- phenixbb - phenix-online.org

Phenix mailing list and web server
by Paul Adams 05 Mar '15

05 Mar '15

Dear Phenix Mailing List Subscribers many of you will have noticed issues with the Phenix web site, bulletin board and help mail addresses over the last week. This was a result of a serious hardware failure. Today these services should all be back on line and functioning normally. If you encounter any problems please let us know. Many thanks for your patience. Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Test
by Paul Adams 05 Mar '15

05 Mar '15

Test of restored Mailman system. Please ignore. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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get_cc_mtz_pdb for neutron data table
by Maxime Cuypers 26 Feb '15

26 Feb '15

hi, i need the correlation coefficients map/residues for a publication, which command should i use to get phenix.get_cc_mtz_pdb to take into account the neutron scattering tables? seems it uses the x ray tables by default. i can not find it on this page: http://www.phenix-online.org/version_docs/1.8.3-1472/get_cc_mtz_pdb.htm#anc… many thanks for your reply. -- Dr. Maxime Cuypers

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hiding clash dots
by Sebastiano Pasqualato 26 Feb '15

26 Feb '15

Hi all, a quick question: how do I get rid of the clash dots that appear in Coot, when opened from a phenix job? thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit <http://is.gd/IEO_XtalUnit>

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on phenix.cut_out_density
by Smith Lee 26 Feb '15

26 Feb '15

Dear All, Can the mtz file produced by phenix.cut_out_density be used by Phenix refine for refinement? Smith

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a sharp rise of R-free in resolution bin
by Singh, Bishal 25 Feb '15

25 Feb '15

Hello everyone, I am refining a structure at 2.3 A resolution. R-work/R-free is 26/31 and is not reducing further. When I looked into the resolution bin, I notices a sharp rise of R-free between resolution range 2.5-2.6 A (marked in figure below). However R-work is fine. I am doubtful of reducing the resolution to 2.5 A or lower. Please suggest me your opinion. Your words will be highly appreciated. With regards, Bishal Singh PhD Student University of Heidelberg, Germany

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How to define a disulfide bond between symmetry related molecules in phenix.refine
by Michael Hothorn 25 Feb '15

25 Feb '15

Dear all, I am trying to refine an intermolecular disulfide bond in phenix.refine. The disulfide involves Cys 188 in chain A and Cys 188 of chain B of a symmetry related molecule, with symop -X, Y+1/2, Z+1/2. There are two molecules in the AU, SG is P212121. I generated the following SSBOND entry in the pdb header: SSBOND 2 CYS A 188 CYS B 188 1555 3555 2.04 Based on this: http://www.wwpdb.org/documentation/file-format/format33/sect6.html the format seems fine, but the disulfide is not being recognized during refinement. Could someone point out to me how to correctly define this for phenix.refine. Thanks! Michael

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sharp rise of R-free in resolution bins
by Singh, Bishal 25 Feb '15

25 Feb '15

Hello everyone, I am refining a structure at 2.3 A resolution. R-work/R-free is 26/31 and is not reducing further. When I looked into the resolution bin, I notices a sharp rise of R-free between resolution range 2.5-2.6 A (marked in figure below). However R-work is fine. I am doubtful of reducing the resolution to 2.5 A or lower. Please suggest me your opinion. Your words will be highly appreciated. With regards, Bishal Singh PhD Student University of Heidelberg, Germany

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On Ramachandran restraints of Phenix refine
by Smith Lee 25 Feb '15

25 Feb '15

Dear All, If my resolution was between 2.5-3.0 A, and if I did not use Ramachandran restraints in the Phenix refine the Ramachandran outliers would be increased significantly during the refinement process, in this situation may I use Ramachandran restraints in the Phenix refine? I am looking forward to getting your reply. Smith

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Bug? phenix.hyss crashes on reading CNS def file
by Mark A Saper 23 Feb '15

23 Feb '15

I am trying the example described on this documentation page: http://www.phenix-online.org/download/documentation/cci_apps/hyss/examples.… For mbp.hkl the HySS command suggested is: phenix.hyss $CNS_SOLVE/doc/html/tutorial/data/mbp/mbp.hkl 4 yb —symmetry $CNS_SOLVE/doc/html/tutorial/data/mbp/def The software does not expect the “{“ character in the def file. I can send you the Traceback on request. I am running dev-1951. -Mark

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on TLS for Phenix refine
by Smith Lee 22 Feb '15

22 Feb '15

Dear All, For TLS, the document says, "Can I use both TLS and anisotropic ADPs? Yes, but not for the same atoms - since TLS is essentially constrained anisotropic refinement, the two methods are mutually exclusive". In the "Refinment settings" of the Phenix refine graphical interface, will you please tell me which button is for the anisotropic ADP? The individual B-factors, or the Group B-factors, or only the "Optimize X-ray/ADP weight"? I am looking forward to getting your reply. Smith

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Odd behaviour of real-space refinement
by Tristan Croll 21 Feb '15

21 Feb '15

Hi all, I'm just finalising the re-refinement of a 3.6 Angstrom structure. The stats in general are excellent (Rwork/Rfree = 0.219/0.260; Ramachandran outliers 0.12%; Clashscore < 2; rotamer outliers 2.1%) and I've gone through the whole structure to check and double-check fit to the density. I'm very confident that it's effectively correct. When I run through a fairly standard refinement protocol (XYZ coords, Individual B-factors, optimizing weights, secondary structure restraints), all seems fine - the Rfree rattles around within 0.2% or so. But when I include the real-space refinement option, very strange things start to happen. Each rsrl step causes a 3-4% jump in both Rwork and Rfree, and jumps the Clashscore up to 40 or so. Rotamer outliers briefly go to zero but then increase substantially (to 6+%) in subsequent steps, and the number of Ramachandran outliers increases. I thought I'd missed some dreadful error in my structure until I looked more closely at the results. Some very nonsensical changes have been made - for example, an arginine in the middle of a beta-sheet (admittedly with no observable density associated with its sidechain, but register is well determined by surrounding residues and backbone density is clear) was flipped from its original orientation to point directly into the hydrophobic core of the domain. Somewhat surprising, to say the least. Is this a bug in the algorithm, or is it simply that 3.6A is too low resolution for it to work reliably? My version of Phenix is a nightly build from about 2 weeks ago. Happy to share coordinates and log files if necessary. Thanks, Tristan

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Odd behaviour of real-space refinement
by Tristan Croll 21 Feb '15

21 Feb '15

Hi all, I'm just finalising the re-refinement of a 3.6 Angstrom structure. The stats in general are excellent (Rwork/Rfree = 0.219/0.260; Ramachandran outliers 0.12%; Clashscore < 2) and I've gone through the whole structure to check and double-check fit to the density. The only stat that bugs me a little is the rotamer outliers (2.3%). When I run through a fairly standard refinement protocol (XYZ coords, Individual B-factors, optimizing weights, secondary structure restraints), all seems fine - the Rfree rattles around within 0.2% or so. But when I include the real-space option, very strange things start to happen. Each rsrl step causes a 3-4% jump in both Rwork and Rfree, and jumps the Clashscore up to 40 or so. Rotamer outliers briefly go to zero but then increase substantially in subsequent steps, and the number of Ramachandran outliers increases. I thought I'd missed some dreadful error in my structure until I looked more closely at the results. The attached image is an example of what's happened: an exposed arginine in the middle of a beta-sheet (admittedly with no observable density associated with its sidechain, but register is well fixed by surrounding residues) has been flipped from its original orientation (yellow) to point directly into the hydrophobic core of the domain. Somewhat surprising, to say the least. Is this a bug in the algorithm, or is it simply that 3.6A is too low resolution for it to work reliably? My version of Phenix is a nightly build from about 2 weeks ago. Thanks, Tristan

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Re: [phenixbb] Autobuild iterative omit map error
by Terwilliger, Thomas Charles 20 Feb '15

20 Feb '15

Hi Emily, (Back on-list so others can see the answer.) It seems that your PDB file has a "TER" record between residues ASN 446 and ALA 447 of chain B. Our parsing system interprets that as the end of chain B and thinks that ALA 447 is another chain. You can see this by running: phenix.print_sequence xxxxx.pdb I tried deleting the TER record and it looks as though autobuild will get past the interpretation stage with it taken out. Let me know if that doesn't do it! (Also...do you know why the TER record might be there? It is a little surprising!) All the best, Tom T On Feb 20, 2015, at 9:10 AM, Emilia C. Arturo (Emily) wrote: Thank you Tom! Attached are the reflections file, sequence file, input model pdb file, and the log file from phenix. Emily. On Fri, Feb 20, 2015 at 11:01 AM, Terwilliger, Thomas Charles <terwilliger(a)lanl.gov<mailto:[email protected]>> wrote: Hi Emily, I'm sorry for the trouble! I'll be happy to try and help with it. If you send me (off-list) the input files you are using and the full log file I'll have a look. All the best, Tom T On Feb 20, 2015, at 7:53 AM, Emilia C. Arturo (Emily) wrote: > Hello. > > I'd like to use phenix's Autobuild iterative omit map tool, but have run into an error I could use some help with. When the process aborts, the message that phenix outputs is that the input file has duplicate chains. I looked at the pdb file and I do not see duplicate chains; could the ANISOU records for each atom generated by TLS refinement be hanging up the process? I had no error with Autobuild when I started the iterative map process using an input file that had been generated by phenix.refine using the same configuration as the TLS refinement had used (except, of course, for the TLS parameters). > > Thanks for your attention. > Emily. > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]> <AutoBuild_run_85_1.log><III-40-C2_justscan3_xscale_cutresto29.mtz><PAH.fa><PAH_C2_ref22plus_refine_84.pdb>

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Autobuild iterative omit map error
by Emilia C. Arturo (Emily) 20 Feb '15

20 Feb '15

Hello. I'd like to use phenix's Autobuild iterative omit map tool, but have run into an error I could use some help with. When the process aborts, the message that phenix outputs is that the input file has duplicate chains. I looked at the pdb file and I do not see duplicate chains; could the ANISOU records for each atom generated by TLS refinement be hanging up the process? I had no error with Autobuild when I started the iterative map process using an input file that had been generated by phenix.refine using the same configuration as the TLS refinement had used (except, of course, for the TLS parameters). Thanks for your attention. Emily.

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on Bulk-solvent and scaling
by Smith Lee 20 Feb '15

20 Feb '15

Dear All, Will you please introduce to me briefly on the function of the step of Bulk-solvent and scaling in the Phenix refine and what is the corresponding mechanism? Smith

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On Phenix refinement
by Smith Liu 20 Feb '15

20 Feb '15

Dear All, The default number of cycles for the Phenix refinement graphical interface is 3 (should be macro-cycles). I have done a refinement with 3 default cycles, and I get the acceptable refinement results. Then I kept everything same, except I changed the cycles of refinement from 3 to 5, however the refinement result was ugly which was unacceptable (Rfree increased). The Phenix document regards 5 macrocycles refine is fine. For my situation, do you think the 3 macrocycles refine result is acceptable or not? If not acceptable, what do you suggest for improvement? I am looking forward to getting your reply. Smith

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erraser for DNA?
by Phoebe A. Rice 19 Feb '15

19 Feb '15

I know phenix has lovely DNA restraints, but I think the backbone of my lowish-resolution DNA structure could use more help. Is there anything like erraser for DNA that will make my DNA backbone as B-like as possible? ++++++++++++++++++++++++++++++++++++++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago PRice(a)uchicago.edu<mailto:[email protected]>

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The discrepancy for determination of Ramachandran outliers by Coot and MolProbity
by Smith Lee 18 Feb '15

18 Feb '15

Dear All, It often finds for the Ramachandran favored determined by Coot, MolProbity regards as Ramachandran outliers. There are earlier posts regards Coot and MolProbity has different database for the determination of the Ramachandran plots. Then will you please let me know the correct way to correct the Ramachandran outliers by Coot in order to meet the MolProbity Standards? I am looking forward to getting your reply. Smith

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SA (torsion angle) along with B factor reset to low value.
by Tarek DawoD 18 Feb '15

18 Feb '15

to remove memory of the old original R-free flags (which is not available) and using a new test set, i reset the B factor and use SA (torsion angle) i got this error: not implemented: support of different sites. individual and sites.torsion_angles selection. what does that mean? thank you in advance TK_DawoD

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on HIS ** both conformations clash in the flipping
by Smith Lee 17 Feb '15

17 Feb '15

Dear All, In the log output of the Phenix refine, for the flipping of the N/Q/H residues before XYZ refinement, it often occurs something like "HIS ** both conformations clash, **PLEASE CHECK MANUALLY**". Will you please tell me what will clash with 1 of the 2 conformations of the specified HIS? I have checked the specified HIS in Coot, and I still do not know what does it mean for "both conformations clash". I am looking forward to getting a reply from you for clarification. Smith

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Computational Crystallography Newsletter - Volume 6, Number 1
by Nigel Moriarty 17 Feb '15

17 Feb '15

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2015 Articles Improved Probabilistic Estimates of Biocrystal Solvent Content Rapid evaluation of non-bonded overlaps in atomic models Short Communications Plan a SAD experiment, scale SAD data, and analyze your anomalous signal Validation of carbohydrate structures in CCP4 6.5 Disulfide bond restraints Fitting Tip #9: Avoiding excess cis peptides at low resolution or high B FAQ - Tips for coordinated metal refinement Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division 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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Quick request for addition to the line at the end of all these mails
by Morten Grøftehauge 16 Feb '15

16 Feb '15

Dear administrators of this list, Could you please add a line at the very end of these mails with: To unsubscribe click: www.somelink.com As it is it seems that some people have trouble getting off the list after they sign up. Because my spam filter keeps sending phenixbb mails into the spam folder. Which is likely because someone out there keeps flagging them as spam. If there's a link like that then gmail will even offer to attempt to unsubscribe for you. Just a thought. Cheers, Morten

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Please comment on the twinning analysis of my data by Xtriage
by Smith Liu 15 Feb '15

15 Feb '15

Dear All, I have done a Xtriage twinning analysis on my data. I summarize the result as following, Twinning analysis summary: The results of the L-test indicate that the intensity statistics below as expected. No twinning is suspected. Multivariate Z score L-test: 1.625. It further shows, Possible twin operators o merohedral twin operator(s) found, 1 pseudo-merohedral twin operator(s) found. Type Axis R metric(%) delta(le Pa) delta (lebed) Twin law PM 2-fold 4.934 2.547 0.036 l -k h Based on the above information, will you please advise me whether I need to input "l -k h" in the "Twin law" in "Other options" in "Refinement settings" in the Phenix refine graphical interface? I am looking forward to getting your reply. Smith

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On the cycles of the Phenix refinement
by Smith Lee 15 Feb '15

15 Feb '15

Dear All, The default number of cycles for the Phenix refinement graphical interface is 3 (should be macro-cycles). I have done a refinement with 3 default cycles, and I get the acceptable refinement results. Then I kept everything same, except I changed the cycles of refinement from 3 to 5, however the refinement result was ugly which was unacceptable. Someone told me once I have corrected the outliers by Coot, I can have a Phenix refinement with macro-cycles as 1, in order to avoid the Ramachandran corrected ones changing backing to Ramachandran outliers (Will you please further comment whether this strategy to correct Ramachandran outliers is acceptable or not). Thus can we regard the macro-cycles of Phenix refinement as one parameter for the refinement? And why the macro-cycles of the refinement can affect the refinement result? I am looking forward to getting your reply. Smith

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Re: [phenixbb] Fw: Fw: Question related to Phenix refinement
by Pavel Afonine 14 Feb '15

14 Feb '15

> From the attached the image, on the x-axis you can see the 4' rsrg and > 5'rsrg. > > I am looking forward to getting an explanation from you. Dear Smith, hope this will lead you to the answer: chevy:/net/chevy/raid1/afonine/sources % which fifig fifig: aliased to libtbx.find_files -g chevy:/net/chevy/raid1/afonine/sources % fifig rsrg ./cctbx_project/mmtbx/refinement/print_statistics.py: "realsrg" : "rsrg", chevy:/net/chevy/raid1/afonine/sources % All the best, Pavel

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Question related to Phenix refinement
by Smith Lee 14 Feb '15

14 Feb '15

Dear All. In the Phenix refine "run status" window, with the progression of the refinement, it occurs 3' bss, 3' rsrl, 3' xyz, 3' adp (for 3rd round of refinement). I guess xyz means the strategy is for x, y, z coordinates? Then what do bss, rsrl and adp mean? I am looking forward to getting your reply. Smith

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Test
by Paul Adams 14 Feb '15

14 Feb '15

-- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Hydrogen adding and real space refinement
by Smith Lee 12 Feb '15

12 Feb '15

Dear All, I find when I add H in the PDB file, in a refinement by Phenix, there is no real space refinement step (rsrl). If I do not add H in the PDB file, there is the rsrl step in the refinement. Somebody told me it was because there was a bug in the Phenix I downloaded, somebody told me if H added, there would be no real space refinement. I myself cannot clarify it by reading documents. Will you please clarify whether no rsrl step after H addition was because of bug or because of H addition leading to no rsrl step? And why H addition can lead to no rsrl step? I am looking forward to getting your reply. Best regards. Smith

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How should we estimate the "uncertainty" of the occupancy of an atom?
by Masaki UNNO 12 Feb '15

12 Feb '15

Hello We determined the structure of an enzyme-substrate complex. The substrate of the enzyme contains some partially occupied atoms. We were able to calculate the occupancies of these atoms using PHENIX_refine. By the way, I would like to know the uncertainties of the occupancies of these atoms. How can I estimate the uncertainties? For example, the occupancy of an atom was calculated as 0.65; can we write it as 0.65 (+/- 0.05) or 0.65 (+/- 0.1)? I know that it is related to B-factor and depends on the resolution (number of diffraction data per parameters), but I would like to know how to estimate (calculate?) the uncertainty. Could someone tell me about this issue? Best regards ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Masaki UNNO Graduate School of Science and Engineering Ibaraki University, JAPAN 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan Tel&Fax +81-294-38-5041 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [phenixbb] How should we estimate the "uncertainty" of the occupancy of an atom?
by Dale Tronrud 11 Feb '15

11 Feb '15

On 2/11/2015 12:34 PM, Keller, Jacob wrote: >> If your interpretation of your model depends on whether the occupancy of this atom is 0.65 or 0.75 crystallography is the tool you need. > > Did you mean *not* the tool...? > > JPK > You are right. I meant crystallography is NOT your tool. Sorry. Dale Tronrud

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Specifying Multiple Twin Operators
by Keller, Jacob 11 Feb '15

11 Feb '15

Dear List, Is it possible to specify multiple twin operators in Phenix? I have tetartohedrally-twinned data. If so, what's the syntax, and an example? And can it be done through the GUI? Thanks, Jacob ******************************************* 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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Question on Torsion-angle NCS
by Smith Liu 11 Feb '15

11 Feb '15

Dear All, For the graphical Phenix refine, if we click the "NCS options" button, a small window will occur. In the small window, will you please tell me how much should I input for "Weigh on NCS-related B-factor restraints"? I am looking forward to getting your reply. Smith

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Calculating map with electron scattering factors
by Omar Davulcu 10 Feb '15

10 Feb '15

Hi, everyone. Probably a silly question, but here goes... I'm trying to calculate a simulated map around a set of coordinates using the electron scattering table. Phenix.maps doesn't appear to allow selection of that particular scattering table. I noticed that phenix.refine allows me to select that table and I thought I would set the number of macro cycles to 0 and turn off all the refinement options and produce a map that way. I thought I would generate the structure factors needed as input with phenix.fmodel, but that also doesn't allow selection of the electron scattering table. So, my (naïve) question is: what am I doing wrong? Is there a way I can calculate this map in phenix? Any help would be greatly appreciated. Thanks much! Omar Davulcu

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on XYZ individual (reciprocal space) refinement
by Dialing Pretty 10 Feb '15

10 Feb '15

Dear All, Will you please tell me the XYZ individual (reciprocal space) refinement is executed by which strategy of the Phnix refinement? By XYZ coordinates, or by Optimize X-ray/ADP weight,or by Optimize X-ray/sterochemistry weight? Dialing

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on my Phenix refinment
by Smith Lee 09 Feb '15

09 Feb '15

Dear All, I have started a Phenix refinement, my strategy including xyz coordinates, real space, individual B-factors, Group B-factors, TLS parameters, Occupancies, optimize X-ray/sterochemistry weight, NCS restraints, and Automatically correct N/Q/H errors. Number of cycles is 3. It is now at the 3' bss stage. But will you please tell me why there is no rsrl stage occurred in the Run Status window (here I mean there is no 1' rsrl stage and 2' rsrl stage) even now it has reached the 3' bss stage? I am looking forward to getting your reply. Smith

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Global metrics for Ramachandran quality beyond %outliers?
by Shane Caldwell 09 Feb '15

09 Feb '15

I'm making a new thread because it's off the topic, but I have a question in response to this point <http://phenix-online.org/pipermail/phenixbb/2015-February/021691.html>: > [Doggy structure improved, as shown by how] The Ramachandran plot tightened This is interesting to me - other than eyeballing the plot, are there any quantitative metrics of Ramachandran distribution quality? At low-res or when refining a bunch of structures side-by-side it could be an additional indicator of quality of the model, without requiring having to inspect the plot. Of course manual inspection is always important in the end, but in early stages a global measure of spread could help guide refinement. I've seen %outliers used for this purpose, but that ignores that while a residue can be "allowed" it can still be far from a statistically likely conformation. From what I've seen, some users only consult Ramachandran to tweak residues until they pop into the "allowed" regions and stop there, which isn't the same as globally improving the geometry. Interested to hear thoughts (or it it's already in use, pointing me in the right direction!), Shane Caldwell McGill University On Thu, Feb 5, 2015 at 5:06 AM, Andreas Förster <docandreas(a)gmail.com> wrote: > Dear Almudena, > > I promise not to make a habit of advertising other programs on the Phenix > mailing list, but just once I would like to encourage you (and the > community) to try all the tools at your disposal. > > Different refinement programs have different strength and weaknesses. > Secondary-structure restraints in Phenix are great for low-resolution data, > but so is jelly-body refinement in Refmac. A dodgy 3.2 Å structure I'm > currently working on was improved dramatically by Buster-TNT. The > Ramachandran plot tightened, and R free plunged by four percentage points. > > > Andreas > > > > On 05/02/2015 10:44, Almudena Ponce Salvatierra wrote: > >> Dear all, >> >> I am refining my structure (data at 3 A), with a model that is complete. >> However the Rs values are: R work= 0.25 and Rfree= 0.32. I have read >> "Improved target weight optimization in phenix.refine" (In the >> computational crystallographic newsletter 2011) and what I understand is >> that just by marking the boxes "improve xray/stereochemistry weight" and >> "improve xray/adp weight" it should work... giving me the best possible >> Rfree. >> >> I'm refining individual coordinates, occupancies, b-factors (isotropic >> for all atoms), TLS, and using secondary structure restraints, automatic >> ligand linking and experimental phases restraints. Also, I chose this >> strategy because I have finished building the structure and according to >> some of the suggestions in "towards automated crystallographic structure >> refinement with phenix.refine". >> >> I am actually quite confused and don't know what to think... is it a >> matter of the weights? is it only that this is as good as it gets? >> >> Any suggestions and comments are welcome. >> >> Thanks a lot in advance, >> >> Best, >> >> Almudena >> -- >> Almudena Ponce-Salvatierra >> Macromolecular crystallography and Nucleic acid chemistry >> Max Planck Institute for Biophysical Chemistry >> Am Fassberg 11 37077 Göttingen >> Germany >> >> >> >> _______________________________________________ >> 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 >

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Scientist BioMAX
by Marjolein Thunnissen 07 Feb '15

07 Feb '15

Beamline manager position open for BioMAX Beamline The MAX IV Laboratory, a part of Lund University, has operated successfully for more than 25 years and is currently building the new MAX IV synchrotron facility in Lund. More than 900 scientists from Sweden and the rest of the world are coming to the MAX IV Laboratory every year to use the x-rays produced by our electron accelerators. They do research in areas such as materials science, structural biology, chemistry, and nanotechnology. 170 people are currently employed at the MAX IV Laboratory. The MAX IV facility, the largest and most ambitious Swedish investment in research infrastructure, will be the brightest source of x-rays worldwide and will replace the existing laboratory, which today consists of the storage rings MAX I, II and III. The new MAX IV facility will become operational in June 2016. One of the first beamline at MAX IV to come into operation will be the macromolecular crystallography (MX) beamline BioMAX. BioMAX will use the unique properties of the MAX IV 3 GeV ring to become a world leading MX beamline with a high degree of automation, microfocus capability, highly parallel beam suitable for large molecular assemblies, high flux, high level of software support and a user friendly environment. We are now looking for a beamline manager for the BioMAX beamline. Link to full posting: http://www.lu.se/lediga-anstallningar-available-jobs?x=0&Dnr=654959&Type=E Job Location: MAX IV-Laboratory, Lund, Sweden Job Title / Reference: Scientist BioMAX / Ref: PEPA 2015/9 Application deadline: Wednesday, February 18, 2015 For further information please contact: Tomas Lundqvist<mailto:[email protected]>, Life Science Director | +46708467688 best regards Marjolein [cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC] Marjolein Thunnissen Science Coordinator Structural Biology MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/> [cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC] Marjolein Thunnissen Science Coordinator Structural Biology MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/>

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allowable completeness limit for the highest resolution shell
by Tarek DawoD 06 Feb '15

06 Feb '15

Dear ALL i would like to ask in general if there is a suggested certain completeness cutoff for the higher resolution shell. for example; the following are the values for the 4 higher resolution shells Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac Rmeas Rpim CC1/2 CC* completeness 1.53 1.50 2.5 1.2 1.2 0.706 0.680 0.596 0.855 0.510 0.547 0.841 73.6 1.50 1.47 2.3 1.1 1.0 0.745 0.742 0.629 0.967 0.613 0.468 0.798 55.3 1.47 1.44 2.0 1.0 1.0 0.725 0.775 0.644 0.000 0.694 0.395 0.752 52.4 1.44 1.41 1.9 0.8 0.8 0.689 0.946 0.681 0.000 0.883 0.371 0.736 33.9 All reflections 44.8 2.5 2.3 0.638 0.044 0.029 0.052 0.028 my question in other word if all statistics for the highest resolution shell are reasonable, good I/sigma, R-fac, ........, CC1/2, ..etc but the completeness is just say 20 or 30, what is allowable completeness limit for the highest resolution shell, 70, 80 or 90??? regardsTK_Dawod

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refinement with anomalous data
by Guangyu Zhu 06 Feb '15

06 Feb '15

Hi, all, I have a question for refinement. I have a data set for refinement at 3.8A (outshell I/sigma ~1.0). When I processed the data, I kept anomalous data I+/I-. Because at that time I think I might have anomalous signal. But later I found that the protein coordinated with wrong metal, so I don’t really have anomalous scatters. I have good model from high resolution data. When I refined the structure, I found that refined against I+/I- give lower R/Rfree (23.0%/27.0%) than against Imean (25.1%/28.3%). When I used I+/I-, I knew I doubled reflections/parameters ratio. I also let Phenix both X-ray stereochemistry/ADP weight. The refined models have similar geometry. So should I use I+/I- for refinement since it gives lower R factor? Guangyu Zhu

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Fwd: [ccp4bb] Absence of contact between layers in a crystal
by Folmer Fredslund 06 Feb '15

06 Feb '15

Hi all, As you might have noticed, there is a discussion going on about the fraudulent 2hr0 pdb deposition on the CCP4BB Searching for 2hr0 I came across http://www.phenix-online.org/documentation/reference/cif_as_mtz.html where 2hr0 is used as an example. Might I suggest that this is changed in the documentation? Best regards, Folmer Fredslund ---------- Forwarded message ---------- From: Kerff Fred <fkerff(a)ulg.ac.be> Date: 2015-02-06 11:58 GMT+01:00 Subject: [ccp4bb] Absence of contact between layers in a crystal To: CCP4BB(a)jiscmail.ac.uk Hello, Looking at structure 2HR0 ("The structure of complement C3b provides insights into complement activation and regulation. »,Abdul Ajees, A., Gunasekaran, K., Volanakis, J.E., Narayana, S.V., Kotwal, G.J., Krishna Murthy, H.M.; (2006) Nature 444: 221-225), I noticed the absence of contacts between layers in the crystal. Is it something that has already been observed in other crystals? Best regards, Fred ----- Frédéric Kerff Chercheur qualifié F.R.S.-FNRS Cristallographie des protéines Centre d'Ingénierie des Protéines Université de Liège 17, Allée du 6 Août - Bat B5a 4000 Liège (Belgium) Tel.: +32 (0)4 3663620 Fax: +32 (0)4 3663772 > Le 6 févr. 2015 à 10:12, Tim Gruene <tg(a)SHELX.UNI-AC.GWDG.DE> a écrit : > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Smith, > > The sca file most likely does not contain flags. pointless can read > the sca file, standardise it to ccp4 standards and freerflag marks > random reflections. You should use the maximum of 500 unique > reflections or 5% of the unique reflections, whichever is larger. > > Best, > Tim > > On 02/06/2015 09:49 AM, Smith Lee wrote: >> Dear All, I have a sca file. Will you please tell me by which >> software or how I can know whether the sca file contains R-free >> tags? If not, by which software or how I can add the R-free tags? >> And how much of the reflections I add the R-free tags? I am looking >> forward to getting your reply. Smith >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > > iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi > j0JFZac4kAh8twpov71MG84= > =XN57 > -----END PGP SIGNATURE----- -- Folmer Fredslund

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Phenix refine - R free does not decrease
by Almudena Ponce Salvatierra 05 Feb '15

05 Feb '15

Dear all, I am refining my structure (data at 3 A), with a model that is complete. However the Rs values are: R work= 0.25 and Rfree= 0.32. I have read "Improved target weight optimization in phenix.refine" (In the computational crystallographic newsletter 2011) and what I understand is that just by marking the boxes "improve xray/stereochemistry weight" and "improve xray/adp weight" it should work... giving me the best possible Rfree. I'm refining individual coordinates, occupancies, b-factors (isotropic for all atoms), TLS, and using secondary structure restraints, automatic ligand linking and experimental phases restraints. Also, I chose this strategy because I have finished building the structure and according to some of the suggestions in "towards automated crystallographic structure refinement with phenix.refine". I am actually quite confused and don't know what to think... is it a matter of the weights? is it only that this is as good as it gets? Any suggestions and comments are welcome. Thanks a lot in advance, 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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Strange behaviour of phenix.maps fill_missing_f_obs
by Tristan Croll 05 Feb '15

05 Feb '15

Hi, I'm working on a package that makes scripted calls to phenix.refine to generate a series of ccp4 formatted maps, and have run into an odd problem. Using the attached parameter file I get a series of perfectly normal-looking maps, except in the case of the filled 2mFo-DFc map (test-3_2mFo-DFc_fill.ccp4 - the second-last map generated). This comes out as a series of disconnected blobs (it looks rather like a mFo-DFc map, but it doesn't match the actual mFo-DFc map). When I take the resulting .mtz file and generate the filled map in Coot (with or without omission of Rfree flags), on the other hand, it seems to come out fine. There are no error messages in the log, but I suspect the default method to fill in the missing F_obs may be returning only the missing F_obs? I've attached a small example image. Red wireframe is the 2mFo-DFc unfilled map at 1 sigma; green translucent is the 2mFo-DFc filled map at 1 sigma; yellow is the mFo-DFc map at 2 sigma. The test structure I'm using is nothing special: 3WSY, picked more-or-less at random off the protein data bank. Phenix version is 1.9.1692, installed in Fedora 21. Have I done something wrong that I'm just not seeing, or is there a bug here? Thanks, Tristan

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off-topic: Faculty position at all levels in structural biology at Stony Brook University, New York
by Markus Seeliger 05 Feb '15

05 Feb '15

We are recruiting for the above position. More details and the application can be found at https://academicjobsonline.org/ajo/jobs/5289 Stony Brook University Department of Pharmacological Sciences *Tenure-Track Structural Biology / Imaging Faculty Position in Conjunction with the Interdisciplinary Biomolecular Imaging Cluster Hiring Initiative* The Department of Pharmacological Sciences ( http://www.pharm.stonybrook.edu/faculty_research/overview) at Stony Brook University seeks applications for a tenure-track faculty position at the level of Assistant, Associate, or Full Professor. Candidates must have an M.D. and/or Ph.D., at least two years of postgraduate research experience, and an outstanding record of research accomplishment. This search is intended to recruit investigators with translational research programs that make use of *NMR, Cryo-EM, or positron emission tomography (PET) coupled with radiotracer synthesis approaches* to pursue fundamental questions relevant to health-connected fields such as cancer, neuroscience, metabolism, and infectious disease. Senior candidates should also have a record of success with extramural funding and training of students and/or fellows. Applicants must be eligible for a faculty appointment in accordance with the criteria established by the School of Medicine (Criteria for Appointment, Promotion and Tenure.) The Department has pre-doctoral and MSTP training grants, a broad infrastructure for research investigation, and newly renovated lab space housing structural biologists with expertise in NMR and x-ray crystallography. Additional structural biologists and PET imagers are found in the Departments of Biochemistry, Physiology, Chemistry, and Microbiology. With the on-going NYSUNY 2020 Challenge Grant awarded to the University and the recent and largest gift ever to public higher education in the State of New York, Stony Brook University is embarking on a transformational expansion of the biomedical research enterprise. Diverse opportunities for collaborative research on campus include the Cancer Center, the Laufer Center for Physical and Quantitative Biology, the Center for Structural Biology, the Institute for Chemical Biology and Drug Discovery, and the interactive Computer Science and Applied Mathematics Departments. Imaging biological molecules is key to understanding their function, providing a starting point for rational drug design and protein engineering. Stony Brook University is becoming a leader in biomolecular imaging through its newly-upgraded high-field NMR facilities including Bruker 700MHz and 850 MHz instruments with cryogenic probes, a strong program in computational structural and physical biology, world-class computational resources, facilities for radiotracer synthesis and human imaging, and proximity to the new third-generation synchrotron facility at Brookhaven National Lab (NSLS-II). The Biomolecular Imaging Cluster has already recruited junior faculty with expertise in super-resolution microscopy and x-ray crystallography. Stony Brook University, home to many highly-ranked graduate research programs, is located 60 miles from New York City on Long Island's scenic North Shore. Our 1,100-acre campus has more than 24,000 undergraduate, graduate, and doctoral students and 13,500 faculty and staff. The University is a member of the prestigious Association of American Universities and co-manager of the nearby Brookhaven National Laboratory, a multidisciplinary research laboratory supporting world-class scientific programs utilizing state-of-the-art facilities. Stony Brook University is also located close to the Cold Spring Harbor Laboratory with which it interacts through graduate program training and faculty collaborations. To apply, use Academic Jobs Online ( https://academicjobsonline.org/ajo/jobs/5289) to submit a State employment application, a complete curriculum vitae including publications, and a 3-page proposed research plan of current and future research, and have three letters of recommendation submitted through the AJO site. The cover letter should indicate whether the applicant wishes to be considered for appointment at the Assistant, Associate, or Full Professor level. Applicants at the Associate or Full Professor level should add a summary of past and current research funding and administrative and teaching experiences. Electronic submission through AJO is required. Questions should be addressed to Ms. Lynda Perdomo-Ayala, Department Administrator ( lynda.perdomo-ayala(a)stonybrook.edu). 631-444-3050 For a full position description, visit www.stonybrook.edu/jobs (Ref. F-9387/14/12.) Stony Brook University is an Affirmative Action, Equal Opportunity Educator and Employer.

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generating xplor map of specific size
by Scott Horowitz 03 Feb '15

03 Feb '15

Hi all, Sorry for yet another map question: what I'd like to do is be able to generate xplor maps with an explicitly defined size and shape from the command line using phenix. Just choosing a buffer around a selection will result in slightly different sizes for different PDB files, which I'd like to avoid. In my comparisons, having exactly the same dimensions and centering for maps I'm calculating from multiple slightly different variants would be very helpful. Is there a way to do this? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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serial MR / refinement
by Eike Schulz 03 Feb '15

03 Feb '15

Dear all, I am looking for a way to automate molecular replacement and refinement runs. >From ligand / fragment screening trials we have many datasets of the same protein with various resolutions (2.8 – 1.2Å). The apo-structure is known and well refined. The cell constants are fairly similar but not in all cases identical, hence I would prefer a MR run prior to the refinement. I am sure this can somehow be realized with some shell-script but maybe there is some more sophisticated way of realising this? I would also be happy for partial solutions to the problem. Best regards Eike

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Young scientist travel awards for Intl Conf. on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology"
by Terwilliger, Thomas Charles 02 Feb '15

02 Feb '15

2-Feb-2015 Dear Colleagues, We are pleased to announce the availability of young scientist travel fellowships to the International Conference on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology", which will be held on the campus of the Weizmann Institute of Science in Rehovot, Israel June 7-11, 2015. This conference is intended to foster international collaboration and to provide an overview for the most recent developments in Structural Biology and Structural Genomics and future impacts on biology, medicine and disease. Web site: http://www.weizmann.ac.il/conferences/ICSG2015 Poster: https://www.dropbox.com/s/i1s3hsg7a0chqi2/ICSG2015_Poster.pdf?dl=0 There are two types of young scientist travel support available (deadlines are both March 31, 2015): Young scientist travel support of up to $1,000 US will be made available to graduate students and post-doctoral researchers to attend ICSG2015. A total of 5 International Structural Genomics Organization (ISGO) - NIH Protein Structure Initiative (PSI) Student Travel Fellowships have kindly been provided by the ISGO and the NIH PSI. Fellowships of €500 for students from Instruct countries will be awarded to attend the pre-conference workshop “Technical and Analytical Approaches to the Translation of Deep Sequencing Data into Three-Dimensions” (7-June-2014 09:00-12:00) and to stay on and participate in the full conference. A total of 8 Fellowships have kindly been provided by Instruct (https://www.structuralbiology.eu). To apply for a student travel fellowship please see http://www.weizmann.ac.il/conferences/ICSG2015/young-scientists-travel-supp… . The International Conference on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology” conference The scientific topics to be covered in ICSG 2015 (see http://www.weizmann.ac.il/conferences/ICSG2015) include: · Deep sequencing for modeling and refinement of macromolecular structures · Membrane protein structure and function using complementary methods · Technological advances in XFEL, Cryo-EM, NMR, SAXS, MS, MX and macromolecular complexes · Combining low and high resolution data and modeling for structural biology · Synergistic use of 3D structures and deep sequencing to realize personalized medicine · Protein design and deep sequencing · Cancer, antibiotic resistance and drug discovery In order to widen the opportunities for younger researchers, we have organized satellite workshops before ICSG 2015 (during the day on June 7, 2015). These include: · Cryo-EM developments for structural biology [Sponsored by FEI] · Approaches to the translation of deep sequencing data into three-dimensions [Sponsored by Instruct] · PHENIX: Automated determination of molecular structures [Tom Terwilliger & Pavel Afonine] · HKL3000: From X-ray diffraction images to structure determination in minutes [Wladek Minor] · Protein expression and characterization workshop [Tamar Unger & Yoav Peleg] · Proteopedia: A Scientific Wiki Bridging the Rift Between 3D Structure & Function [Jaime Prilusky & Joel L. Sussman] Five oral presentations will be chosen from the posters, and six poster prizes will be awarded, so be sure to submit your abstracts by April 15, 2015! Speakers include: Arie Admon (Haifa) Lucia Banci (Florence) Pamela J. Bjorkman (Pasadena) Samir K. Brahmachari (Delhi) Susan Buchanan (Bethesda) Martin Caffrey (Dublin) Mark Gerstein (New Haven) Wayne Hendrickson (New York) Yvonne Jones (Oxford) Roger Kornberg (Stanford) Luhua Lai (Beijing) Michael Levitt (Stanford) Michal Linial (Jerusalem) Abraham Minsky (Rehovot) John Moult (Rockville) Nathan Nelson (Tel Aviv) Stefan Raunser (Dortmund) Monica Roth (Piscataway) Dinakar M. Salunke (Gurgaon) Eran Segal (Rehovot) Philip Selenko (Berlin) Sachdev Sidhu (Toronto) Rotem Sorek (Rehovot) Jan Steyaert (Brussels) Shamil Sunyaev (Boston) Dan Tawfik (Rehovot) Janet Thornton (Hinxton) The FEBS National Lecturer Gunnar von Heijne (Stockholm) Soichi Wakatsuki (Stanford) Shigeyuki Yokoyama (Yokohama) Ada Yonath (Rehovot) Mingjie Zhang (Hong Kong) We are looking forward to welcoming you to the Weizmann Institute in the June of 2015! Sincerely yours, ICSG 2015 Local Organizing Committee Joel L. Sussman, Gideon Schreiber, Tamar Unger and Israel Silman, Weizmann Institute ICSG 2015 International Organizing Committee Cheryl Arrowsmith, (Structural Genomics Consortium, Toronto) Lucia Banci, (University of Florence, Florence) Jacqui Beckmann, (Swiss Institute of Bioinformatics, Lausanne) Mark Gerstein, (Yale University, New Haven) Yvonne Jones, (University of Oxford, Oxford) ------------------------------------------------------------------------- Prof. Joel L. Sussman www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel> Department of Structural Biology tel: +972 (8) 934 4531 www.weizmann.ac.il/ISPC<http://www.weizmann.ac.il/ISPC> Weizmann Institute of Science fax: +972 (8) 934 6312 www.proteopedia.org<http://www.proteopedia.org> Rehovot 76100 ISRAEL www.weizmann.ac.il/conferences/ICSG2015<http://www.weizmann.ac.il/conferences/ICSG2015> -------------------------------------------------------------------------

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Output file of the Phenix refine
by Smith Liu 01 Feb '15

01 Feb '15

Dear All, Will you please tell me which Phenix refine output file contains the information on my input files, my strategies and my parameters for the refinement? Smith

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Question related to Phenix refinement
by Smith Lee 01 Feb '15

01 Feb '15

Dear All, Which strategy or parameter input can be used to reduce the rotamer outliers? Which strategy or parameter input can be used to reduce the bond outliers? For all the Phenix refine strategies, can you sequence it from rough refinement to fine refinement in order? I am looking forward to getting your reply. Smith

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Rwork and Rfree
by Dialing Pretty 31 Jan '15

31 Jan '15

Dear All, After a Phenix refinement (for crystal 2.5A), my Rwork is about 0.19, and my Rfree is about 0.26. Is the gap between Rwork and Rfree too karge? If too large, why it is too large and how to avoid it? I am looking forward to getting your reply. Dialing

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