Search results for "look through"

Re: [cctbxbb] flex index

by Ralf Grosse-Kunstleve

Yes, that's true, the padded arrays are a permanent struggle. A few days ago Nat changed the fft_map.real_map_unpadded() method to do the unpadding in place by default, to avoid memory overhead. That's probably the way to go in most situations. Ralf On Tue, Oct 18, 2011 at 4:20 AM, Monarin Uervirojnangkoorn < monarin(a)biochem.uni-luebeck.de> wrote: > Thanks!. very useful. although doesn't really work with padded array (as in > the case of real_map object). but found my way round. > > best > mona > > On Oct 18, 2011, at 11:17 AM, Ralf Grosse-Kunstleve wrote: > > Hi Mona, > > Try this: > > from scitbx.array_family import flex > a=flex.double([1,4,5,7,5,6,6,1]) > a.set_selected(a > 5, 5) > print list(a) > > Or in smaller steps: > > bool_selection = a > 5 > assert bool_selection.size() == a.size() > print list(bool_selection) > a.set_selected(bool_selection, 5) > print list(a) > > You can also call a.set_selected(bool_selection, b) > where b is an array with as many elements as you have True in the > bool_selection. > > This kind of working with selections is very typical within cctbx/phenix. > If you look through our sources you'll find a lot of examples; in passing, > we have two types of selections, bool selections as above, and integer > selections. The latter are useful for permutations, e.g. to sort array > elements, or if you know you select only a small number of elements from a > large array. Let me know if you have more questions about selections and > I'll be happy to explain. (I guess one day I should write a "Working with > selections" tutorial.) > > Ralf > > On Tue, Oct 18, 2011 at 2:54 AM, Monarin Uervirojnangkoorn < > monarin(a)biochem.uni-luebeck.de> wrote: > >> Hi, >> >> I'm using flex and 'd like to get an access to elements fall beyond/ below >> certain value. eg. >> a=[1,4,5,7,5,6,6,1] >> anything beyond 5 should be set to 5. (in matlab then a(a>5)=5;) >> if you could tell me how to do this quickly for flex, that would be great. >> for now i use loop and that is... pretty slow. >> >> many thanks. >> mona >> >> >> >> ^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^ >> Institute of Biochemistry, >> Institut für Neuro- und Bioinformatik, >> Graduate School for Computing in Medicine and Life Sciences >> University of Lübeck, >> Ratzeburger Allee 160 >> Lübeck 23538 >> Germany >> Tel: +49451-5004072 >> Fax: +49451-5004068 >> >> >> >> >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > > > ^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^ > Institute of Biochemistry, > Institut für Neuro- und Bioinformatik, > Graduate School for Computing in Medicine and Life Sciences > University of Lübeck, > Ratzeburger Allee 160 > Lübeck 23538 > Germany > Tel: +49451-5004072 > Fax: +49451-5004068 > > > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > >

14 years, 3 months

Re: [phenixbb] phenix.refine problems with my pdb

by Nicholas Noinaj

matt, >>> Number of atoms with unknown nonbonded energy type symbols: 308 just curious, did you have 308 waters? as peter said, hard to determine exact problem without some files or examples to look at. also phenix does a good job with water picking, in my little experience. just one more question, when you do get the refinement to work, is your ligand(s) included with the protein model? just no waters, right? it wasn't completely clear from your message. if the ligands aren't included, i recommend adding it(them) back and see if refinement works. then if that works, try water picking within phenix. again, best of luck. cheers, nick -----Original Message----- From: Matthew Bowler <mwb(a)mrc-dunn.cam.ac.uk> To: noinaj(a)uky.edu, PHENIX user mailing list <phenixbb(a)phenix-online.org> Date: Thu, 15 Mar 2007 14:15:45 +0000 Subject: Re: [phenixbb] phenix.refine problems with my pdb Thanks for replies so far.... I removed all ligands and then waters - the waters seem to be the problem as the protein model is now refining, do they need to be treated/marked in a different way for phenix? Thanks again, Matt. On 15 Mar 2007, at 13:32, Nicholas Noinaj wrote: > matt, > > can't offer much help, but have you tried to remove the ligand and > try refinement? it would let you know if the pdb file or the > presence of the ligand is the problem. at least let you would know > where you should focus your attention. > > if all else fails, have you tried getting parameters for your > ligand from the PRODRG Server and using that for inputing the > ligand parameters into phenix.refine directly when you setup the > refinement job? (I think i have done this before???) > > here is the website in case you aren't familiar... > http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ > > Again, Best of luck! > > > > cheers, > nick > > > -----Original Message----- > From: Matthew Bowler <mwb(a)mrc-dunn.cam.ac.uk> > To: phenixbb(a)phenix-online.org > Date: Thu, 15 Mar 2007 13:00:42 +0000 > Subject: [phenixbb] phenix.refine problems with my pdb > > Dear All, > I am trying to run phenix.refine but I keep getting the message: > > > Sorry: Fatal problems interpreting PDB file: > Number of atoms with unknown nonbonded energy type symbols: 308 > Please edit the PDB file to resolve the problems and/or supply a > CIF file with matching restraint definitions. Note that > elbow.builder is available to create restraint definitions. > > I have run my ligands through elbow and used the output .cif but I > still get the same message. I can find no info on this problem in > the manual or the BB, can anyone help? Thanks in advance, yours, > Matt. > > > > > > Matthew Bowler > MRC Dunn Human Nutrition Unit > Wellcome Trust / MRC Building > Hills Road > Cambridge CB2 2XY > Tel: 0044 (0) 1223 252826 > Fax: 0044 (0) 1223 252825 > > _______________________________________________ > 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 Matthew Bowler MRC Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 2XY Tel: 0044 (0) 1223 252826 Fax: 0044 (0) 1223 252825

18 years, 10 months

Re: [phenixbb] Joint X-ray / neutron refinement

by Billy Poon

Hi Kristoffer, Are you running from the command-line? The current GUI in 1.21 does not support joint refinement. We will release 1.21.1 to add support. If you use the command-line, the presence of the xray and neutron scopes will switch the parser to process the parameter file for joint xn refinement. You should see a log that looks like Starting phenix.refine on Sat Feb 24 05:50:17 2024 by bkpoon =============================================================================== Processing files: ------------------------------------------------------------------------------- Found phil, params.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ params.eff Switching to joint x-ray/neutron refinement mode ------------------------------------------------------------------------------- The 1.21.1 release will probably be next week. I'm currently testing the GUI. Thanks! -- 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 Fri, Feb 23, 2024 at 11:58 AM Tim Gruene <tim.gruene(a)univie.ac.at> wrote: > Hello Kristoffer, > > maybe this is related to the first paragraph at the link that you > provide ("The paradigm and implementation of the joint X-ray and > neutron refinement were changed in the fall of 2023, as documented > here: https://pubmed.ncbi.nlm.nih.gov/37942718/"): > > It is better to use the information from an X-ray dataset via > geometric restraints and refine against neutron data only (cf. DOI > 10.1107/S1600576713027659), so that you focus on the information from > the neutron data. > > Cheers, > TIm > > On Fri, 23 Feb 2024 10:58:17 +0000 Kristoffer Lundgren > <kristoffer.lundgren(a)compchem.lu.se> wrote: > > > Hello phenixbb, > > > > When trying to do joint refinement in phenix.refine 1.21-5207 using > > the suggested joint_xn.eff file found at > > > https://phenix-online.org/documentation/reference/refinement.html#neutron-a… > > as a template I get some error messages (running phenix.refine from > > the command line): > > > > Unrecognized PHIL parameters: > > ----------------------------- > > xray.refinement.refine.strategy (file "joint_xn.eff", line 33) > > xray.refinement.main.simulated_annealing (file "joint_xn.eff", > > line 36) xray.refinement.main.ordered_solvent (file "joint_xn.eff", > > line 37) xray.refinement.main.number_of_macro_cycles (file > > "joint_xn.eff", line 38) neutron.refinement.refine.strategy (file > > "joint_xn.eff", line 45) neutron.refinement.main.simulated_annealing > > (file "joint_xn.eff", line 48) > > neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line > > 49) neutron.refinement.main.number_of_macro_cycles (file > > "joint_xn.eff", line 50) > > > > Can you please advice on how to proceed? It looks like the options > > supplied are not recognized at all by phenix.refine. > > > > Best regards > > Kristoffer > > > > > > From: <phenixbb-bounces(a)phenix-online.org> on behalf of Derek Logan > > <derek.logan(a)biochemistry.lu.se> Date: Monday, 22 January 2024 at > > 09:39 To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> > > Cc: Ulf Ryde <ulf.ryde(a)compchem.lu.se>, "esko.oksanen_ess.eu" > > <esko.oksanen(a)ess.eu> Subject: ***SPAM*** [phenixbb] Joint X-ray / > > neutron refinement > > > > Hi phenixbb, > > > > I'm trying to understand the current status of joint X-ray/neutron > > refinement in phenix.refine. The announcement of the latest release > > mentions a change in the algorithm as described in the recent > > publication. In the documentation: > > > > Structure refinement in > > PHENIX< > https://phenix-online.org/documentation/reference/refinement.html#neutron-a… > > > > phenix-online.org< > https://phenix-online.org/documentation/reference/refinement.html#neutron-a… > > > > > > [AURqZhI53yp3gAAAABJRU5ErkJggg==]< > https://phenix-online.org/documentation/reference/refinement.html#neutron-a… > > > > > > > > > > it's described how you can run joint refinement using a parameter > > file. Does this mean that it is *only* possible in this way and not > > through the GUI? The GUI was very useful in the past as it > > automatically opened Coot with the maps for both X-rays and neutrons, > > and the refinement statistics for both were displayed in the GUI. As > > far as I can see joint refinement via the GUI last worked in version > > 1.19.2-4148 from 2021. > > > > Best regards > > Derek > > > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

1 year, 11 months

Re: [cctbxbb] Git

by Nicholas Sauter

>From the DIALS-West perspective, the switch to git has been a stumbling block to participation. I would have to agree with Ralf that git seems to be a tool for very smart people but not for folks who just want a simple tool for managing code. I can't agree with Markus that a linear history is dispensable. In fact, this is one feature in svn that I've found very helpful over the years. If a feature is broken today, but I know for a fact that it worked sometime in the past, I simply do a svn update -r "[datestamp]" to narrow down the exact date when the feature became broken, then I isolate the exact commit and look at the code. Can this be done with git or does it even make sense if there is no concept of linear change? The git environment seems a bit chaotic, and not conducive to close cooperation, from what I can see now. More experience with it may convince me otherwise. Nick Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713 On Tue, Jan 12, 2016 at 2:22 AM, <luis.fuentes-montero(a)diamond.ac.uk> wrote: > Hi fellows, > > > > I believe it is not a bad idea to move to https://github.com (the > servers) and later on decide if move to use *git* (the CLI tool). This > can an incremental way to do transition. And will allow really old fashion > developers (those who refuse to learn *git*) or conservative policies to > survive and still move to a new more reliable code repository. > > > > Just my thoughts, > > > > Greetings, > > > > Luiso > > > > > > > > *From:* cctbxbb-bounces(a)phenix-online.org [mailto: > cctbxbb-bounces(a)phenix-online.org] *On Behalf Of * > markus.gerstel(a)diamond.ac.uk > *Sent:* 12 January 2016 09:56 > *To:* cctbxbb(a)phenix-online.org > *Subject:* Re: [cctbxbb] Git > > > > Dear Luc, > > > > We actually had a look at the quality of the Github svn interface when we > prepared for the DIALS move. My verdict was that it is surprisingly useful. > > All the possible git operations are mapped rather well onto a linear SVN > history. All the branches and tags are accessible either by checking out > the root of the repository, ie. > > svn co https://github.com/dials/dials.git (not recommended, as, > say, any new branch/tag will probably result in a huge update operation for > you) > > or by checking them out directly, ie. > > svn co https://github.com/dials/dials.git/branches/fix_export > > or svn co https://github.com/dials/dials.git/tags/1.0 > > > > Forks by other people are, as is the case when using git, simply not > visible. I agree that looking at the project history through SVN may not be > as clear as the git history. I wonder how relevant this is though, as you > can explore the history, without running any commands, on the Github > website, eg. https://github.com/dials/dials/network, > https://github.com/dials/dials/commits/master, etc. > > > > Creating new branches and tags and merging stuff via SVN would be a major > operation. However, that has always been the case with SVN, and for that > reason one generally just does not do these things in SVN. > > But for an SVN user group those operations would not be important – you > every only need to merge stuff if you create branches – so I don’t really > see the problem. If you want to tag releases you can do that on the Github > website as well as with a git command. > > > > In summary, I do recognize that SVN users will have difficulties > participating in branched development, and in particular will not be able > to quickly switch between branches. > > But I don’t think that this will be a problem, or that there is a need for > a policy to keep the history linear. > > > > Best wishes > > -Markus > > > > > > *From:* cctbxbb-bounces(a)phenix-online.org [ > mailto:[email protected] > <cctbxbb-bounces(a)phenix-online.org>] *On Behalf Of *Luc Bourhis > *Sent:* 11 January 2016 16:45 > *To:* cctbx mailing list > *Subject:* Re: [cctbxbb] Gi, > > > > Hi Graeme, > > > > Can we revisit the idea of moving to git for cctbx? > > > > This brings to mind a question I have been asking myself since the subject > has been brought forth. The idea Paul wrote about on this list was a move > to Github. I guess some, perhaps many, developers will keep interacting > with the repository using subversion. I am worried this would clash with > the workflow of those of us who would go the native git way. By that I mean > creating many branches and merge points, which one would merge into the > official repository when ready. I am worried the history would look very > opaque for the subversion users. I would even probably create a fork on > Github, making it even more opaque for a tool like subversion. Has anybody > thought about such issues? My preferred solution would be for everybody to > move to git but I don’t think that’s realistic. At the other end of the > spectrum, there is putting in place a policy to keep the history linear. > > > > Best wishes, > > > > Luc > > > > > > -- > > 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 > > > > > -- > > 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 > >

10 years

Re: [phenixbb] temp files

by James Holton

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 > <mailto:[email protected]>> 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 >> <mailto:[email protected]>> wrote: >> >> Thank you Li-Wei >> >> Definitely not placing blame on one program. Phenix.autobuild >> is another >> big temp file producer. So is XDS. Clearly this ligand run >> was a case >> of a misconfigured, runaway task that never finished. >> However, the files >> lingered on disk, eating up inodes for 3 years! >> >> The reason I'm asking is I think there are significant >> performance >> increases to be gained by using fast, local storage for >> scratch files. >> This is not just in speed but storage and overall system/cluster >> performance. Very few things are more expensive than an NFS >> write! >> >> Does anyone know how to change the default temp file location >> across >> phenix ? Is this a cctbx thing? >> >> Thanks >> >> -James >> >> >> On 4/23/2021 9:38 PM, Li-Wei Hung wrote: >> > Hi James, >> > >> > I'll leave the global Phenix temp aspect to Billy. >> > For ligand identification specifically, the working >> directory is where >> > all the files are located. The program will purge most of the >> > intermediate files upon completion. If the user interrupted >> the runs >> > or if the program crashed at certain spots, the purge >> mechanism might >> > not kick in. Even so, it'd take many runs to accumulate >> 20e6 (2e7?) >> > files. In any case, you've got a point and I'll look into >> salvaging >> > intermediate files of ligand identification as soon as they >> are not >> > needed in the process. >> > >> > Thanks, >> > >> > Li-Wei >> > >> > On 4/23/2021 7:03 PM, James Holton wrote: >> >> Hello all, >> >> >> >> Is there a way to configure phenix at install time (or >> perhaps >> >> post-install) to put temporary files under /tmp ? I just >> had to >> >> delete 20e6 temp files over NFS from a single user's >> phenix ligand >> >> identification run. The delete took almost a month. >> >> >> >> Apologies if I am neglecting to look somewhere obvious in the >> >> documentation, >> >> >> >> Happy Weekend! >> >> >> >> -James Holton >> >> MAD Scientist >> >> >> >> _______________________________________________ >> >> phenixbb mailing list >> >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> >> http://phenix-online.org/mailman/listinfo/phenixbb >> <http://phenix-online.org/mailman/listinfo/phenixbb> >> >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> <mailto:[email protected]> >> > >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb >> <http://phenix-online.org/mailman/listinfo/phenixbb> >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> <mailto:[email protected]> >> >> >> >> -- >> Thomas C Terwilliger >> Laboratory Fellow, Los Alamos National Laboratory >> Senior Scientist, New Mexico Consortium >> 100 Entrada Dr, Los Alamos, NM 87544 >> Email: tterwilliger(a)newmexicoconsortium.org >> <mailto:[email protected]> >> Tel: 505-431-0010 >> > > > > -- > Thomas C Terwilliger > Laboratory Fellow, Los Alamos National Laboratory > Senior Scientist, New Mexico Consortium > 100 Entrada Dr, Los Alamos, NM 87544 > Email: tterwilliger(a)newmexicoconsortium.org > <mailto:[email protected]> > Tel: 505-431-0010 >

4 years, 9 months

Re: [phenixbb] Autosol: MIRAS

by ash.k＠aol.com

@Gabor: Thanks Gabor! I'll try MR-SAD. Hope it works. @Andre: I have tried Shelx and Phenix. Se sites from both of them were not the same. I tried giving Shelxd output to Phenix also. That also did not help. I have not tried Autosharp yet. I'll see that too.. However, what now I am primarily looking at is the way to get Se-substructure from the MIRAS run. Is there a way to get that? autosol gives only one heavy atom in the output! Since I have a map which looks promising, so before going to the output of another run I want to explore all the possibilities from this. Se locations in this map should help. AK -----Original Message----- From: Gabor Bunkoczi <gb360(a)cam.ac.uk> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Sent: Thu, Sep 6, 2012 5:52 am Subject: Re: [phenixbb] Autosol: MIRAS Dear AK, if you just need the Se positions, you can run Phaser MR-SAD (available from the GUI) using your partial model as a starting point, together with the Se-Met data. Dependending on the model quality (and the model does not have to be very good), it may be able to locate the Se-sites. BW, Gabor On Sep 6 2012, ash.k(a)aol.com wrote: > Satisfactory map means: I am expecting a coiled coil or helix bundle type > of assembly and I could see some densities appropriate for helices. There > are proper solvent channels and continuous stretches of densities. > > More to add about data on this: the data is anisotropic and the longer > 'c' axis and alignment of helical density along c axis support this. This > also makes me think that perhaps map is sensible. > > Few rounds of model building, refinement and DM has been successful to > assign around 10 polyala helices and their distribution looks sensible > from packing point of view. Now the problem is to assign the side chain. > I was hoping to make use of Se locations for this. R and Rfree are still > random, in the range of 50%. I am not sure, but it could be perhaps > because most of the scattering material is still unassigned. > > > > > > >-----Original Message----- >From: Francis E Reyes <Francis.Reyes(a)colorado.edu> >To: PHENIX user mailing list <phenixbb(a)phenix-online.org> >Cc: phenixbb <phenixbb(a)phenix-online.org> >Sent: Thu, Sep 6, 2012 8:07 am >Subject: Re: [phenixbb] Autosol: MIRAS > > > This one is solvable, but with extreme difficulty. I recently completed a > structure solution with experimental phases starting at 5.0 A using phase > information from multiple derivatives. > > >How would you describe a somewhat satisfactory map? > > >F > >On Sep 5, 2012, at 7:08 PM, ash.k(a)aol.com wrote: > > > > > > > >Hi Shya, > > I did wavelength scan, got a good signal for Se and used appropriate > wavelengths for data collection and also used experimental f' and f'' > values for phasing. I think the reasons SAD or MAD for SeMet data is not > working are (i) low resolution: 3.7 for SeMet (Anomalous data is up to > 4.8A) (ii) I should have mentioned this earlier: 3 out of 6 Se are very > close to N-terminus, possible they are disordered. Unit cell is also some > what big..100, 120 and 320A; F222 space group. > >AK > > > >-----Original Message----- >From: Shya Biswas <shyabiswas(a)gmail.com> >To: PHENIX user mailing list <phenixbb(a)phenix-online.org> >Sent: Thu, Sep 6, 2012 7:29 am >Subject: Re: [phenixbb] Autosol: MIRAS > > >Hi AK, >Did you do a wavelength scan when you collected the SE dataset you >need to put the values of f' and f'' from your wavelength scan in >order to locate the heavy atom sites, 6 methionine should be enough to >phase your molecule. >Shya > >On Wed, Sep 5, 2012 at 9:25 PM, <ash.k(a)aol.com> wrote: >> Hi all, >> >> I am trying to solve a structure through experimental phasing using >> AUTOSOL. I have a couple of heavy atom derivative datasets (Hg, La, Eu, >> Cd) and also a SeMet data. Unfortunately all the datasets are of low >> resolution (3.7-4.2A) and there are possibly 4-8 molecules in the asu. >> MIR, SAD and MAD alone did not give any convincing solution. >> >> However, MIRAS, with a combination of few heavy atom datasets and the >> anomalous data from SeMet crystals, gave a somewhat satisfactory map. >> But the heavy atom site picked by AUTOSOL list only one of the heavy >> atoms i.e. Lanthanum. In another set of run, the solution of which was >> not convincing, the heavy atom substructure had only Hg. There are 6 Met >> out of 200 residues in one molecule and mass spec results show that Se >> incorporation is 100%. >> >> Now, my doubt is that why does the heavy atom substructure contain only >> La and how can I get the substructure involving Se from this solution >> (or the datasets used)? Se location is going to help me a lot for >> finding a starting point to assign side chains. >> >> Any suggestion would be greatly appreciated. >> >> Thanks >> AK >> >> _______________________________________________ >> 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 > > > > >_______________________________________________ >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 > > > -- ################################################## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ################################################## _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

13 years, 5 months

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

by Martin Uhrin

Dear cctbxers, I've finally found the time to play around with a C++ version of the KG algorithm and I've come across a result I don't understand. I've tried both David's C++ and the cctbx python niggli_cell() implementations and they both give the roughly the same answer. I'm reducing the following cell with two, equivalent, representations (a, b, c, alpha, beta, gamma): Before: 1: 4.630811 4.630811 4.630811 90 90 90 2: 3.27448 5.67156 5.67156 99.5941 106.779 90 After: 1: 4.63081 4.63081 4.63081 90 90 90 2: 3.27448 5.67154 5.67156 99.5941 90 106.778 Looking at the trace, cell 1 undergoes step 3 and finishes while cell 2 undergoes steps 2, 3, 7 and 4. Does anyone know why these haven't converged to the same cell? Many thanks, -Martin On 23 March 2012 17:12, Ralf Grosse-Kunstleve <rwgrosse-kunstleve(a)lbl.gov>wrote: > 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 >> >> > > _______________________________________________ > 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

13 years, 9 months

Re: [cctbxbb] some thoughts on cctbx and pip

by Luc Bourhis

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> 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… <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/ <https://www.python.org/dev/peps/pep-0513/>). For example, numpy is built according to this standard (see https://pypi.org/project/numpy/#files <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/ <https://www.python.org/dev/peps/pep-0571/>). This is likely a more attainable target (note though by default C++11 is not supported on Centos 6). > > If we built a manylinuxX version of cctbx and uploaded it to PyPi, the user would need all the non-python dependencies. There's no way to specify these in pip. For example, cctbx requires boost 1.63 or better. The user will need to have it in a place their python can find it, or we could package it ourselves and supply it, similar to how the pip h5py package now comes with an hd5f library, or how the pip numpy package includes an openblas library. We'd have to do the same for any packages we depend on that aren't on pip using the manylinux standards, such as wxPython4. > > Further, we need to think about how dials and other cctbx-based packages interact. If pip install cctbx is set up, how does pip install dials work, such that any dials shared libraries can find the cctbx libraries? Can shared libraries from one pip package link against libraries in another pip package? Would each package need to supply its own boost? Possibly this is well understood in the pip field, but not by me :) > > Finally, there's the option of providing a source pip package. This would require the full compiler toolchain for any given platform (macOS, linux, windows). These are likely available for developers, but not for general users. > > Anyway, these are some of the obstacles. Not saying it isn't possible, it's just a lot of effort. > > Thanks, > -Aaron > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb

6 years, 5 months

Re: [phenixbb] phaser MR

by Randy Read

Hi, If you're unlucky, a combination of pseudo-symmetry and twinning gives only weak indications of twinning, because the twin-related reflections are correlated but the twinning tests assume that they are not. It might be worth considering that possibility. You could try solving the structure in lower symmetry space groups to see whether you get a solution that does not exactly obey the higher symmetry. Are you really certain about the space group? If one symmetry operator is wrong (e.g. a 2-fold instead of a 2-fold screw), some of the symmetry operators are still right, and you can get an apparent solution that partly explains the data. It might be worth running tests in all the variants of P422 as well. Best wishes Randy Read On 23 Jul 2009, at 22:54, sbiswas2(a)ncsu.edu wrote: > Hi Francis, > Thanks for your response. The matthews coefficient suggests two > molecules > in the AU. Phaser also finds two molecules. I ran the dataset through > phenix xtriage it did not indicate twinning though. The molecule also > exists in nature as a monomer. > Shya > > >> Twinning? What's your matthews coefficient say? Do you know if your >> structure is a multimer (biochemistry, etc)? Does it agree with the >> matthews coefficient? >> >> If the unit cell is not big enough to hold all of the contents,then >> this is an indicator for twinning . >> >> FR >> >> On Jul 23, 2009, at 3:09 PM, sbiswas2(a)ncsu.edu wrote: >> >>> Hi all, >>> >>> I was trying to solve a structure by molecular replacement. I scaled >>> the >>> data in P4222 space group (resolution 2.7A) with two molecules in >>> the >>> assymmetric unit (molecule A and B) I ran phaser with my model and >>> got a >>> Zscore of 5.1. When I look at the map that I got from phaser I could >>> easily see good electron density for both molecules, However upon >>> inspection of the electron density map there were considerable >>> interaction >>> or clashes with molecule B and a symmetry atom. Molecule A had no >>> clashes >>> however with the symmetry atoms. I was wondering if anyone knows how >>> to >>> resolve this. Could it be a problem of space group. The statistics >>> are >>> good for space group P4222 and the I/sigI was good till 2.7A. >>> Any advice is appreciated, >>> Shya >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> --------------------------------------------- >> Francis Reyes M.Sc. >> 215 UCB >> University of Colorado at Boulder >> >> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D >> >> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D >> >> _______________________________________________ >> 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 ------ 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

16 years, 6 months

Re: [phenixbb] Selecting ellipsoid of data

by Kay Diederichs

Hi Frank, "such a tool" is at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Aniso_cutoff where it's meant to be applied to INTEGRATE.HKL which comes out of XDS. Doing it this way has the benefit that the statistics printed out by XDS' CORRECT (or SCALA/TRUNCATE; there are people who prefer that route) match the data you refine agains. HTH, Kay > Message: 1 > Date: Thu, 15 Jul 2010 06:32:40 +0100 > From: Frank von Delft<frank.vondelft(a)sgc.ox.ac.uk> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: [phenixbb] Selecting ellipsoid of data > Message-ID:<4C3E9D78.5030203(a)sgc.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, is there a tool in phenix that allows me to select an ellipsoid of > data -- specified e.g. by the highest resolutions in three reciprocal > lattice directions. (Yes, I'm playing with anisotropy, "playing" being > the operative word.) > > phx > > > ------------------------------ > > Message: 2 > Date: Wed, 14 Jul 2010 22:47:30 -0700 > From: "Ralf W. Grosse-Kunstleve"<rwgk(a)cci.lbl.gov> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Selecting ellipsoid of data > Message-ID:<201007150547.o6F5lUoL018490(a)cci.lbl.gov> > Content-Type: text/plain; charset=us-ascii > > Hi Frank, > >> Hi, is there a tool in phenix that allows me to select an ellipsoid of >> data -- specified e.g. by the highest resolutions in three reciprocal >> lattice directions. (Yes, I'm playing with anisotropy, "playing" being >> the operative word.) > > I'm not aware of such a tool. > > Ralf > > > ------------------------------ > > Message: 3 > Date: Thu, 15 Jul 2010 07:15:58 +0100 > From: Frank von Delft<frank.vondelft(a)sgc.ox.ac.uk> > To: "Ralf W. Grosse-Kunstleve"<rwgk(a)cci.lbl.gov>, PHENIX user mailing > list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Selecting ellipsoid of data > Message-ID:<4C3EA79E.2030503(a)sgc.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ralf > > Yeah, I figured. So if I want to use cctbx, where do I start? Just a > pointer to a) package and b) function where I'll see the syntax. > > So equation for ellipsoid is x^2/a^2 + y^2/b^2 + z^2/c^2 = 1; so I > imagine I take each reflection, convert each of h,k,l to 1/reso, and > with a = 1/res(a*), I just check whether the above is< 1. > > The main thing I still need is to convert h,k,l into orthogonal > coordinates.... or do I? I suppose I don't, as what I care for is not > whether it's "really" an ellipsoid, only whether it cuts through miller > index space anisotropically. > > Hmmmm... I may be able to do it in sftools; but if you can in<1minute > give me a link to where to look to get started in cctbx, that would be > awesome. > > (Thanks for listening :) > > > > >> Hi Frank, >> >> >>> Hi, is there a tool in phenix that allows me to select an ellipsoid of >>> data -- specified e.g. by the highest resolutions in three reciprocal >>> lattice directions. (Yes, I'm playing with anisotropy, "playing" being >>> the operative word.) >>> >> I'm not aware of such a tool. >> >> Ralf

15 years, 6 months

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