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Test
by Paul Adams 15 Feb '15

15 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 13 Feb '15

13 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 13 Feb '15

13 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 12 Feb '15

12 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 12 Feb '15

12 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 12 Feb '15

12 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 11 Feb '15

11 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 11 Feb '15

11 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 10 Feb '15

10 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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