Search results for "look through"

Re: [phenixbb] SAD related query

by Thomas C. Terwilliger

Hi Tara, It sounds like autosol was not able to find a very good solution to your structure. I would not be too optimistic from what you have said so far, but here is a list of things to check over (from the about-to-be-released phenix manual...!) all the best, Tom T Autosol SAD tutorial: What to do if I do not get a good solution: If you do not obtain a good solution, then it's not time to give up yet. There are a number of standard things to try that may improve the structure determination. Here are a few that you should always try: * Have a careful look at all the output files. Work your way through the main log file (e.g., AutoSol_run_1_1.log) and all the other principal log files in order beginning with scaling (dataset_1_scale.log), then looking at heavy-atom searching (p9_se_w2_PHX.sca_ano_1.sca_hyss.log), phasing (e.g., phaser_1.log or phaser_xx.log depending on which solution xx was the top solution) and density modification (e.g., resolve_xx.log). Is there anything strange or unusual in any of them that may give you a clue as to what to try next? For example did the phasing work well (high figure of merit) yet the density modification failed? (Perhaps the hand is incorrect). Was the solvent content estimated correctly? (You can specify it yourself if you want). What does the xtriage output say? Is there twinning or strong translational symmetry? Are there problems with reflections near ice rings? Are there many outlier reflections? * Try a different resolution cutoff. For example 0.5 A lower resolution than you tried before. Often the highest-resolution shells have little useful information for structure solution (though the data may be useful in refinement and density modification). * Try a different rejection criterion for outliers. The default is ratio_out=3.0 (toss reflections with delta F more than 3 times the rms delta F of all reflections in the shell). Try instead ratio_out=5.0 to keep almost everything. * If the heavy-atom substructure search did not yield plausible solutions, try searching with HYSS using the command-line interface, and vary the resolution and number of sites you look for. Can you find a solution that has a higher CC than the one found in AutoSol? If so, you can read your solution in to AutoSol with sites_file=my_sites.pdb. * Was an anisotropy correction applied in AutoSol? If there is some anisotropy but no correction was applied, you can force AutoSol to apply the correction with correct_aniso=True. > Dear all, > I am a novice user of phenix. I am trying to obtain phases for SAD > dataset > collected at 2.5 angs from autosol.But when i give the phases to > autobuild, > the R-factor is not decreasing below 49%. Also, in warp, it is unable to > built with a message "encounterd an unknown element". Can someone suggest > me > what could be the problem. > > Thanks for any suggestion in advance. > Tara Kashav > > On 9/3/07, phenixbb-request(a)phenix-online.org < > phenixbb-request(a)phenix-online.org> wrote: >> >> Send phenixbb mailing list submissions to >> phenixbb(a)phenix-online.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> or, via email, send a message with subject or body 'help' to >> phenixbb-request(a)phenix-online.org >> >> You can reach the person managing the list at >> phenixbb-owner(a)phenix-online.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of phenixbb digest..." >> >> >> Today's Topics: >> >> 1. command-line Patterson maps (Bryan W. Lepore) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 2 Sep 2007 00:07:51 -0500 (CDT) >> From: "Bryan W. Lepore" <bryanlepore(a)mail.utexas.edu> >> Subject: [phenixbb] command-line Patterson maps >> To: phenixbb(a)phenix-online.org >> Message-ID: >> < >> Pine.LNX.4.64.0709020001190.16588(a)cpe-70-116-17-26.austin.res.rr.com> >> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed >> >> will phenix calculate Pattersons from trial sites or a reflection file >> on >> the command line? i.e. something besides hacking what is already there. >> >> e.g. cns has predict_patterson.inp. i can't seem to find a way to do it >> from the command line - such as `phenix.patterson --sg=94 >> reflections.mtz`. i saw phenix.maps but that looks like electron >> density >> only. >> >> -bryan >> >> >> ------------------------------ >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> End of phenixbb Digest, Vol 22, Issue 1 >> *************************************** >> > > > > -- > Tara Kashav, > Dr. S. Gourinath's Lab, > Lab No 430, > School of Life Sciences, > Jawaharlal Nehru University, > New Delhi - 110067 > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

17 years, 9 months

Re: [phenixbb] Dummy atoms

by Edward A. Berry

I think it is very important to be able to include unknown atoms in a deposited pdb file (with echoing the caveat about flooding the structure with UNK's to lower the R-factor). For one thing, these structures are produced not just for structure-factor calculation and validation. Many of the end users will never even bother to do a structure factor calculation. It important for the depositor to be able to refer to an unknown but likely significant ligand and for the reader to be able to go and look at that position (ideally surrounded by electron density). For another thing, the structure factor calculation will give exactly the same result whether the dummy atoms are omitted or are flagged with zero occupancy or atom-type X to be ignored in sf calculation. In the first case the person calculating structure factors can feel good because the results are exactly right for that model. In the second case he feels bad because he wasn't able to correctly account for those atoms. But the first case is actually a better model. Better to get a slightly wrong value for better model than the correct result for the less good model, especially when the two results are exactly the same. Essentially we are faced with an insurmountable problem: we cannot do a proper job of calculating sf's because of the unk atoms. Better to include but ignore them in sf calc, I think, than to eliminate them and kid ourselves that now we have the right answer. However if the depositor has refined them (suggested by the B-factors present in some of the files), and perhaps chosen an atom-type which results in B-factors compatible with surrounding, it should be possible to include the atom type so his R-factor can be reproduced. This runs the risk of someone over-interpreting the PDB ("I thought I knew what the UNK residue is, but my candidate has 3 C and one N where the UNK has 4 C"). my 2 cents, Ed Pavel Afonine wrote: > Hi Frank, > > thanks a lot for your feedback - as always very useful and critical > which is great! > >> the 2nd-last one of the validation pack, where you recommend against >> the use of UNK atoms, but don't say why: >> >> <snip> >> Some programs and people tend to interpret unknown density using “dummy >> atoms”. In PDB files it typically looks like this: >> ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 X >> ATOM 11 O UNK 2 6.994 -12.600 10.740 1.00 7.16 X >> ATOM 12 O UNK 2 6.028 -13.737 10.607 1.00 6.58 X >> ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28 >> ATOM 14 DUM UNK 2 5.099 -13.727 11.792 1.00 7.15 >> - *Do not deposit this in PDB*, especially if chemical element type is >> undefined >> (rightmost column) >> </snip> > > Sorry for not saying "why". If it ever happens for me to show these > slides again in whatever School I promise to improve the slides to be as > clear as possible. > > The problems with records like: > > ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 X > ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 > ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28 > ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28 X > > are: > > - the chemical element type (column 77-78 ?) (that one that use in Fcalc > calculation and also may provide the charge) is undefined (simply blank > or "X"), so there is no way to include these dummy atoms into structure > factor calculations; > > - even if you have "O" like in the first example this often contradicts > with "X" in rightmost column, so you have to use guesswork, which is not > good for interpreting well defined formatted data files. Plus, of > course, not way to tell the charge; > > - even if you have "O" like in the second example the element type in > rightmost column is missing. Therefore it is a weak information to take: > we cannot reliably extract scattering type from atom label - classical > example CA (Calcium) and CA (C-alpha); > > - of course, we can make the program simply ignore these atoms (hm... > sounds like a bad practice: don't read it if you can't read it - this > way we may end up being ignorant -:) ). But are we sure that the > original program that put these dummies was also not using them in Fcalc > calculation? Or may be it was using some default scattering factor for > them? Which one: H or O or N (N better approximates than O)? > > - furthermore, since we are lacking such a fundamental property of these > dummy atoms as scattering type, it it laughable to assign some B-factors > to these atoms! Look through PDB: you will find a some smart looking > B-factors, such as 8.06 A**2 for an non-existing element X -:) > > In summary: > > - do not put there anything hoping that future generation smarter > software will find out what it is; > - if you want to put something there (which has valid reasons actually - > this will improve the overall map quality which is good - then please > properly define it). > > All the best! > Pavel. > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

14 years, 11 months

Re: [phenixbb] Autobuild

by Terwilliger, Thomas C

Hi Heather, Hmm... a little hard to tell what the problem is. So first: autobuild should have refined this model as one of the first things it did. Did it get about the same R that you got when refining it directly with phenix.refine? If no, then have a look at the refinement .eff files (the autobuild one is in AutoBuild_run_1_/TEMP0 unless that was cleaned up) and see what is different. Next....what happens if you just run phenix.refine to get a map, also take the map from this autobuild run, and look at them along with your model. Is one a lot better than the other? If you take your best working map and run phenix.fit_loops with this model...how does that do? All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Heather L Condurso [condurso(a)bc.edu] Sent: Friday, September 06, 2013 3:54 PM To: PHENIX user mailing list Subject: [phenixbb] Autobuild I'm a bit confused about what is going on with my autobuild run. I solved a structure from anomalous data to 2.7A but many loops are missing. I ran phaser with the current model and native data that extends to 2.4A and got a solution and started autobuild from there. I used mostly the default settings and rebuild_in_place=False. After a pretty short time I realized the run was over and at the bottom of the log I see this: Cycle 3 R/Rfree=0.28/0.35 Built=488 Placed=467 AutoBuild_build_cycle AutoBuild Run 162 Fri Sep 6 14:33:39 2013 Deciding if we should continue... Recent R change per cycle: 0.0 Ending these build cycles as the recent change in R per cycle has been 0.0 and the required value of change is -0.005 and the R is somewhat acceptable at 0.276670644792 All done with build cycles in this region AutoBuild_set_up_build AutoBuild Run 162 Fri Sep 6 14:33:40 2013 All omit/non-omit regions completed finished AutoBuild Run 162 Fri Sep 6 14:33:40 2013 Finishing AutoBuild Run 162 Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat AutoBuild Run 162 Summary of model-building for run 162 Fri Sep 6 14:33:40 2013 Files are in the directory: /Users/heather/Desktop/M/AutoBuild_run_162_/ Starting mtz file: /Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz Sequence file: /Users/heather/Desktop/M/m.pir Best solution on cycle: 2 R/Rfree=0.26/0.33 Summary of output files for Solution 1 from rebuild cycle 2 --- Model (PDB file) --- pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb --- Model (CIF file) --- cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif --- Refinement log file --- log_refine: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine --- Model-building log file --- log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log --- Model-map correlation log file --- log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT --- refine_map_coeffs: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- refine_data: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz --- Density-modified map coefficients FWT PHWT --- denmod_map_coeffs: /Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz You might consider making one very good model now with: phenix.autobuild \ data=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz \ model=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \ rebuild_in_place=True \ seq_file=/Users/heather/Desktop/M/m.pir My full sequence is 325 amino acids so only about 75% is build in. I am hoping autobuild can help find at least some of these missing residues. Why would the change in R be zero? What is meant by "You might consider making one very good model now with:"? I tried running autobuild with these new files and rebuild_in_place=true and get the same type of message. Is this the best that autobuild can do? I also ran the phaser solution through refinement and can significantly lower the Rs from 0.26/0.33 to 0.22/0.30. I appreciate any advice on how best to proceed. I am using 1.8.2-1472 if that matters. Thanks, Heather

11 years, 9 months

Re: [phenixbb] Rosetta refinement fail on Mac

by Andy Watkins

I'm happy to try to debug this but since I don't ordinarily go through the Rosetta refinement protocol -- that's the protein side, which Frank is expert in -- I will probably need to know what Rosetta command line is generated by the above. On Wed, Aug 22, 2018 at 5:51 PM Billy Poon <BKPoon(a)lbl.gov> wrote: > Hi Aaron, > > This looks like a High Sierra issue since this excessive amount of memory > usage is not seen on 10.12. We are tracking this down and will be > contacting the Rosetta developers. It looks like any version of Rosetta > will cause this problem (I tested back to Rosetta 3.7). > > -- > 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 Wed, Aug 22, 2018 at 4:53 PM Aaron Oakley <aarono(a)uow.edu.au> wrote: > >> System: macOS 10.13.6 >> Phenix version: phenix-1.14rc1-3177 >> Rosetta version: 3.9 (rosetta_src_2018.09.60072_bundle) >> >> So I rebuilt rosetta 3.9 as root and can now run "Rosetta refinement". >> However...Rosetta refinement ran for 2 hours, slowly gobbling memory up to >> a maximum of 25GB before failing (error below). >> Also gobbled up disk space, creating a 78 GB file “outtmp.map”. >> >> A memory leak issue? >> >> Thanks, >> >> a++ >> >> >> >> RuntimeError : File 'None' not found. >> Traceback: >> File >> "/Applications/phenix-1.14rc1-3177/modules/cctbx_project/libtbx/runtime_utils.py", >> line 179, in run >> return_value = self.target() >> >> File >> "/Applications/phenix-1.14rc1-3177/modules/cctbx_project/libtbx/runtime_utils.py", >> line 74, in __call__ >> result = self.run() >> >> File >> "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/command_line/rosetta_refine.py", >> line 304, in run >> return run(args=list(self.args)) >> >> File >> "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/command_line/rosetta_refine.py", >> line 191, in run >> debug=params.output.debug) >> >> File >> "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", >> line 313, in __init__ >> self.run_jobs() >> >> File >> "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", >> line 388, in run_jobs >> check_result(result) >> >> File >> "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", >> line 383, in check_result >> raise RuntimeError("File '%s' not found." % result.file_name) >> >> _______________________________________________ >> 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

6 years, 10 months

Re: [cctbxbb] after SourceForge awakens

by Graeme.Winter＠diamond.ac.uk

Hi Aaron I guess like our other projects, cctbx developers have a bunch of stuff to commit before migrating, and as Nigel says there’s a phenix release RSN anyhow. However I for one am very worried that this message says we’ve found half of the svn repo data, we don’t know when we will be able to tell you that you should be expecting service to be restored. Given that the frequency of updates seems to be every two days it would suggest we will know when svn likely to be back on Friday at earliest. We’re part way through moving xia2 to git on github before even being able to merge latest change sets. It’s looking more and more like that was a good choice. Best wishes Graeme On 22 Jul 2015, at 21:51, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: FYI: * SourceForge Allura Subversion (SVN) service – offline, filesystem checks complete, data restoration at 50%. Restoration priority after Git and Hg services. ETA TBD, Future update will provide ETA. >From this update that just went live: http://sourceforge.net/blog/sourceforge-infrastructure-and-service-restorat… Looks like we'll be waiting longer for SVN access to be restored. Seems like migrating to github makes more and more sense, indeed... -Aaron On Mon, Jul 20, 2015 at 1:20 PM, <Graeme.Winter(a)diamond.ac.uk<mailto:[email protected]>> wrote: Hi Nigel We're thinking along the same lines moving xia2 across first then maybe dials, depending on how people feel. Moving all of it across in the longer term would work well. Thanks Graeme On 20 Jul 2015 20:42, Nigel Moriarty <nwmoriarty(a)lbl.gov<mailto:[email protected]>> wrote: Folks I have not read the emails regarding the current SourceForge situation. However, we had been planning to move to github in the near future. SF has been very reliable so I don't think it was too much of pain given the long use we've had from them. It does, however, come at a time when we are trying to get out a major release of Phenix. To that end, it would be helpful if any commits were bug fixes only to minimise the risk of breaking to the codebase. We will be actively evaluating the options regarding to github after Phenix 1.10 is safely away... Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709<tel:510-486-5709> Email : NWMoriarty(a)LBL.gov<mailto:[email protected]> Fax : 510-486-5909<tel:510-486-5909> Web : CCI.LBL.gov<http://cci.lbl.gov/><http://CCI.LBL.gov<http://cci.lbl.gov/>> -- 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<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb

9 years, 11 months

Re: [phenixbb] question on bad geometry

by Pavel Afonine

Hi, I agree with Tom. Here is an example. A 3ifk structure deposited in PDB (resolution 2.03A) has the following statistics: - reported Rwork/Rfree = 0.237/0.293 - recomputed Rwork/Rfree (using phenix.model_vs_data) = 0.2306/0.2835 - Molprobity scores (computed using phenix.model_vs_data): Ramachandran plot, number of: outliers : 4 (2.35 %) allowed : 1 (0.59 %) favored : 165 (97.06 %) Rotamer outliers : 28 (18.67 %) Cbeta deviations >0.25A : 10 All-atom clashscore : 61.61 (steric overlaps >0.4A per 1000 atoms) After running this model through PHENIX AutoBuild and then refining it with phenix.refine using fix_rotamers option and H atoms added, I'm getting the following numbers: - Rwork/Rfree = 0.2097/0.2402 - Molprobity scores: Ramachandran plot, number of: outliers : 2 (1.18 %) allowed : 2 (1.18 %) favored : 166 (97.65 %) Rotamer outliers : 5 (3.57 %) Cbeta deviations >0.25A : 1 All-atom clashscore : 37.14 (steric overlaps >0.4A per 1000 atoms) As you can see, the change is pretty significant and no manual work at all to achieve it! Good luck! Pavel. P.S.: All files are here: http://cci.lbl.gov/~afonine/example_3ifk/ 3ifk.mtz - original data file pdb3ifk.ent - model from PDB pdb3ifk.mvd - result of "phenix.model_vs_data 3ifk.mtz pdb3ifk.ent > pdb3ifk.mvd " command autobuild.mvd - result of "phenix.model_vs_data autobuild.pdb 3ifk.mtz > autobuild.mvd " command autobuild.pdb - model after AutoBuild and phenix.refine On 8/31/10 7:08 PM, Thomas C. Terwilliger wrote: > Hi Fengyun, > > That does look like a lot of outliers to me. You could try improving the > model by "rebuilding in place" with autobuild with the keyword > "rebuild_in_place=True" which will try to rebuild your model without > changing the sequence alignment. This procedure takes a while and it is > useful to use a multiprocessor machine with nproc=5. > > You should also have a careful look at your model, as some manual > rebuilding might improve it a lot. > > All the best, > Tom T > >>> Hi everyone, >>> >>> I have a structure at 2.3 A refined in phenix to R/Rfree=0.23/0.28. >>> However, the geometry is not that good, the followings are the output >>> from phenix.model_vs_data, >>> >>> Stereochemistry statistics (mean, max, count): >>> bonds : 0.0080 0.0547 3244 >>> angles : 1.1669 12.1085 4374 >>> dihedrals : 15.7241 85.6280 1202 >>> chirality : 0.0706 0.2831 536 >>> planarity : 0.0036 0.0246 573 >>> non-bonded (min) : 2.1217 >>> Ramachandran plot, number of: >>> outliers : 17 (4.02 %) >>> allowed : 37 (8.75 %) >>> favored : 369 (87.23 %) >>> Rotamer outliers : 30 (8.62 %) goal:< 1% >>> Cbeta deviations>0.25A : 0 >>> All-atom clashscore : 40.51 (steric overlaps>0.4A per 1000 >>> atoms) >>> >>> I tried to use fix_rotamer=True, but it doesn't help at all. As to the >>> rotamer outliers, the value is far higher than the ideal one. Does >>> that mean I need to manually adjust the model? Or will autobuild help >>> improve the geometry? >>> >>> Thanks! >>> Fengyun >>> >>> _______________________________________________ >>> 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, 10 months

Re: [phenixbb] Problems placing second component in Phaser

by Morten Groftehauge

Hi Gabor, Sounds good but I was hoping for something I could tell phenix.mr_rosetta that would allow it to find a good second solution. Phenix insists on rerunning place model even if you tell it that the model is already placed. So instead of continuing with the placement that worked I end up with one chain based on my original model another one scattered all over the place... I'll try with AMPLE and see what happens there. Cheers, Morten On 18 February 2013 13:01, Gabor Bunkoczi <gb360(a)cam.ac.uk> wrote: > Hi Morten, > > this is weird. One way around is to manually superpose the mr_rosetta > model onto the original in the full solution, and just do a refinement with > Phaser (you can (kind of) do this automatically by running MRage with both > models). Another idea is to decrease the rotation peak cutoff when finding > the second molecule (PEAKS ROT CUTOFF keyword). > > BW, Gabor > > > On Feb 18 2013, Morten Groftehauge wrote: > > Hi guys, >> >> So I have a solution that covers some of target and I ran it through >> phenix.mr_rosetta and I am actually kinda happy with the output from >> there. >> However, while I can place both (NCS=2) with the original model I only >> seem >> to be able to place one of the rosetta models, even with 'packing >> function' >> set to 'all' or 'allow'. >> Original model - >> Refinement after placing component 1: LLG 175 >> Refinement after placing component 2: LLG 620 >> Rosetta model (packing 'all') - >> Refinement after placing component 1: LLG 295 >> Refinement after placing component 2: LLG 390 >> Rosetta model (packing standard) - >> Refinement after placing component 1: LLG 295 >> Refinement after placing component 2: LLG 350 >> >> More notably there is little to no increase in TFZ with the placement of >> the second component... >> >> There are more residues in the Rosetta model and I would expect more >> clashes but this looks weird. >> >> Cheers, >> Morten >> >> >> > > ______________________________**_________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/**mailman/listinfo/phenixbb<http://phenix-online.org/mailman/listinfo/phenixbb> > -- Morten K Grøftehauge, PhD Pohl Group Durham University

12 years, 4 months

Re: [phenixbb] phenix refinement of cryoEM data

by Pavel Afonine

Hello, > I am a relative newcomer to Phenix. I have a large multimeric protein > structure docked into an electron density map, and I would like to > further refine it by rigid-body refinement using Phenix. Is this a > realistic strategy? yes, this is a perfectly valid intent. Have a look at https://www.dropbox.com/s/imv2yzwodik13in/afonine_etal_wcpcw2015.pdf?dl=0 that overviews and summarizes Phenix refinement tools for cryo-EM. > I have made some attempts, first by converting the .mrc map file to > .mtz as outlined here: > https://www.phenix-online.org/documentation/reference/map_to_structure_fact… If you follow the above link you will see that it is best to refine the model directly against the map (in real space, that is), instead of taking a "detour" through reciprocal space. So my suggestion to you is: - get latest Phenix from nightly builds (it is essential that you use recent Phenix): http://phenix-online.org/download/nightly_builds.cgi - run phenix.real_space_refine (sorry, no GUI yet!): phenix.real_space_refine model.pdb map.ccp4 If you expect the model to make large movements to fit the map, you can enable morphing or/and rigid-body, and also increase number of refinement cycles: phenix.real_space_refine model.pdb map.ccp4 run=minimization_global+rigid_body+morphing macro_cycles=10 > Then I tried to refine using rigid body refinement in Phenix. However, > the program quits but doesn’t really tell me why. Here’s the last part > of the log file: > > Number of unique models: 24 > Time building chain proxies: 36.85, per 1000 atoms: 0.26 > Number of scatterers: 142296 > At special positions: 0 > Unit cell: (342, 342, 342, 90, 90, 90) > Space group: P 1 (No. 1) > Number of sites at special positions: 0 > Number of scattering types: 4 > Type Number sf(0) > S 264 16.00 > O 27720 8.00 > N 25872 7.00 > C 88440 6.00 > sf(0) = scattering factor at diffraction angle 0. > > Writing MTZ file: > /Users/xxx/Documents/Phenix/TEST/Refine_1/Test_refine_data.mtz > > Sorry > > > Can anyone give me any ideas as to what went wrong? Still, I would like to debug this.. Could you please send me the following files: - original map; - MTZ file that you get as result of conversion of this map into structure factors and the command you use to do this; - input PDB file with the model; - phenix.refine command (or GUI setup: .eff file and .log file) that crashes with the above error message. All files will handled confidentially. Files may be large, so please use Dropbox or any similar file sharing utilities. > Also, is there a better way to do this? Yes, see suggestions above! Please let me know if you have any questions or need any help! Pavel

10 years, 2 months

[phenixbb] postdoctoral position at the Institute for Protein Innovation in Boston, USA

by Christopher Bahl

The Bahl Lab <http://function-structure.org/> at the Institute for Protein Innovation (IPI) in Boston is recruiting Postdoctoral Fellows. We use protein design to accelerate drug discovery and to engineer new lead therapeutic molecules. In addition to traditional academic collaborations, we work closely with pharmaceutical and biotech companies, as well as venture capital firms. We are looking for translationally-minded scientists who want their work to have a direct impact on the world. We will provide training in computational protein design using Rosetta, including de novo protein design and the design of protein function and biophysical properties. Postdoctoral Fellows at IPI leverage our high-throughput automated laboratory infrastructure. We are especially excited to expand our work in the following research areas: - prediction and design of protein developability for therapeutic applications - engineering of de novo miniprotein/peptide lead therapeutics for oncology, infectious disease, hypertension and diabetes, etc. - antibody design, including de novo paratope design - enzyme design Strong candidates will have demonstrated expertise in one or more of the following: - protein biochemistry: protein production and biophysical characterization, enzymology - structural biology: cryo-EM, X-ray crystallography, NMR - immuno-oncology: cell culture models, fluorescence activated cell sorting - traditional protein engineering: directed evolution, library construction, yeast and/or phage display - computational biology: machine learning, data science, molecular dynamics and/or modeling If you are excited to join a team of protein designers working to tackle audacious projects aimed directly at improving human health, please send your CV to: chris.bahl(a)proteininnovation.org About IPI The Institute for Protein Innovation is a non-profit organization that is advancing protein science to accelerate research and improve human health. The Institute is located at Harvard Medical School. IPI uniquely combines the freedom of academic exploration with the high-throughput scaling of industry to take on transformative protein-based initiatives that no other laboratory or organization can or will pursue. IPI is deploying state-of-the-art technologies to build a repository of powerful protein tools and reagents and share them through licensing and collaboration. These will enable new biomedical and therapeutic discovery for researchers in academia and industry alike. This constellation of vanguard technology and expertise positions IPI to train the next generation of entrepreneurs and protein scientists to lead the discovery of new medicines. The IPI is an equal opportunity employer and prohibits discrimination based on ethnicity, religion, sexual orientation, gender identity/expression, national origin/ancestry, age, disability, socioeconomic status, marital or veteran status, etc. Candidates from underrepresented backgrounds are especially encouraged to apply. -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you.

4 years, 11 months

Re: [phenixbb] Using the Same Test Set in AutoBuild and Phenix.Refine

by Thomas C. Terwilliger

Hi Dale, Can you try something else: phenix.refine AutoBuild_run_12_/overall_best.pdb \ refinement.input.xray_data.file_name=\ AutoBuild_run_12/exptl_fobs_freeR_flags.mtz \ refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \ /usr/users/dale/geometry/chromophores/bcl_tnt.cif This differs from your run only by substituting AutoBuild_run_12/exptl_fobs_freeR_flags.mtz for your 2 refinement data files. This is the exact file that is used in refinement by AutoBuild. I agree that you should be able to use your original data file instead. A possible reason why this has failed is that the original data file has a couple reflections for which there is no data...and which were tossed by AutoBuild before creating exptl_fobs_freeR_flags.mtz . Two files that differ only in reflections with no data will still give different checksums, I think. All the best, Tom T > Hi Dale, > >>> 1) Why you specify reflection MTZ file twice in phenix.refine script? >>> >>> >> I put the mtz in twice because if I put it in once phenix.refine >> complains that I have no free R flags. It seems to want one file with >> the amplitudes and another with the flags. Since I have both in the >> same file I put that file on the line twice and phenix.refine finds >> everything it needs. >> > > phenix.refine looks for free-R flags in your main data file > (1M50-2.mtz). Optionally you can provide a separate file containing > free-R flags (I have to write about this in the manual). However, if > your 1M50-2.mtz contains free-R flags then you don't need to give it > twice. So clearly something is wrong at this step and we need to find > out what is wrong before doing anything else. Could you send the result > of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your > data file? Or I can debug it myself if you send me the data and model. > >> If the MD5 hash of the test set depends on the resolution then >> certainly >> I could be in trouble. > > No. It must always use the original files before any processing. > >> Does the resolution limit affect the MD5 hash of the test set? >> > > No. If it does then it is a very bad bug. I will play with this myself > later tonight. > >> >>> 3) Does this work: >>> >>> (...) >> >> I'll try these but it will take a bit of time. >> > > Don't run it until completion. Just make sure it passed through the > processing step. > > Pavel. > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

17 years, 6 months

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