February 2015 - phenixbb - phenix-online.org

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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

6 17

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

1 0

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 *******************************************

2 1

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

2 1

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

2 3

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

2 1

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

2 2

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 >

5 4

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/>

1 0

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

2 1