- phenixbb - phenix-online.org

twinning detection
by Ursula Schulze-Gahmen 06 Jun '16

06 Jun '16

I have an extremely low resolution data set to 6.5 A. The data were collected on a Pilatus detector, indexed and further processed in XDS, space group P321. Pointless determines spacegroup to P3221 or P3121 and L-test shows no twinning. Phenix X-triage indicates twinning, but the twin fraction varies enormously depending on the method used: Britton analysis 0.337, H-test 0.260, ML 0.022. The UCLA twin server also thinks that data are twinned. How do I evaluate which information is right? Also, I think I found a molecular replacement solution that is correct using these twinned data. 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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GPU acceleration of phenix.real_space_refine?
by Oliver Clarke 02 Jun '16

02 Jun '16

Hi all, phenix.real_space_refine takes a very long time to run on large systems when using any of the more computationally expensive options (e.g. morphing). I was wondering if there has been any consideration towards optimizing this code (and maybe that of phenix.map_to_model) for GPU acceleration? There is somewhat of a shift occuring in the EM community towards using GPU workstations for data processing - if we could use already purchased capabilities to accelerate model refinement as well that would be a huge bonus. I saw a discussion on the bb from a while back concerning the same question applied to phenix.refine, and the conclusion was that in that case the benefits would be minimal, but I'm not sure whether the same applies to real space operations. Cheers, Oli. PS has there been any consideration of including an option to allow users to supply two half maps at run time, one "work" and one "test" map for cross validation purposes? It is possible to do this with two separate runs right now but having the option integrated would be wonderful.

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phenix.real_space_refine GUI
by Pavel Afonine 01 Jun '16

01 Jun '16

Hi Phenix users, since I had to answer this very same question off-list three times in past 48 hours, I thought I post this for future reference... Yes, thanks *Billy* there is a GUI for phenix.real_space_refine (tool to refine atomic models against maps, such as cryo-EM maps)! To give it a try, you need: 1) Get the latest nightly build, dev-2427 for instance: http://phenix-online.org/download/nightly_builds.cgi 2) Enable alpha-test programs in Phenix GUI. To do this: -- start Phenix GUI; -- go to Preferences and tick "Enable alpha-test programs and features" box; -- restart the GUI (close down, then start again); -- phenix.real_space_refine will be available in Refinement section on the right (Real-space refinement [alpha]). Note, it has a very handy feature to see/explore/edit secondary-structure restraints graphically. Also note that *this is alpha-test version meaning that glitches are not unexpected*! However your feedback will help to improve it, so please let us know should you encounter problems, have suggestions or found bug(s)! All the best, Pavel

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r-free flag cell constant mismatch
by wtempel 01 Jun '16

01 Jun '16

Dear Phenix experts, our project involves crystals *A* and *B*, which are nearly isomorphous and of a protein’s complexes with two different small molecules, respectively. *A* diffracts better than *B*. The r-free flag from *A* was “attached” to *B*‘s input reflections with the CCP4 cad command and is still associated to *B*‘s slightly different cell dimensions. Would/should this be reason enough for refine to throw an error? The error message suggests changing the refinement.input.symmetry_safety_check setting. Can this setting be changed in the GUI? Thank you. Wolfram Tempel

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Berkeley Server Downtime (6/3/2016)
by Billy Poon 01 Jun '16

01 Jun '16

Dear all, On Friday, June 3, our servers will be shutdown starting at 6:30 am Pacific for scheduled maintenance in our building (7 - 8 am). This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) We expect that the servers will be available by 8:30 am Pacific at the latest. Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- 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

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Gordon Research Conference on Diffraction Methods
by Edward Snell 01 Jun '16

01 Jun '16

While not a Phenix posting, we do encourage attendance from the usual suspects! We'd like to remind you to register for the Gordon Research Conference on Diffraction Methods to be held at Bates College in Lewiston, Maine, July 17th-22nd 2016. The conference is themed around "Probing the structure and dynamics of macromolecules" and details of the program are at https://www.grc.org/programs.aspx?id=11655. The closing date for applications is June 19th 2016, about 5 weeks away, however GRC conferences have a limited number of participants and we will close registration early if that number is reached. Please join us in Maine this summer for the 40th anniversary of this meeting. If you are planning on attending, please note the deadline, and the growing potential that registration may close earlier. Thanks, Eddie Snell and Arwen Pearson - Chair and co-chair for 2016. Edward Snell Ph.D. CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Heisenberg was probably here!

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rosetta_refine connecting non-consecutive residues around break in chain
by wtempel 27 May '16

27 May '16

Hello, can one prevent rosetta_refine from connecting two residues that surround a gap? For example, how do I keep near-by residues 108 and 115 apart when 109 through 114 are missing? Thank you. Wolfram Tempel

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Fwd: Re: Scultor model with gaps included
by Gabor Bunkoczi 26 May '16

26 May '16

Apologies, this should have been directed to the mailing list. Gabor -------- Original Message -------- Subject: Re: [phenixbb] Scultor model with gaps included Date: 2016-05-25 14:33 From: Gabor Bunkoczi <gb360(a)cam.ac.uk> To: Joseph Brock <joseph.brock(a)ki.se> Dear Joseph, apologies for the late response, and sorry for the trouble. Please find some answers inlined. On 2016-05-24 15:10, Joseph Brock wrote: > Dear Phenix community, > > I was hoping if someone could help me with using Phaser correctly, > since I can't seem to produce the desired search model. > > The first thing that I was wondering about is that the CLUSTAL > alignment from the log file is quite different to the .aln alignment I > made with phenix --> other tools --> multiple sequence alignment. Why > is a sequence alignment required as input if sculptor performs it's > own internally? Sculptor can perform sequence alignment, but the algorithm is relatively basic, and you can get much better results with an external method (such as HHPRED), and hence alignment input is preferred over the target sequence. The alignment selected is printed into the logfile for reference. On the other hand, Sculptor does align the structure of your model chain to the sequence of your model (this is a surprisingly non-trivial task). However, this alignment should be close to 100% identical, unless a mistake has been made (such as using the wrong alignment file). You should get a warning if the sequence identity is too low. It is normally OK to have a couple of mismatches (such as having SeMet in the model structure with translates to "X" and not as "C"). > > My model sequence aligned to my target sequence in the log file has > several gaps in the alignment . For e.g., > > MASTER ......AASFIMV...... > CHAIN_A ......AKM--MF....... > > I would like to great a search model in which the residues aligned to > gaps in the MASTER chain are included, however the resulting sculptor > .pdb file has these residues removed. Shouldn't they be inserted so > that the rest of the chain is in the correct register? You need to do homology modelling to achieve this, as an insertion can affect the whole structure. Sculptor is designed for quick model improvement, and just renumbers/renames residues. However, the new residues numbers should reflect your sequence, i.e. in your example alignment the two methionines on both sides of the gap will get a non-consecutive number and are displayed as non-bonded in e.g. Coot. > > If anyone can let me know the parameters to allow this, I would > greatly appreciate it. I tried unselecting 'gap' in main-chain > deletion scope and some other variations, but this didn't seem to > help. > > I seem to get the same result even if I change the target index from 1 > to 2 in the associated .aln alignment. Does anyone know why this is? Hmm, this does not sound right. Can you send me the logfile so that I can have a look (please use my direct email address)? Best wishes, Gabor > > Apologies if this is quite obvious, I have been reading the > documentation but can't seem to figure it out. > > All the best, > > Joseph. > > Joseph Brock | PhD > Division of Physiological Chemistry II > Department of Medical Biochemistry and Biophysics > Karolinska Institutet > Scheeles väg 2 > SE-171 77 Stockholm, Sweden > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org -- ################################################## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##################################################

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Appropriate model_vs_data usage over part of a structure
by Andy Watkins 25 May '16

25 May '16

Perhaps necessary preface: I am largely learning as I go, and large parts of Phenix (and the details of refinement data file formats) are still black boxes for me. Suppose I have a model of one chain of a complex and an .mtz describing the entire complex. I have performed some refinement procedure altering the model of that single chain. My aim is to determine how this refinement procedure has affected the fit to the experimental data--or, really, the subset of the experimental data expected to be relevant for my model. For obvious reasons, phenix.model_vs_data chain_A.pdb whole_complex.mtz phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz are undesirable: they evaluate the model of a single chain against the whole complex's data, and there's obviously a lot of unsatisfied electron density. So, while this command *works*, it reports an unrepresentative fit. (In theory, one solution to my problem would be to re-combine each chain's refined version, then run model_vs_data on the recombined, refined complex. I'm interested nonetheless in how it would work on the chains separately. Now, during the refinement procedure, we of course generate .ccp4 density maps for the individual chain models: phenix.maps chain_A.pdb whole_complex.mtz which produces the ccp4 file as well as, crucially, chain_A_map_coeffs.mtz. Attempting to employ that resulting .mtz file, i.e. phenix.model_vs_data chain_A.pdb whole_complex.mtz phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz leads to an evocative error: Sorry_No_array_of_the_required_type: No reflection arrays available. My highest suspicion is that I need to alter maps.params in a particular way so that reflection arrays are also output to model_map_coeffs.mtz. I could also imagine that I need to be using another program entirely! Thanks in advance for whatever help you can provide; unfortunately, I can't provide any input files.

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July ACA meeting in Denver early registration still open!
by Terwilliger, Thomas Charles 24 May '16

24 May '16

?Hi Phenix colleagues! Heading to Denver for ACA's Annual Meeting in July? Early registration ends May 31 (abstracts still being accepted too!) See: http://www.amercrystalassn.org/2016-meeting-homepage ?All the best, Tom T Tom Terwilliger (2016 ACA President)

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