- phenixbb - phenix-online.org

Modifications for Ca-binding site
by Keller, Jacob 30 Dec '15

30 Dec '15

I am getting a lot of problems with my calcium binding sites--there is clear density for the calciums and the protein side chains, but Phenix keeps sucking the side chains out of their density towards the calciums and also the calciums show some positive difference density, perhaps due to too-high b-factors (or potentially partial occupancy by Na?). I think what might work best is to turn off the Ca-O bond length restraints somehow, but don't see where/how to do that. I tried releasing them from geometrical restraints, but that made things worse, since things went haywire in the sidechains themselves. Is it possible to make Phenix ignore the Ca-O bond distance restraints? JPK ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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RSRZ in Phenix?
by Keller, Jacob 30 Dec '15

30 Dec '15

Dear Crystallographers, Is there any place in Phenix where RSRZ or a similar measure is shown? All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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Coot add DNA base or mutate DNA base
by Xiao Lei 25 Dec '15

25 Dec '15

Hi All, I'm using coot to build DNA, when I click "add residue" to one end of DNA, coot automatically add an "A" base to it, but I'd like to add "G" base, is it a way to mutate the A base to G base, I know coot can mutate amino acid residue, is is a way to mutate DNA residue in coot GUI? Thanks ahead. Xiao

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Trouble refining following molecular replacement
by Tyler Liban 22 Dec '15

22 Dec '15

Hello all, We are currently working with a dataset for a trimeric protein complex at 3A that is giving us some issues. The space group seems to be P21 ( 59.5, 61.6, 99.6 , 90, 98, 90) and the Mathews coefficient (2.6) suggests 2 copies of this 35kDa complex in the ASU. We are using a homolog as the search model that is 80% identical, and Phaser is able to find 2 molecules in P21 when searching in the same point group and gives good TFZ scores (TFZ = 9 or 10). However, these solutions do not refine well following Phaser (Rfree ~.50), and after removing parts of the model that look incorrect the Rfree still stays between .46 and .50. We ran the data through Xtraige and saw no signs of twinning based on the L-test, and the Patterson map has one small off-origin peak that is only 5%, indicating that there is no significant pseudotranslation. We have also tried finding MR solutions in P1, but haven’t had much luck. Any ideas on where to go from here would be greatly appreciated. Tyler

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command line for reflection file editor
by Zheng Zhou 22 Dec '15

22 Dec '15

Dear phenix experts, How do I combine Rfree from one dataset with the new dataset under command line? I can do this using reflect file editor GUI easily. But I tried to look up the documentation for phenix.reflection_file_converter and could not find a solution. I am trying to write a script to handle several datasets scaled from HKL2000. I could do this easily in ccp4, but looks like Ctruncate's French&Wilson made the completeness worse than scale.log. Thanks for your help in advance. Best, Zheng

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mmCIF file must contain at least one data block
by Ursula Schulze-Gahmen 18 Dec '15

18 Dec '15

I am getting this thie error message mmCIF file must contain at least one data block when trying to run readyset or phenixrefine I cannot find anything wrong wqith my input files. What is the problem? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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remove old phenix version but keep the processed data
by Xiao Lei 17 Dec '15

17 Dec '15

Hi Phenixbb member, As I updated Phenix version on my Macbook pro (OS X 10.10), I found the newer version phenix did not automatically replace the old versions. Is there a way to remove the old version Phenix safely and only keep the newer version, but at the same time keep the processed data (data from phenix refine and xtriage)? Thanks ahead. Xiao

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ML with Twinning?
by Keller, Jacob 16 Dec '15

16 Dec '15

Is Phenix able yet to use the ML target function with twinned data? Is it in the works? All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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differences in refinement stats between phenix-dev-2219 and -1.9-1692
by Ezequiel Noguera 16 Dec '15

16 Dec '15

Thank you very much, Pavel. I don't save H's when I modify the model in coot (the input PDB file that I sent you was the output from coot). I did the refinement again, now in version 2247, without NCS. I got the same results, higher R factors and RMS deviations for the newer version. I got better results when I used "update waters" (both in Rfactors and RMS). Below, I list the statistics for refinement without updating waters. Significant differences remain. Could it be any difference in settings of default parameters between versions? version: dev-2247 Start: r_work = 0.1687 r_free = 0.2011 bonds = 0.046 angles = 1.321 Final: r_work = 0.1753 r_free = 0.2040 bonds = 0.030 angles = 0.593 version: 1.9-1692 Start: r_work = 0.1651 r_free = 0.2018 bonds = 0.013 angles = 1.409 Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011 angles = 1.321

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Re: [phenixbb] -differences in refinement stats between phenix-dev-2219 and -1.9-1692
by Pavel Afonine 13 Dec '15

13 Dec '15

Hi Ezequiel, just to make it clear: torsion-angle NCS, Optimize X-ray/stereo weight are *not* the default settings, therefore you did customize the refinement parameters. At this resolution (1.3A) you do not need to use NCS restraints. Also, you say you used "Automatically add H's" however the PDB file you sent me does not contain any H atoms. Furthermore, the PDB file header says H are present: REMARK MODEL CONTENT. REMARK ELEMENT ATOM RECORD COUNT OCCUPANCY SUM REMARK C 1275 1047.00 *REMARK H 2029 1649.00 * REMARK O 559 488.50 REMARK N 315 263.00 REMARK S 6 6.00 REMARK Cu 4 2.89 REMARK TOTAL 4188 3456.39 So overall this make an impression that something has gone wrong. Way forward: 1) Take the file you sent me; 2) Add H atoms: phenix.reduce model_no_h.pdb > model_with_h.pdb 3) Use new file with H atoms added to run refinement. The only setting different from defaults should be "Optimize X-ray/stereo weight". Perhaps you can also enable automated water update. I just did all this myself and got nicely refined model with Final: r_work = 0.1624 r_free = 0.1939 bonds = 0.010 angles = 1.030 Corresponding PDB and MTZ are sent in a separate email that goes to you only (off mailing list). Pavel On 12/6/15 07:59, Ezequiel Noguera wrote: > Hi Pavel, thank you very much for your help. I attach the data. I > didn´t customize parameters. The refinement stategy of the last job > was: XYZ coords, Real-space, Individual B-factors, torsion-angle NCS, > Optimize X-ray/stereo wght and X-ray/ADP wght, Automatically add H's > and correct N/Q/H errors. > > > Hi Ezequiel, > > deviations are not unexpected in general but not that large as you > report, so I wonder what's going on.. Could you please send me input > data and model files, as well as any ligand files you used. If you > customized some parameters, telling what were those would be helpful too. > > Please send all files off-list to my email directly. > > Thanks, > Pavel > > >> Hello, I'm working in a refinement that I started some time ago. I >> noted that repeating the same refinement task using a newer version >> of phenix, the refinement statistics Before and After refinement are >> different from values of the old version (I used "restore job" from >> the Job history to repeat the same task in the two versions installed >> in the same PC). Any explanation? I'm worried about the rms >> deviation. Thanks in advance. >> >> new version: >> R-work: start=0.1697, final=0.1761 >> R-free: start=0.2011, final=0.2053 >> Bonds: start=0.046, final=0.029 >> Angles: start=1.321, final= 0.631 >> >> old version: >> R-work: start=0.1651, final=0.1657 >> R-free: start=0.2018, final=0.2009 >> Bonds: start=0.013, final=0.013 >> Angles: start=1.409, final= 1.411

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