- phenixbb - phenix-online.org

Refinement
by mohamed noor 25 Mar '15

25 Mar '15

Dear all I have a structure at 1.4 A currently with an Rfactor of 21/26 %. I notice from the plot by cycle that everytime the RMS bonds/angles reduce, the Rfactor increases a few percent. Is there any way of telling phenix.refine to not 'restrain' the model too much? I have already used automatic weighting. Also, RINGER identified a few alternate conformations, so I'm thinking that modeling this might account for a better model. However, as I have an NCS of 4, this can be tedious to do by hand, and AFAIK, phenix.refine does not create new conformations. Is there an alternative? Final question, some residues were flagged as having high B factors but not in all the copies. How do I deal with this? Some background: I initially had problems with refinement being stuck at 30-35 % in SG P 3 2 1 (as suggested by Pointless and Xtriage). However, the beamline scientist suggested that there could've been lattice translocation and that it is actually P 3. Reintegrating seems to have solved the problem. With integrated data up to 1.2 A, I tried cut-off at 1.4, 1.3 and 1.2 A. Together with CC1/2 and refinement results, I chose 1.4 A, but should I cut it a bit lower? Thanks.

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PhD position in Structural Biology in Norway
by Hans-Petter Hersleth 24 Mar '15

24 Mar '15

Dear all, A 3- or 4-year PhD position in Structural Biology / Biophysics / Biochemistry starting August 2015 is available at University of Oslo, Department of Biosciences, Section for Biochemistry and Molecular Biology in the Metalloprotein group. The project is in the field of structural biology, biophysics and biochemistry with an emphasis on protein crystallography and spectroscopy (UV-vis, Raman and EPR) in combination with other biochemical and biophysical methods. The project is dealing with different redox proteins involved in oxygen activation and electron transfer. The focus will be on some enzyme systems like ribonucleotide reductase and nitric oxide synthase, their reaction mechanism and redox activation pathways. More information about the project, position and application procedure is found on the website: http://uio.easycruit.com/vacancy/1352831/96323?iso=no Applicants must hold a Master's degree or equivalent in structural biology, bioinorganic chemistry, biochemistry, biophysics, protein crystallography or related fields. We are seeking a highly motivated candidate that should have skills and experience in working with proteins or bioinorganic molecules. It would be advantageous with hands-on experience within topics like cloning, protein expression, purification, crystallisation, protein crystallography, spectroscopy, bioinorganic chemistry, protein-protein interactions, enzyme kinetics and redox-, radical- and metalloproteins. Candiates without a Master's Degree have until 30 June 2015 to complete the final exam. Application deadline is 13th April 2015 through the website: http://uio.easycruit.com/vacancy/1352831/96323?iso=no For further information please contact: Dr. Hans-Petter Hersleth, (h.p.hersleth(a)ibv.uio.no) ---------------------------------------------------------------------------------------------- Hans-Petter Hersleth, PhD Project Leader, Researcher and Senior Lecturer Department of Biosciences, University of Oslo Section for Biochemistry and Molecular Biology P.O.Box 1066 Blindern, NO-0316 Oslo, Norway Phone: +47 2285 4631 Fax: +47 2285 4726 Mobile: +47 413 33 126 http://www.hersleth.org/ -----------------------------------------------------------------------------------------------

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on Phenix's "Generate "Table 1" for journal"
by Smith Liu 23 Mar '15

23 Mar '15

Dear All, With the Phenix refine PDB and mtz file, I just prepared a "Table 1" for journal with Phenix. Here I find something special, which I hope I can get your advice. First, for the "Total reflections" and "Multiplicity", they are empty (no data given). Wil you please tell me why? Secondly, it writes, "Statistics for the highest-resolution shell are shown in parentheses". Suppose my crystal resolution is 2.5-45.6, then the the highest-resolution value should be 2.5, rather than 45.6, right? In addition, what is the diffrence between highest-resolution shell in the Table 1 and highest-resolution bin in the "Results" of Phenix refine? What is R-merge, R-meas,CC1/2 and CC*? I can get these data from MOSFLM output mtz file. But is my images were processe by HKL, which I have no experience, then how can I get the R-merge, R-meas,CC1/2 and CC*? I am looking forward to getting your reply. Smith

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question related to phenix produced PDB file
by Dialing Pretty 21 Mar '15

21 Mar '15

Dear All, In my Phenix refine produced PDB file, I find in REMARK 3, there is a sentence "PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED): 42.3. Does 42.3 means 42.3%? Is it too high? I am looking forward to getting your reply. Dialing

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error message in phenix refine
by Almudena Ponce Salvatierra 20 Mar '15

20 Mar '15

Hi everyone, I have merged 3 mtz files into one and done successfully Molecular replacement with it. However when I try to refine, I get the following error message: "cctbx error: merge_equivalents_exact: imcompatible flags for hkl (0, 0, 16) (mismatch between Friedel pairs). How can I fix this? Thank you very much 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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fixing rotamers with coot
by Benoît Masquida 19 Mar '15

19 Mar '15

Dear all, I am using Coot 0.7.2 and phenix 1.9-1692 on Ubuntu 13.10 and I have the following error message when I try to regularize zone, edit Chi angles or fix rotamer outliers. Error message :"Refinement setup failure. Failed to find restraints for : 'residue list' " Apparently a cif dictionary is missing that should be output by phenix to be used by coot. Does anyone has any idea? Thanks in advance. Benoit --

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on Phenix refine
by Smith Liu 19 Mar '15

19 Mar '15

Dear All, Will you please tell me which strategy of Phenix refine is for reciprocal space refinement? In the log, I often see "XYZ individual (reciprocal space)", will you please let me know whether "XYZ individual (reciprocal space)" is caused by "XYZ coordinates" or by "Optimize X-ray/sterochemistry weight"? Smith

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on the eff file
by Smith Liu 19 Mar '15

19 Mar '15

Dear All, Someone told me from the refine eff file, I can know what is my strategy for my refinement. I have run 2 refines with the same input files, For one refine, in the graphical interface I have checked xyz-coordinates, Real-space, Individual B-factors, Occupanies, Optimize X-ray/sterochemistry weight, Automaticaly orrect N/Q/H erros. For the other refine, I only checked XYZcoordinates, Real-space and Autonomously correct N/Q/H errors. I have checked the eff files from the 2 diffrent refines, but I cannot find any diffrence in the eff file. Thus will you please tell me how to find the diffrence in the 2 eff files? Or my strategies for each refine was recorded in the other files? I am looking forward to getting your reply. Smith

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the command to open the *.eff file
by Smith Lee 18 Mar '15

18 Mar '15

Dear All, Will you please tell me the command to open the *.eff file? I want to get the stratgies for my refinement. Smith

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phenix.development.optimize_model
by Colin Levy 18 Mar '15

18 Mar '15

Hi, I am running a Phenix development installation (dev_1977) and used the phenix.development.optimize_model option on a project of mine refined at 1.9Å. The output has certainly improved the R factors but I was curious as the refined model which is a rather globular structure has been refined utilising 17 TLS groups and anisotropic B factors. In its current state of development, how robust are these refinement choices and on what basis are they being determined? They differ somewhat from what I might have invoked manually? Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk On 12/03/2015 15:19, "phenixbb-request(a)phenix-online.org" <phenixbb-request(a)phenix-online.org> wrote: >Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > >To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb >or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > >You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of phenixbb digest..." > > >Today's Topics: > > 1. Announcement and call for abstracts: Structural > Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, > Croatia (Capitani Guido (PSI)) > 2. how to correct residuess with missing atoms (Smith Liu) > 3. Re: how to correct residuess with missing atoms (Joel Tyndall) > 4. RESOLVE density modification (Mark A Saper) > 5. Re: RESOLVE density modification (Terwilliger, Thomas Charles) > 6. Nitric Oxide metal.edits not working? (Yarrow Madrona) > 7. Re: Nitric Oxide metal.edits not working? (Edward A. Berry) > 8. Group B factor refinement not working for low resolution data (??) > 9. Re: Group B factor refinement not working for low resolution > data (Pavel Afonine) > 10. Re: Group B factor refinement not working for low resolution > data (Phoebe A. Rice) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Fri, 6 Mar 2015 13:29:51 +0000 >From: "Capitani Guido (PSI)" <guido.capitani(a)psi.ch> >To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> >Subject: [phenixbb] Announcement and call for abstracts: Structural > Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, Croatia >Message-ID: > <D324C9581FD3114280044EDC6357A3E51BCE66CD(a)MBX114.d.ethz.ch> >Content-Type: text/plain; charset="us-ascii" > >Dear Colleagues, > >The 29th European Crystallographic Meeting (ECM29), to be held on August >23-28 in Rovinj, Croatia, will feature a Structural Bioinformatics >microsymposium >(http://ecm29.ecanews.org/programme/microsymposia/#ms10). All structural >bioinformatics topics with relevance to macromolecular crystallography >are welcome. >Abstract submission (for oral or poster presentation) is available at >http://ecm29.ecanews.org/participate/abstract-submission/, with deadline >March 23. >The final program will encompass two 30-min talks from invited speakers, >three 20-min talks chosen from the submitted abstracts, and poster >presentations. >Looking forward to many interesting contributions; with best regards, > >Guido Capitani > > > >Dr. Guido Capitani >Paul Scherrer Institute >OFLC/110 >5232 Villigen PSI >Switzerland >guido.capitani(a)psi.ch >Tel. +41 56 310 47 22 >http://www.psi.ch/lbr/capitani_-guido >http://www.eppic-web.org > > > > > > >------------------------------ > >Message: 2 >Date: Sun, 8 Mar 2015 18:11:19 +0800 (CST) >From: "Smith Liu" <smith_liu123(a)163.com> >To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> >Subject: [phenixbb] how to correct residuess with missing atoms >Message-ID: <46870f8b.b136.14bf8de1901.Coremail.smith_liu123(a)163.com> >Content-Type: text/plain; charset="gbk" > >Dear All, > >Is any function of Phenix or some other software which can be used to >correct residuess with missing atoms in the PDB file? > >I am looking forward to getting your reply. > >Smith >

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