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R vs Geometry (branched off from: [ccp4bb] Rfree at low resolution: how reliable is it, really?)
by Keller, Jacob 03 Aug '15

03 Aug '15

Dear Crystallographers, In following the thread on Rfree reliability, and in the context of a structure I am currently polishing, I have started to wonder what is the ideal way to weight geometry versus R values. I had always thought the rationalization for using geometric restraints was actually to help R values to decrease eventually, since the truth about one’s protein structure is much more likely to agree with the thousands of molecules already solved than with the particularities of the model one has built or the reflection data under consideration. What happens, though, when one’s R values are, say, 2% or even 5% lower with less weight on geometry? It seems to me that this is a gray area, and it would be great to have some sort of general rule. I know that Phenix has a weight-optimization protocol which uses parallel runs with different weights, but I am curious what method is used to decide which one was best? There may not, however, be such a general rule, since I suppose this question is one we always encounter in science. For example, in fitting a few data points, when does one abandon the use of a linear model in favor of something more sophisticated? Or maybe, indeed, someone *has* discovered some reasonable way of approaching this? All the best, Jacob Keller

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symmetry file for Phenix merging statistics
by Xiao Lei 03 Aug '15

03 Aug '15

Hi Phenixbb members, I am trying to use "phenix merging statistics" tool, and I have an unmerged sca file from HKL2000, because the unmerged HKL2000 output does not have unit cell information, so I also need to input a symmetry file, how can I find the symmetry file? Is there a way to generate a symmetry file? Thanks ahead. Xiao

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Anisotropic B-factors with Trucated Data
by Keller, Jacob 02 Aug '15

02 Aug '15

Dear Crystallographers, I have a dataset which was artificially truncated at 1.7 Ang by the limitations of our setup, but the resolution is probably 1.5 Ang or so. I would like to try running anisotropic B refinement in Phenix, but am not sure how to tweak to get this to happen. I know about the parameter:measurement ratio concept, but I think it may still be better than isotropic. NB the dataset is also 42% twinned. 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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Radiation-sensitive dataset and molecular replacement
by mohamed noor 31 Jul '15

31 Jul '15

Dear all I have a crystal that diffracted to about 3.5 A for the first 5 degrees and rapidly decayed after that. With xia2, I can get a good dataset to 6 A (CC1/2, I/sigma etc.) using all the frames. I can also process the first good frames with obviously low completeness (20%). As I only want to check if molecular replacement can be done before investing time on experimental phasing (not expecting miracles here and not publishing this yet), should I bother running Phaser? The closest search model only covers about 20 % of the protein with 20 % identity. Thanks.

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Berkeley Server Downtime
by Paul Adams 30 Jul '15

30 Jul '15

Dear Colleagues, as part of final commissioning of our new building there will be a power outage to the Computational Crystallography Initiative server room. As a result several structural biology web services will be offline for a short while. These include: - 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/) The servers will be shutdown at 5pm Pacific time on Thursday 30th (i.e. tonight). Services should resume by the morning of Friday August 31st. During the downtime bug reports and emails requesting help should be queued and received by us once the servers are back online. We greatly appreciate your understanding, and hope that this doesn’t present too much of an inconvenience. 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 33, Room 347 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 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Re: [phenixbb] mr_rosetta pause & resume
by Juergen Koepke 30 Jul '15

30 Jul '15

Dear Tom, I found in the phenixbb exactly my case discribed as you wrote on July 22nd, 2013 on reply of Morten Grøftehauge: Hi Morten, Yes, you'll need to specify the start_point (otherwise it will start from the beginning considering the solutions you have in the .pkl file along with ones that it finds along the way). I don't know if rosetta3.5 makes a difference in mr_rosetta; I'd be happy to hear from anyone on this. All the best, Tom T but unfortunately after launching the command "phenix.mr_rosetta mr_rosetta_params.eff start_point=rosetta_rescore mr_rosetta_solutions=./rebuild_results.pkl" I get the following error message: Sorry: Unable to create temporary directory MR_ROSETTA_3 Error message is: The directory MR_ROSETTA_3 could not be created (it may already exist) but this looks not logical to me since I am in directory MR_ROSETTA_3 because I want to restart were the program stopped after the crash. Do I have to restart the program from within another directory or what ist the trick? I must admit I first started without the start_point=rosetta_rescore until I realized the program had started my job from the very beginning. Thus i killed the processes again and tried the above with the start_point included. Has my previous attempt already confused something? __________________________________ Dr. Juergen Koepke Project Leader ESFRI-Instruct Core Centre Max-Planck-Inst. of Biophysics Dept. Molecular Membrane Biol. Max-von-Laue Str. 3 D-60438 Frankfurt/Main Germany T: [49] 69 6303 1055 F: [49] 69 6303 1002 C: [49] 151 2263 6736 Email: juergen.koepke(a)biophys.mpg.de URL: https://registration.cc.biophys.mpg.de

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Re: [phenixbb] Extract coordinates from PDB file
by Zhijie Li 29 Jul '15

29 Jul '15

With a little modification it can be more specific ;) : grep -e '.\{12\} CA .\{61\}C' 1PRW.pdb But not so ideal for multi-model NMR structures: grep -e '.\{12\} CA .\{61\}C' 1cff.pdb Zhijie -----Original Message----- From: Pavel Afonine Sent: Wednesday, July 29, 2015 5:59 PM To: Tanner, John J. ; phenixbb(a)phenix-online.org ; Ashok Nayak Subject: Re: [phenixbb] Extract coordinates from PDB file John, that may include Calcium or similarly called atoms in ligands -;) But if you know there are none in your structure then your solution would do the job and much faster! Pavel On 7/29/15 14:53, Tanner, John J. wrote: > grep " CA " file.pdb > ca.pdb > > Sent from Jack's iPhone > >> On Jul 29, 2015, at 4:15 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: >> >> Hi, >> >>> I wish to extract xyz coordinates of Calpha atoms from the PDB file of >>> my interest. >>> Is there a program in Phenix or CCP4 for the same? >> some examples: >> >> - this will select all CA atoms: >> >> phenix.pdb_atom_selection model.pdb "name CA" >> >> - this will select CA atoms in chain A and chain B: >> >> phenix.pdb_atom_selection model.pdb "name CA and (chain A or chain B)" >> >> - this will select all Carbon atoms: >> >> phenix.pdb_atom_selection model.pdb "element C" >> >> - this will select all atoms with alternative conformation id A: >> >> phenix.pdb_atom_selection model.pdb "altloc A" >> >> etc etc etc - this can be very detailed and flexible. >> >> Pavel >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

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Extract coordinates from PDB file
by Ashok Nayak 29 Jul '15

29 Jul '15

Dear Phenix BB, I wish to extract xyz coordinates of Calpha atoms from the PDB file of my interest. Is there a program in Phenix or CCP4 for the same? Suggestions are highly appreciated. Thanks in advance Ashok Nayak Grad Student GN Ramachandran Structural Biology Lab., MSB Div CSIR-CDRI Lucknow India

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weird problem with autosol
by Almudena Ponce Salvatierra 28 Jul '15

28 Jul '15

Dear all, I give autosol a list of HA sites generated with SHARP, an mtz file and the sequence of my protein and I get the following: "Invalid MTZ column_types for the given miller_array." DO you know if this is a bug? Or something else? my mtz contains all the relevant columns, so I don't understand why I get such a message. 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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Covalent Linker
by Courtney Daczkowski 27 Jul '15

27 Jul '15

We are currently trying to build a model that has a nonstandard ligand that is covalently bonded to two peptide chains. We've placed the ligand and linked it using Coot, but phenix.refine keeps removing the links. We generated the restraints using Elbow and wrote the .edits file using phenix.link_edits, but phenix.refine is still removing the links. We also tried turning on automatic ligand linking in phenix.refine, but that didn't work either. Any advice? Thanks. Courtney

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