April 2015 - phenixbb - phenix-online.org

on the convergence of the Phenix refine
by Smith Liu 22 Apr '15

22 Apr '15

Dear All, Suppose I have a refine of 10 cycles, it get stablized from cycle 7. But sometimes I noticed that from the end of the cycle 10 to the end of the whole refinement, the stablization from 7 to cycle 10 can be destroyed a little, which makes me concern whether the final refinement can be regarded as convergent or not. Will you please explain why the stablization from 7 to cycle 10 can be destroyed a little from the end of cycle 10 to the end of the whole refinement? More critically, in the other situation, suppose I have a refine of 10 cycles, it get relatively stablized from cycle 5, from the end of cycle 5 to the end of cycle 10 the Rfree increase very slightly each cycle of the refine, which makes at the end of cycle 10 the Rfree is slightly higher than the Rfree at the start of the whole refinement. But from the end of cylce 10 to the end of the whole refinement, there is a slight decrease of Rfree, which makes the Rfree at the end of the whole refinement slightly lower than Rfree at the start of the whole refinement. It seems to increase the cycles of the refinement would not help further. Will you please explain the above phenomenon and to see whether the refine result can be acceptable, or do you have any suggestions for improvement? Smith

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Off-topic: Hydrogen images
by mohamed noor 21 Apr '15

21 Apr '15

Dear all I will be presenting about protein crystallography to a group of PhD-level physicists and need some images from the community. Would anyone have high-quality images of density maps that show hydrogen atoms at 1. high and ultra-high X-ray resolution (say, about 1.2 A to about 0.5 A) 2. low or medium X-ray resolution (where H atoms are not visible) compared with neutron data (with H). Ideally these images should be from the same protein so that I can show the power of complementary beam source for the diffraction. A side question - what is the community's preference to get deuterated samples? Is it crystal soaking or growing E. coli in deuterium? All contributions will be credited. Thanks.

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citation
by Sneha Rangarajan 21 Apr '15

21 Apr '15

Hello, What is the correct way to cite Phenix MRage? Thanks, Sneha

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Standard settings for map generation in phenix.refine
by Tristan Croll 21 Apr '15

21 Apr '15

Hi all, In the phenix.refine GUI, the default options for the maps auto-generated in Coot include the R-free set in the map coefficients. Is this the best choice? It's fairly natural for the user to immediately inspect/correct their structure using the helpfully-provided Coot window - which, as per a recent discussion thread on this list, can easily lead to over-fitting. I suspect I've been looking at such a case over the last week or so - a mid-3A structure refined in Phenix with an amazingly low Rfree (0.234) and Rfree-Rwork (~0.016), despite clear (albeit non-disastrous) errors in a number of loops, and moderate-poor statistics in structural quality metrics. Tellingly, the Rfree goes up quite substantially upon re-refinement after correcting these issues. If maps generated with the Rfree set included should only ever be used for final display, wouldn't it be better to have them excluded by default? Best regards, Tristan Tristan Croll Lecturer Faculty of Health School of Biomedical Sciences Institute of Health and Biomedical Engineering Queensland University of Technology 60 Musk Ave Kelvin Grove QLD 4059 Australia +61 7 3138 6443 This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.

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on importing CIF structure factors and cutting out density
by Smith Liu 21 Apr '15

21 Apr '15

Dear All, By importing CIF structure factors of the Phenix graphical interface, I converted a CIF file to a mtz file. But when I tried to cutting out the density by Phenix with the converted mtz file, it request the map labels, which the converted mtz file seems does not have. Will you please let me know how to have the issue settles? Smith

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phenix refinement of cryoEM data
by Ali Malay 17 Apr '15

17 Apr '15

Dear all, 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? 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… <https://www.phenix-online.org/documentation/reference/map_to_structure_fact…> 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? Also, is there a better way to do this? Thanks very much in advance!! A.M.

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find difference peaks
by Alejandro Virrueta 16 Apr '15

16 Apr '15

Hello, I'm working on a small project, and need some feedback. I am trying to rebuild methionine side-chains by looking at the difference peaks for a given Fo-Fc map. I envision a process as follows: 1. Delete the MET side-chain of a PDB file 2. Refine structure to get Fo-Fc map 3. Get a list of the peak positions relative to the coordinates of the PDB file I used 4. Filter list by keeping peaks near the MET C alpha/beta PDB coordinate. 5. Try to rebuild side-chain after anchoring the sulfur atom (assuming sulfur is located at the highest peak and within some distance to C beta) What functions should I use to achieve step 3? I am also trying to implement this process within the ringer program (phenix/cctbx_project/mmtbx/command_line/ringer.py). If anyone is familiar with this, what commands would work best within this ringer program? i.e. what functions can operate on difference_map (which is sampled by a point using tricubic_interpolation under 'def sample_angle')? I hope this makes some sense to someone. Thanks! Alex

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reflections file editor
by Almudena Ponce Salvatierra 14 Apr '15

14 Apr '15

Dear all, I would like to merge two datasets containing anomalous signal. If have done so earlier for native data within phenix in the reflections editor by selecting the arrays corresponding to FP and SIGFP and then running the program. However when I try to do so for the anomalous datasets it writes FP SIGFP and FP2 SIGFP2 instead or merging them, so it does with the anomalous signal... so I guess I have basically only one file containing two datasets but not a merged dataset. How can I solve it? Would it be possible, on the other hand, to merge a dataset with anomalous signal with a native one? The intention behind is to extend the resolution to the one of the native data. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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sugar puckering refinement with phenix refine
by Almudena Ponce Salvatierra 14 Apr '15

14 Apr '15

Dear all, does anyone know how phenix.refine deals with the sugar puckering of an RNA or a DNA strand? Does it refine it? Or does it leave it as it was built? Thank you very much in advance. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Link NGA and THR
by Cory Brooks 13 Apr '15

13 Apr '15

Hello! I am refining a structure with O-link glycosylation (GalNAc linked to Thr). Phenix seems to remove the link during refinement. Can anyone suggest a solution that will maintain the bond during refinement? Regards, Cory Cory Brooks,Ph.D.

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