- phenixbb - phenix-online.org

reference_xray_structure
by yamei yu 06 Dec '17

06 Dec '17

Dear all, I want to use “reference model” in a low resolution structure refinement. Do I need to set this parameter “reference_xray_structure”? What does “reference_xray_structure” stand for? Many thanks and best wishes ************************************************ Yamei Yu Associate Professor State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyuxtal(a)gmail.com ymyuxtal(a)163.com yamei_yu(a)scu.edu.cn

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Re: [phenixbb] Is it harmful to to use Imean SigImean in Phenix Refine by default?
by Jeffrey, Philip D. 04 Dec '17

04 Dec '17

To put this in context: I originally wrote that page when phenix.refine used a |F|>0 cutoff in refinement. Given that I<0 often results in |F|=0 after the conversion the program threw out data for which we knew something (i.e. it was weak) albeit imprecisely. That was a self-evidently bad idea. However the defaults in phenix.refine have changed and as Ed Berry observes it does emulate CCP4's TRUNCATE now (in "truncate yes" mode, probably). I convert my data with CCP4's TRUNCATE or CTRUNCATE programs. For strong data I don't apply the French and Wilson intensity data remapping. For weak data I do - but only for refinement purposes, not for SAD/MAD phasing. My standard ploy is to use CAD to strip out Imean and SigImean from the MTZ file so that phenix.refine cannot attempt to "outsmart" me again. And by outsmart I really mean "usurp my intentions". I would suggest that everyone do the same - or at least test the difference. My known bias is to trust CCP4 programs more. Cheers Phil Jeffrey Princeton ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Xiao Lei [xiaoleiusc(a)gmail.com] Sent: Saturday, December 02, 2017 9:05 PM To: PHENIX user mailing list Subject: [phenixbb] Is it harmful to to use Imean SigImean in Phenix Refine by default? Dear All, I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF. I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful" ( web link http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead." This may force rejecting weak data according to the post. The latest Phenix version may be updated from the version the post author used, I wonder if this risk is still in the newest version of Phenix ?

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Is it possible to restrain Cartesian NCS for ligands?
by Edward A. Berry 04 Dec '17

04 Dec '17

Is it possible to restrain cartesian NCS for ligands in phenix.refine? I included a ligand in an paired ncs-group and it seems to be omitted from the listing of those groups in the log file. When I made an ncs_group including only ligands, it halted complaining of empty selection. Ed

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Is it harmful to to use Imean SigImean in Phenix Refine by default?
by Xiao Lei 04 Dec '17

04 Dec '17

Dear All, I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF. I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful" ( web link http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead." This may force rejecting weak data according to the post. The latest Phenix version may be updated from the version the post author used, I wonder if this risk is still in the newest version of Phenix ?

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 21 Nov '17

21 Nov '17

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the January 2018 issue is 20 December 2017. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. 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

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Bug in 2.10.3 with scrolling
by Mark Saper 20 Nov '17

20 Nov '17

If one scrolls an alignment (not WRAP mode), the names of the sequences scroll but not the sequences with it. Using the scroll bar works correctly. Running 2.10.3 on MacOS 10.12.6 with Java version: 1.8.0_151. Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

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Ligand library error in Phenix.Refine
by Gyanendra Kumar 17 Nov '17

17 Nov '17

Hi there, My Phenix.Refine run crashes because of non-availability of dictionary file for "ACP", a non-hydrolyzable ATP. Could this ligand be added to the next nightly build? Phenix.Refine suggested using "ReadySet", but that also failed. I sent the error reports to bugs(a)phenix-online.org, all emails bounced back. Refmac runs fine. Thanks! -Gyan -- Gyanendra Kumar, PhD Associate Scientist, St. Jude Children's Research Hospital, Department of Structural Biology, 262, Danny Thomas Place, MS-311 Memphis, TN 38105 Cell: 631-875-9189 https://www.linkedin.com/in/gyanendrakumar https://scholar.google.com/gyanendrakumar <https://scholar.google.com/citations?user=lnil0IQAAAAJ&hl=en> https://www.researchgate.net/profile/Gyanendra_Kumar3 http://stjude.academia.edu/GyanendraKumar -------------------------------------------------------

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(no subject)
by Rajendra Sharma 15 Nov '17

15 Nov '17

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Max_reasonble_bond_distance error in phene.resl.space.refine
by Rune Thomas Kidmose 15 Nov '17

15 Nov '17

I have been playing around with phenix.real.space.refine as part of a small pipeline I am making for EM structures. Testing various deposited EM structures and their corresponding maps, within my pipeline, I sometimes run in to the below error: RuntimeError: Bond distance > max_reasonable_bond_distance: 79.8663 > 50: Followed by a list of distances between, what I am assuming is, atom numbers and the actual distance. I can get past it simply by changing the max_reasonable_bond_distance for the run to, in this case, 80. But I tend to see, that the final results gets significantly worse when I use this bypass. This is based on very similar models going through the pipeline, where the ones which yields the error, scores much worse when using the above mentioned bypass, compared to the models that showed no max_reasonable_distance_error. So I was wondering: A: What does "max reasonable bond distance" actual mean? B: Any ide what I can do, to avoid running into this bond distance problem? I know the latter is asking a lot, as I have not disclosed any of the details surrounding how the error arose etc. but if such info is needed, I would prefer to do so off list and then return with the solution on list, if possible. Maybe I was hoping for a setting that ignores the outliers, without changing the max value. But that all depends on, what the setting actual is, which I dont know Cheers Ruki

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Twin refinement problem
by Leonid Sazanov 15 Nov '17

15 Nov '17

Dear all, there seems to be a problem with twin refinement of some of our datasets, and I wanted to see if that is something specific to our data or if anybody else has seen it. These crystals have been reproduced many times and are always twinned in P21 space group with twin operator: -h,-k,h+l and twin fraction in the range 0.45 - 0.49. Data always refines fine in Refmac and in many cases in Phenix as well, giving similar twin fraction in both programs. However, with some datasets (at 3.4-3.6 A resolution) in Phenix there is a problem: refinement of twin fraction is unstable and jumps each macro-cycle between about 0.40 (wrong?, giving high R-factors) and 0.47 or so (true?, giving much lower R-factors). This can be clearly seen from log file extract: cycle stage r-work r-free twin_fraction 0 : 0.3002 0.3084 1_adp: 0.2511 0.2701 0.49 2_adp: 0.2724 0.2837 0.42 3_adp: 0.2296 0.2465 0.47 4_adp: 0.2464 0.2587 0.40 5_adp: 0.2230 0.2420 0.47 6_adp: 0.2393 0.2554 0.40 7_adp: 0.2225 0.2423 0.47 8_adp: 0.2416 0.2590 0.40 9_adp: 0.2184 0.2376 0.47 10_adp: 0.2380 0.2556 0.40 end: 0.2393 0.2568 0.39 ------------------------------------------- The same dataset refines with stable twin fraction = 0.48 in refmac. When Phenix accepts higher twin_fraction with its lower R-factors, it does cycles 0 and 1 of twin fraction refinement once, while when it fails to update and falls back to low twin_fraction, it does this twice, as shown below. Updates OK: =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2383 0.2381 0.2565 n_refl.: 191608 twin_fraction=0.40 re-set all scales: r(all,work,free)=0.2926 0.2926 0.2950 n_refl.: 191608 twin_fraction=0.40 cycle 0: update twin fraction: r(all,work,free)=0.2910 0.2910 0.2933 n_refl.: 191608 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2910 0.2910 0.2933 n_refl.: 191608 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2910 0.2910 0.2933 n_refl.: 191608 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2249 0.2246 0.2473 n_refl.: 191608 twin_fraction=0.48 cycle 1: update twin fraction: r(all,work,free)=0.2249 0.2246 0.2472 n_refl.: 191608 twin_fraction=0.47 update scales twin start: r(all,work,free)=0.2249 0.2246 0.2472 n_refl.: 191608 twin_fraction=0.47 reset f_part, k_(total,mask): r(all,work,free)=0.2910 0.2911 0.2934 n_refl.: 191608 twin_fraction=0.47 bulk-solvent and scaling: r(all,work,free)=0.2249 0.2246 0.2472 n_refl.: 191608 twin_fraction=0.47 r_work=0.2246 r_free=0.2472 twin_fraction=0.47 twin_law=-H,-K,H+L ============================ Set refinement target ============================ Falls back: =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2216 0.2214 0.2408 n_refl.: 191608 twin_fraction=0.47 re-set all scales: r(all,work,free)=0.2855 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.47 cycle 0: update twin fraction: r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 cycle 1: update twin fraction: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 start: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 re-set all scales: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 cycle 0: update twin fraction: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2330 0.2329 0.2486 n_refl.: 191509 twin_fraction=0.48 cycle 1: update twin fraction: r(all,work,free)=0.2306 0.2305 0.2458 n_refl.: 191509 twin_fraction=0.40 update scales twin start: r(all,work,free)=0.2306 0.2305 0.2458 n_refl.: 191509 twin_fraction=0.40 reset f_part, k_(total,mask): r(all,work,free)=0.2781 0.2780 0.2846 n_refl.: 191509 twin_fraction=0.40 bulk-solvent and scaling: r(all,work,free)=0.2295 0.2293 0.2439 n_refl.: 191509 twin_fraction=0.40 r_work=0.2374 r_free=0.2522 twin_fraction=0.40 twin_law=-H,-K,H+L ============================ Set refinement target ============================ With some other datasets Phenix just gets stuck at apparently in-correctly low twin fraction - each cycle it tries to update to 0.47-0.48 (and R factors are better in this case) but then it always falls back to 0.36-0.40 again. So I wonder if anybody else has seen this with their data? Many thanks for any info! Leonid -- Prof. Leonid Sazanov IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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