd > have to look at the two algorithms in greater detail to be sure. > > All the best, > -Martin > > > On 22 March 2012 22:00, Ralf Grosse-Kunstleve <rwgrosse-kunstleve(a)lbl.gov>wrote: > >> Hi Martin, >> You're very welcome to add a C++ version of the Krivy-Gruber algorithm to >> cctbx if that's what you had in mind. >> I'm not sure what's better, generalizing the fast-minimum-reduction code, >> or just having an independent implementation. >> Ralf >> >> On Thu, Mar 22, 2012 at 2:24 PM, Martin Uhrin <martin.uhrin.10(a)ucl.ac.uk>wrote: >> >>> Dear Cctbx community, >>> >>> Firstly I'd like to say thank you to Rolf, Nicholas and Paul for their >>> expertly thought through implementation of the reduced cell algorithm. >>> I've found it to be extremely useful for my work. >>> >>> My code is all in C++ and I'd like to be able to use the Krivy-Gruber >>> algorithm. My understanding is that only the reduced (Buerger) unit cell >>> algorithm is implemented in C++ [1] which guarantees shortest lengths but >>> not unique angles. From my understanding the Krivy-Gruber would also >>> guarantee me uniqueness of unit cell angles, however this is only >>> implemented in Python [2]. Sorry to be so verbose, I just wanted to check >>> that I was on the right page. >>> >>> Would it be possible for me to implement the Krivy-Gruber in C++ by >>> adding in the epsilon_relative to the parameter and following the procedure >>> found in the python version? >>> >>> Many thanks, >>> -Martin >>> >>> [1] >>> http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1uctbx_1_1fas… >>> [2] >>> http://cctbx.sourceforge.net/current/python/cctbx.uctbx.krivy_gruber_1976.h… >>> >>> >>> >>> -- >>> Martin Uhrin Tel: +44 >>> 207 679 3466 >>> Department of Physics & Astronomy Fax:+44 207 679 0595 >>> University College London >>> martin.uhrin.10(a)ucl.ac.uk >>> Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk >>> >>> _______________________________________________ >>> 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 >> >> > > > -- > Martin Uhrin Tel: +44 > 207 679 3466 > Department of Physics & Astronomy Fax:+44 207 679 0595 > University College London > martin.uhrin.10(a)ucl.ac.uk > Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > >

13 years, 3 months

Re: [phenixbb] temp files

by Tom Terwilliger

Hi James, Not the code (I hope), just any scripts that use these methods. Like this: mkdir /var/tmp/autosol phenix.autosol p9.sca 2 se temp_dir=/var/tmp/autosol Now the temp files go in /var/tmp/autosol and the output files go in AutoSol_run_xxx/ as usual All the best, Tom All the best, Tom T On Sat, Apr 24, 2021 at 11:59 AM James Holton <jmholton(a)lbl.gov> wrote: > 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> 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 >> >> 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 > > > > -- > Thomas C Terwilliger > Laboratory Fellow, Los Alamos National Laboratory > Senior Scientist, New Mexico Consortium > 100 Entrada Dr, Los Alamos, NM 87544 > Email: tterwilliger(a)newmexicoconsortium.org > Tel: 505-431-0010 > > > -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

4 years, 2 months

Search results for query "look through"