Search results for "look through"

Re: [phenixbb] temp files

by Billy Poon

Hi James, By default, the GUI should try to delete AutoBuild temporary files. However, if the jobs crash, the cleaning up might not take place. In that case, the deletion of temporary files can be manually run by selecting "Projects" in the menu bar, then "Clean up large files", and then selecting the project directory. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Sat, Apr 24, 2021 at 2:56 PM James Holton <jmholton(a)lbl.gov> wrote: > What if people are using the GUI ? > > On 4/24/2021 2:51 PM, Tom Terwilliger wrote: > > 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 > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

4 years, 2 months

Re: [phenixbb] alternatives to RMSD

by Morten Grøftehauge

Hi Patrick, The quick and easy way of doing this would be to use Rob Nicholls' ProSMART in CCP4. It does a local structure alignment and gives you a value for the superposition of main chain atoms. I don't know of any tool in Phenix that does this. Cheers, Morten On 8 July 2014 14:56, MARTYN SYMMONS <martainn_oshiomains(a)btinternet.com> wrote: > 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 > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > -- Morten K Grøftehauge, PhD Pohl Group Durham University

10 years, 11 months

Re: [phenixbb] helix/sheet outliers

by Oleg Sobolev

Hi Casper, > I am doing real space refinement on a protein model build from a cryo-em > map. I run the refinement with Amber gradients turned on and with secondary > structure restraints (otherwise, more or less default settings). > Amber gradients should not be relevant to the issue. SS filtration is based on input model geometry before any coordinate refinement was done. > I have some issues with helix and sheet outliers. > > Every time I run the refinement (after making sure that the bond distance > in the helices are within the 3.5 Å) > I get a lot of bad annotation remarks, but with outliers just above 3.5 Å > (see .log below): > > > > … > > removed outlier: 3.576A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " > (cutoff:3.500A) > > Proline residue: A 180 - end of helix > > removed outlier: 3.681A pdb=" N PHE A 188 " --> pdb=" O LEU A > 184 " (cutoff:3.500A) > > removed outlier: 3.628A pdb=" N PHE A 189 " --> pdb=" O ILE A > 185 " (cutoff:3.500A) > > removed outlier: 3.521A pdb=" N ILE A 190 " --> pdb=" O ALA A > 186 " (cutoff:3.500A) > > Processing helix chain 'A' and resid 219 through 228 > > removed outlier: 3.737A pdb=" N MET A 227 " --> pdb=" O GLU A > 223 " (cutoff:3.500A) > > … > > > > Is this something that I just need to fix in several rounds of refinement > or is there an explanation? > If you believe the distances you see in the log are wrong, I'm happy to investigate. Please send me the model file (off-list) with an explanation why do you think so. The distances (even 3.5) suggest a rather poor helix geometry since the target distance is 2.9A. If you are sure your annotations are correct, you may try to relax the threshold by setting parameter "distance_cut_n_o" to some larger value than default 3.5. Then the restraints will be imposed and hopefully the geometry of the helix will become good during refinement. > In addition, I have some bad sheet annotations such as: > > > > … > > removed outlier: 6.987A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " > (cutoff:3.500A) > > removed outlier: 4.659A pdb=" N VAL B 442 " --> pdb=" O LEU B > 431 " (cutoff:3.500A) > > removed outlier: 6.296A pdb=" N LEU B 431 " --> pdb=" O VAL B > 442 " (cutoff:3.500A) > > removed outlier: 5.062A pdb=" N ALA B 444 " --> pdb=" O THR B > 429 " (cutoff:3.500A) > > removed outlier: 6.129A pdb=" N THR B 429 " --> pdb=" O ALA B > 444 " (cutoff:3.500A) > > … > > > > When I look at the model, the residues are definitely a part of the sheet > – the long distance between the N-O atoms is due to the O being “flipped” > (hope it makes sense). > > Is this because of wrong annotation? > If you believe the residues are part of the sheet - then the annotation is correct, the model is wrong. If you believe the O needs to be "flipped" - go ahead and flip it. Do any other adjustments you deem necessary to improve the model and hydrogen-bonding pattern. This may result in proper distance between N and O and established restraint. Such big model changes are better done manually rather than during refinement with restraints. Some relevant tutorials are: https://www.youtube.com/watch?v=9dCkAdR1RDk&feature=youtu.be https://www.youtube.com/watch?v=qB8W_6yuw5k&feature=youtu.be Relevant documentation and links in it: https://www.phenix-online.org/documentation/reference/secondary_structure.h… Please let us know if you have more questions. Best regards, Oleg Sobolev. > > > > > Best > > Casper > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

5 years, 2 months

Re: [phenixbb] Solving MR solution without sequence information

by Tom Peat

Hello Eric, You've had some good responses as to things to do already, but I'll throw in one 'old school' method. When I had this situation (although with somewhat higher resolution data), I went through the density with Coot and tried to put in residues where I thought I could identify them (Trp, Phe, Cys, Pro, etc). I did this iteratively (with some refinement) until I came up with a stretch of say 8-10 residues where I thought the sequence fit the density reasonably well. I then did a search for that sequence. In your case, if you obtained the protein from E. coli, then I would just search the E. coli set of proteins using something like UniProt. You obviously need to take into account that you won't be able to tell the difference between Asp/Asn and Glu/Gln, so don't look for 100% matches. This allowed me to narrow down the possible proteins to just one or two and I then had a full sequence to work with. Might be worth a shot. Best of luck, tom ________________________________ From: phenixbb-bounces(a)phenix-online.org <phenixbb-bounces(a)phenix-online.org> on behalf of Rosenberg, Eric (NIH/NCI) [F] <eric.rosenberg(a)nih.gov> Sent: Saturday, February 4, 2023 7:22 AM To: phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> Subject: [phenixbb] Solving MR solution without sequence information You don't often get email from eric.rosenberg(a)nih.gov. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi all, I’m in a bit of bind here and am seeking some advice. For context, a former graduate student in our lab set crystal trays of an MBP fusion protein, the fused part after MBP being ~400 amino acids long. This region is also predicted to be mostly unstructured, but has a C-terminal SH3 domain. Our graduate student then graduated and before throwing out some of her trays a year or two later, we found some hits of the MBP fusion protein that actually diffracted to 2.9 Angstrom. I spent some time working on it after we collected the data (June 2021), but because I didn’t know what crystallized specifically, it was impossible to phase, and replicating seemed next to impossible, too. The Matthew’s coefficient was predicting ~130 amino acids in the ASU, space group C222 or C2221. Since whatever crystallized was clearly a degradation product of the MBP fusion, I tried phasing with SH3 domains and a lot of other things to no avail. As a final last ditch effort I eventually submitted the .mtz file to SBGrid to perform a Wide Search MR job, and low and behold it actually found MR solutions that had TFZ scores ~17 in space group C2221! So here’s my current situation—I have been able to phase the data set using the MR search model, but again, I don’t know what specifically it is that I’ve crystallized. I’m currently able to get the Rfree to ~0.4, but can’t seem to improve it. I am really at a loss of what to do, since there are obvious backbone issues with the protein (as seen from iterative build composite omit maps), but every time I try to manually correct them it seems to make the Rfree worse. The MR solution does not align very well at all to the MBP fusion, only ~20 identity, and again, I don’t know to which ~130 amino acids I crystallized out of the ~400 of the MBP fusion. Is it one continuous stretch, two copies of a shorter stretch, etc.? I tried phasing with a polyalanine model of the MR search model and then tried autobuilding just a polyalanine sequence to get the backbone right, but that doesn’t seem to work. Autobuild also fails when trying to various fragments of the MBP fusion sequence. Other than opening coot and manually building the entire polypeptide chain, is there an easier method? I think that once the backbone is totally right the phases will improve so I can start putting in side chains, but I’m not sure. My latest effort is to just use Sculptor prior to Phaser in order to force the sequences to match, but again, I don’t know precisely what sequence was crystallized. I have tried both the Phenix and CCP4 software suites, for reference. Any and all help would be much appreciated (and yield an acknowledgement on a paper, if this ever works). Best, Eric Rosenberg CRTA Postdoctoral Fellow Randazzo Lab Laboratory of Cellular and Molecular Biology National Cancer Institute, US

2 years, 5 months

Re: [cctbxbb] Making branches by accident

by Nigel Moriarty

Markus I was a non-rebaser but I have set it to true on my second machine. So my question is regardind branches. I have made a branch, made some changes and merged the master into the branch. I will make some more changes during testing. I assume that I merge into the master at some point. Will the commits appear in the log based on the time of the merge or the time I committed in the branch? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Thu, Dec 8, 2016 at 12:14 AM, <markus.gerstel(a)diamond.ac.uk> wrote: > I use a custom prompt so I can see what is going on when I am in a git > repository folder. > > This is the code one could add to their ~/.bashrc: > https://gist.github.com/Anthchirp/dfc9a4382f8dfc9a97fe1039c9e6789a > > This is what it looks like: > https://postimg.org/image/8c9h72qwd/ > > This is what happens in the image: > * yellow brackets indicate you are in git territory, and contain the > current branch name > * red branch name = uncommitted changes in repository > * positive number: number of commits the local repository is ahead of the > remote repository > * the 'git pull' command causes an implicit merge commit, which I undo > with the next command > * negative number: number of commits the local repository is behind the > remote repository > * both negative and positive number: branches have diverged > > Maybe someone finds it useful. > > -Markus > > > ________________________________ > From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] > on behalf of Pavel Afonine [pafonine(a)lbl.gov] > Sent: Wednesday, December 07, 2016 18:24 > To: cctbxbb(a)phenix-online.org > Subject: Re: [cctbxbb] Making branches by accident > > This happened to me a few times now, and just double-checked that my > .gitconfig contains "rebase = true". Let's see if it happens again.. > Pavel > > On 12/7/16 00:02, Graeme.Winter(a)diamond.ac.uk<mailto: > Graeme.Winter(a)diamond.ac.uk> wrote: > Morning all > > I am seeing a certain amount of “Merge branch 'master' of github.com: > cctbx/cctbx_project” coming through on the commits – this usually means > you did not do a git pull –rebase before the git push. This can be set to > the default by using the spell Markus sent out > > git config --global pull.rebase true > > This will need to be done on each machine you push from, else getting the > habit of doing a git pull –rebase before push is a good one. > > We have had this on and off with DIALS but it tends to pass easily enough. > > What bad happens? Nothing really but the history becomes confusing… > > So: may be worth checking that you have the pull.rebase thing set? > > Cheerio Graeme > > > > -- > > 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<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 >

8 years, 6 months

Re: [phenixbb] reflection file utility and use of modified phases in refinement

by Engin Ozkan

Hi Tom, My second question was about autobuild recommending modified phases to be used in further refinement. This is the end of the log file printed by autobuild. See the line for "Data for refinement": Summary of output files for Solution 3 from rebuild cycle 4 --- Model (PDB file) --- pdb_file: AutoBuild_run_1_/cycle_best_4.pdb --- Refinement log file --- log_refine: AutoBuild_run_1_/cycle_best_4.log_refine --- Model-building log file --- log: AutoBuild_run_1_/cycle_best_4.log --- Model-map correlation log file --- log_eval: AutoBuild_run_1_/cycle_best_4.log_eval --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PH FOFCWT --- refine_map_coeffs: AutoBuild_run_1_/cycle_best_refine_map_coeffs_4.mtz --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz --- Density-modification log file --- log_denmod: AutoBuild_run_1_/cycle_best_4.log_denmod --- Density-modified map coefficients FP PHIM FOM --- hklout_denmod: AutoBuild_run_1_/cycle_best_4.mtz If HLAM, HLBM, HLCM and HLDM are density-modified phases, it looks like that's what autobuild suggests. Thanks again, Engin On 8/28/09 7:07 AM, Thomas C. Terwilliger wrote: > Hi Engin, > > I'm not sure about your main question...I hope that Nat or Pavel will > answer you on that. > > On the use of density-modified phases in refinement: AutoBuild expects > experimental phases in the data file, with experimental HL coefficients, > and it by default it will use those HL coefficients in refinement with an > MLHL target. > > The phase probabilities from resolve statistical density modification are > pretty accurate, and not inflated, so you could use them in refinement if > you wanted to. I don't suggest it, however, because the > density-modification phase information is not fully independent of the > other information used in refinement (e.g., a flat solvent is implicit in > your refinement already, so including that through density modification is > partially redundant). > > ps: I hope AutoBuild doesn't recommend using density-modified phases in > refinement, so if you could send me the text where it says that, I will > check that out! > > All the best, > Tom T > > >>> Hi everybody, >>> >>> I had some trouble with the reflection file utility today. I've been >>> trying to import Rfree-flag column from one of the mtz's to my combined >>> mtz, and it never does. The R-free flag is always left out of the output >>> even when I have it selected. Have you guys seen this (I'm using 147)? >>> >>> Another question I have is about the output of phenix.autobuild. >>> Phenix.autobuild tells me to use modified phase probabilities (HLAM, >>> etc.) in refinement. I am assuming this is density-modified phases. But >>> I've always thought that this would be bad practice (possibly because of >>> unrealistically high FOMs and possible flattening of loops, etc, but >>> maybe resolve does a better job than, say DM). Any ideas on that one? >>> >>> Thanks, >>> >>> Engin >>> >>> -- >>> Engin Özkan >>> Post-doctoral Scholar >>> Dept of Molecular and Cellular Physiology >>> Howard Hughes Medical Institute >>> Stanford University School of Medicine >>> ph: (650)-498-7111 >>> >>> _______________________________________________ >>> 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 > -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111

15 years, 10 months

Re: [cctbxbb] CBF compositing

by Graeme.Winter＠diamond.ac.uk

Hi Frank, OK, so we have done something recently which I think would be very similar, converting tiff files and "dat" files (don't ask) to full 'n' proper cbf files. It worked sensibly and would work in your case, but as you point out it would involve some post processing. In this example however the postprocessing was done by cbflib, which makes it a little more kosher. In essence, the program does this: - read tiff files -> numpy arrays -> sum - read dat file - write cbf header with empty image using template and dat file contents - read / write this file through cbflib adding the image data in flight You should be able to do this all in one go, looking at pycbf_test4.py in the new distribution of cbflib / pycbf, but you may find it a bit of a fiddle constructing the full cbf file ab initio. Cheerio, Graeme -----Original Message----- From: cctbxbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Frank Murphy Sent: 03 December 2012 13:19 To: cctbx mailing list Subject: Re: [cctbxbb] CBF compositing Graeme, Unfortunately, my intent is to write out the image as a proper CBF. Your email is exactly correct, as I was at first quite happy to find how simple it was to add the images together, but then disappointed as I have struggled writing out a proper CBF in one step. I, of course, can write the CBF out and then hack the header, but this wastes a lot of time, having to effectively write a CBF twice. I was able to write a header and CBF data separately and then concatenate them, but the header for the CBF data file needs edited... Frank On Dec 3, 2012, at 5:01 AM, <Graeme.Winter(a)diamond.ac.uk> wrote: > Hi Frank, > > It would be easy to write one, as pycbf is included in there as is some code to unpack the byte-offset compression quickly in iotbx.detectors - > > from iotbx.detectors import ImageFactory > > image = ImageFactory(filename) > image.read() > image.get_raw_data() > > You would however need to create and pack the data to a new CBF file, which IIRC requires some new additions to the pycbf bindings - I asked Herbert B about this a while back and he needed to make some patches as it was not generally possible. That said, what I was after was creating a full cbf not e.g. miniCBF. > > Adding the new version to a live version of cctbx/python is easy enough. > > I take it as a given that this is for visualizing - you're not too worried about the image headers? Otherwise this will be somewhat more tricky. > > Email from Herbert B follows. It went to the imgCIF mailing list so is public already :o) > > Best wishes, > > Graeme > > ------------- > > > Dear Graeme, > > I have made a new example that uses setters and writes a byte-offset compressed image. Testing revealed some bugs in the wrapper for some of the setters, so I have also updated the release kit. The whole thing is available on the CBFlib_bleeding_edge svn on sourceforge as well as a release kit > > http://downloads.sf.net/cbflib/CBFlib-0.9.2.6.tar.gz > > Please give it a try and take a look at pycbf/pycbf_test4.py for an example of writing a byte-offset CBF. Let me know if it does what you need. If not, tell me what is missing or wrong and I'll be happy to fix things and add more pycbf examples to the kit. > > Regards, > Herbert > > P.S. This was a very useful question because it relate to testing the HDF5 changes. > > -----Original Message----- > From: cctbxbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Frank Murphy > Sent: 01 December 2012 14:22 > To: cctbx mailing list > Subject: [cctbxbb] CBF compositing > > Hello, > > Does anyone have a CCTBX-based method for compositing multiple CBFs to a single image a la merge2cbf? > > Thanks in advance, > Frank Murphy > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > 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 Frank Murphy frankvmurphy(a)gmail.com _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org 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

12 years, 7 months

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

by Randy John Read

Hi, Thanks for sending the log files! The jobs turn out not actually to be identical. The GUI automatically chose to use the intensity data (which is what we prefer for use in Phaser) whereas your job run from a script is using amplitude data. The issue I alluded to earlier occurs only for intensity data, because the analysis of those data involves applying different equations, which use a special function (tgamma from the Boost library). For some reason I don’t understand, when the Intel version of the tgamma algorithm is computed using the Rosetta functionality to run it on an ARM processor, it’s much much slower than other calculations. Just last week (right after I finally got an M2 MacBook Pro), we tracked this down and replaced the calls to Boost tgamma with alternative code, and that problem should exist any more. You can use it already in Phenix by getting a recent nightly build, and I’ve asked the CCP4 people to compile a new version of Phaser and release it as an update to CCP4 as well. Best wishes, Randy > On 4 Jul 2023, at 12:05, Xavier Brazzolotto <xbrazzolotto(a)gmail.com> wrote: > > 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>. > > <command_line_PHASER.log><GUI_phaser.log> ----- 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 Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

2 years

[phenixbb] Re: for autobuild full sequence?

by Pavel Afonine

Hi James, Yes, that makes sense, and it’s what I suspected. Creating a string of residues that matches your sequence is, as I mentioned, a ten-minute exercise in CCTBX. However, ensuring that it folds within the allowed volume, avoids self-clashes, and meets other geometric quality metrics is a more complex challenge—but not impossible. My approach would be to create a map where all voxels occupied by existing atoms have negative values. Then, assuming the start and end points of your chain are known, I’d generate a rough path through non-negative voxels. From there, a round of real-space simulated annealing could refine the structure. But that’s starting to sound like a full project now! Pavel On 4/1/25 13:23, James Holton wrote: > Yes, but I don't want it to clash with other molecules in the unit > cell, including itself. > > When I was an undergrad, Steve Mayo called this an "amorphous > builder". Trivial in concept, but you need to do a "bump check" after > adding each atom, and then have a plan for what to do if you hit a bump. > > Make sense? > > -James > > > On 4/1/2025 1:10 PM, Pavel Afonine wrote: >> Hi James, >> >> Are you just looking to string residues together in a line from start >> to end according to your sequence? That’s a quick 10-minute exercise >> using CCTBX, but I suspect that’s not exactly what you need. >> >> Pavel >> >> On 4/1/25 12:28, Tom Terwilliger wrote: >>> Hi James, >>> I think there is no way to force AutoBuild to build a full sequence >>> when there is no density. >>> All the best, >>> Tom T >>> >>> >>> On Tue, Apr 1, 2025 at 10:26 AM James Holton <jmholton(a)lbl.gov> wrote: >>> >>> Hey all, >>> >>> Don't worry, nothing is funny today. I have a real question: >>> >>> Is there a way to force phenix.autobuild to build in the entire >>> sequence? As in: the full length of the actual molecule that is >>> in the >>> crystal, such as what is supposed to go into SEQRES, regardless of >>> "visible" density? I am trying to come up with a pipeline for >>> prepping >>> MD simulations of protein crystals. It seems proper to me that the >>> molecule being simulated should be the actual molecular species, >>> disordered bits an all. However, we don't seem to have good >>> technology >>> for building protein chains into "nothingness". Yes, I know >>> Alphafold is >>> a thing, but it is rubbish at clashes in the context of a crystal. >>> >>> I mean, I could write something, but does this tool already exist? >>> >>> Cheers, and happy Tuesday, >>> >>> -James Holton >>> MAD Scientist >>> >>> >>> _______________________________________________ >>> phenixbb mailing list -- phenixbb(a)phenix-online.org >>> To unsubscribe send an email to phenixbb-leave(a)phenix-online.org >>> Unsubscribe: phenixbb-leave@%(host_name)s >>> >>> >>> >>> -- >>> 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 >>> >>> >>> _______________________________________________ >>> phenixbb mailing list --phenixbb(a)phenix-online.org >>> To unsubscribe send an email tophenixbb-leave(a)phenix-online.org >>> Unsubscribe: phenixbb-leave@%(host_name)s >

3 months

Re: [phenixbb] Molecular replacement with fixed solution

by Muhammed bashir Khan

Thanks Randy for your detail reply. Its worked out.. On Fri, January 16, 2015 21:06, Randy Read wrote: > Hi, > > There are two ways to do this, and I’ve just tested them both using the > beta-lactamase:BLIP tutorial from the Phenix distribution. > > 1. The easy way, which is what users are generally meant to do. Define > all the necessary background information (data, both ensembles: beta and > blip, composition with sequence files). Specify one search for one > component, e.g. beta. When this finishes, go to the main “Input and > general options” pane of the GUI and, in the “Use partial solution from > previous job” pulldown, choose the job that placed the beta component. > Now go to the “Search procedure” pane and uncheck “beta” for the search > model and check “blip” instead. Run the search, and it will place the > blip component in the context of the already placed beta-lactamase > component. This could go wrong if the user is obsessively tidy and > deletes the definition for the “beta” ensemble between the first and > second jobs, because the partial solution information specifies how to > place a defined ensemble (which therefore still has to be defined), but it > does not store the placed ensemble. > > 2. The harder way, which is probably what you were trying to do. After > placing the first component, define a new ensemble, giving the PDB file > from the phaser subdirectory created in the first search (I called this > ensemble “beta_placed”). For this one, check the box labelled “Ensemble > is fixed partial solution”. Again, in the “Search procedure” pane, > uncheck “beta” and check “blip”, then run the search. Note that you’re > not specifying any search for the already placed component. This way of > doing things was really only created so people could come in halfway > through a structure solution with another molecular replacement program, > not as the way you would choose to do it with Phaser. > > Actually, the very easiest way, which I hope most users do by default, is > to decide at the beginning what you are hoping to find in the structure > solution and specify all the copies of all the components you’re looking > for in one job. That approach gives Phaser the most flexibility to use an > adaptive search strategy. So, in the tutorial, users are instructed to > set up two searches in the one job, searching for both “beta” and “blip”. > > Let me know if that doesn’t clarify things. > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > Wellcome Trust/MRC Building Fax: +44 1223 336827 > Hills Road > E-mail: rjr27(a)cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > On 16 Jan 2015, at 18:56, Muhammed bashir Khan > <muhammad.bashir.khan(a)UNIVIE.AC.AT> wrote: > >> Hi There; >> >> I want to solve the structure with molecular replacement using phaser in >> phenix GUI. When I get solution from the one, how I can use as it as >> already solution using phenix in the next run. I use the "ensamble is >> fixed partial solution" but seems its not working. Any suggestion will >> be >> highly appreciated. Thanks >> >> Regards >> >> >> -- >> Muhammad Bashir Khan >> ************************************************** >> Department for Structural and Computational Biology >> Max F. Perutz Laboratories >> University of Vienna >> Campus Vienna Biocenter 5 >> A-1030 Vienna >> Austria >> >> Austria >> >> Phone: +43(1)427752224 >> Fax: +43(1)42779522 >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > > -- Muhammad Bashir Khan ************************************************** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522

10 years, 5 months

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