- phenixbb - phenix-online.org

Ensemble refinement
by mohamed noor 04 Apr '15

04 Apr '15

Using the FEM map, I managed to remove more bad waters and add instead ions from the crystallization mix. I tried phenix.ensemble_refinement but the Rfactor increased by 2 % (originally 19/22 % from phenix.refine). Before it crashes at the validation point all the time, it prints out the validation summary with 0.53-3.48 % and 1.87-7.22 % Ramachandran outlier (from 0.3 %, supported by density) and a Molprobity score of 1.57-1.92 and 1.82-2.14 depending on pTLS used (original single model score was 2.08). The clashscore in both settings (pTLS=0.6 and 1) are 0. Do I still go by the Rfactor and decide to not use ensemble refinement at all? Thanks.

3 2

Structure with pseudo-NCS translation
by Mark A Saper 03 Apr '15

03 Apr '15

I know that Phaser takes account of NCS translation in the likelihood statistics ( Read, Adams, McCoy (2013) Intensity statistics in the presence of translational non crystallographic symmetry”). Has this also been incorporated into phenix.refine? I have a structure with pseudo NCS translations because of NCS rotational symmetry. One suggestion that I found in the archives, was to explicitly LS target refinement rather than ML. Any comments? Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

4 5

refinement
by Almudena Ponce Salvatierra 02 Apr '15

02 Apr '15

Dear all, I am using Phenix.refine after MR and I have a complete model and data to 2.8 Angstrom resolution. However, for some reason, Phenix does not place any water molecules. Is there a setting I could change in order to see whether this situation changes? What could the reason be? 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

2 1

twinning
by Shun Liu 01 Apr '15

01 Apr '15

Dear all, Recently I have got a data set that diffracts to 1.7 angstrom. Images look good. During data processing I did not find anything that looks strange. However, when I was doing Phaser-MR, I got a warning: “ Intensity moments suggest significant twinning (>5%). Tests based on possible twin laws will be more definitive.” What does this mean? A twinning data set? I still found a solution and refined the model step by step, using the data (20-1.7 angstrom). It seems that the final model and map are acceptable. But R-factors are 0.24/0.28, very high. Does the twin cause the high R-factors? Is there a solution to detwin? Or are the R-factors acceptable for a twinning data set? Any suggestions are appreciated and thanks in advance! Best, Shun

5 10

a question on henix refine
by Smith Liu 01 Apr '15

01 Apr '15

Dear All, For the Phenix refine, the default for the Scattering table in "other options" in the graphical interface is n_gaussian, in which situation to use electron is much better? And how much would be the benefit to use electron instead of n_gaussian? Smith

2 1

Maps
by mohamed noor 01 Apr '15

01 Apr '15

Dear developers What is the difference between MEM and FEM maps? I read the documentation and my understanding is both are supposed to create beautiful maps :) My problem is I have a structure at 1.9 A (a different protein than the one referred to in my previous question), the Rfactor is around 20/22 %, Rms bonds is 0.03 and Rms angles is 1.845. If the bonds/angles get lower, the Rfactor jumps up (same problem as the other structure). Looking in Coot, there are positive and negative density and missing density for the side chains of residues with high B factor. For some reason, phenix.refine keeps on adding water at strange places even at regions that I suspect to be just noise. For this reason, I want to see if the noise is really noise. A second reason is I have density that seem to be too big for a water molecule but waters were placed anyway, so I want to know if these are real positive density. The dataset was obtained from only 50 degrees, SG is P 61 2 2. Including more images brought up the Rmerge to 30-40% and Rfactor being stuck at 30 %. For some reason, I don't find the X-ray statistics from the phenix.model_vs_data logfile but in essence, I have: 28-1.9: 82 % 6 A - infinity: 95 % in the shells (2.25-2.14, 2.14-2.04, 2.04-1.97, 1.97-1.9) my completeness is around 85-62 % and CCwork is at least 70 % and CC1/2 of the dataset is 60 % at the highest resolution shell. Thanks.

2 1

continuously Rfree lower than Rwork
by Smith Liu 31 Mar '15

31 Mar '15

Dear All, If in a Phenix.refine proces, the Rfree continuously lower than Rwork, what does it mean? Smith

4 3

Twinning
by Shun Liu 31 Mar '15

31 Mar '15

Dear all, Recently I have got a data set that diffracts to 1.7 angstrom. Images look good. During data processing I did not find anything that looks strange. However, when I was doing Phaser-MR, I got a warning: “ Intensity moments suggest significant twinning (>5%). Tests based on possible twin laws will be more definitive.” What does this mean? A twin data set? I still found a solution and refined the model step by step, using the data (20-1.7 angstrom). It seems that the final model and map are acceptable. But R-factors are 0.24/0.28, a little high. Does the twin cause the high R-factors? Is there a solution to detwin? Or are the R-factors acceptable for a twin data set? Any suggestions are appreciated and thanks in advance! Best, Shun

1 0

First-Science Discussions for Life-Science Beamlines at NSLS-II: April 21-22, 2015
by Robert Sweet 27 Mar '15

27 Mar '15

We will hold a "First Science at the ABBIX Beamlines" meeting on Tuesday - Wednesday, April 21-22, 2015, pertaining to the National Institutes of Health (NIH)-sponsored "Advanced Beamlines for Biological Investigations with X-rays" (ABBIX) Project. These three state-of-the-art beamlines are now under construction at the National Synchrotron Light Source (NSLS)-II facility at Brookhaven National Laboratory (BNL). Two of the beamlines are for macromolecular crystallography (MX), and the third is for life sciences applications of x-ray scattering. Visit this web site for further information and registration materials: http://workshops.ps.bnl.gov/?w=ABBIXApr2015 Briefly, the MX beamline called FMX - Frontier MX - is optimized to address microbeam applications, and the other called AMX - Highly Automated MX - is optimized for highly automated throughput. The scattering beamline called LIX - High Brightness X-Ray Scattering for Life Sciences - will offer multiple modes of study. The MX beamlines view canted undulator sources, and the scattering beamline views a single undulator, providing world-leading brightness. Current plans are to conclude construction by the end of 2015 and start commissioning then. During the commissioning period, opportunities will arise to perform early experiments before the general user programs of the beamlines commence in 2016, and it is the upcoming meeting's purpose to explore and discuss scientific areas and opportunities on which early operation of the beamlines could capitalize. Note: Registration is required. There is no registration fee. Visit this site to register: http://workshops.ps.bnl.gov/?w=ABBIXApr2015 Those who registered for the original meeting planned for January must re-register for the new occurrence in April. Contributed presentations describing experiments that exploit the capabilities of the ABBIX beamlines will be selected from submitted abstracts. The meeting will consist of both plenary and parallel sessions. The plenary session will begin with presentations on science topics in research fields that the beamlines are designed to address, followed by facility presentations to update the community about the early scientific capabilities at the suite of ABBIX beamlines and, in addition, of the Life Science and Biomedical Technology Research Resource (LSBR), sponsored by the NIH and the Department of Energy Office of Biological and Environmental Research (DOE BER). Two parallel sessions on Tuesday afternoon will focus on MX and x-ray scattering, consisting mainly of presentations that will address specific opportunities in these areas. These will be followed by two more parallel sessions on Wednesday morning, also focusing on MX and x-ray scattering, which will include contributions. If you wish to give a contributed presentation during one of the parallel sessions, please submit an abstract here: http://workshops.ps.bnl.gov/abstracts/default.aspx?w=ABBIXApr2015 The parallel sessions are designed to provide forums to facilitate more detailed discussions about potential first experiments at specific beamlines and the formation of the experiment teams. Specifically, each parallel session group will be charged to accomplish these goals: 1. Identify key research projects and the associated first experiments that may be performed at the suite of ABBIX beamlines, emphasizing those projects that will take advantage of NSLS-II properties and ABBIX beamline capabilities. 2. Facilitate the formation of research teams to generate first experiment proposals for submission. 3. Identify key additional team members in such areas as theory and analysis, ancillary measurements, and specimen preparation, needed to achieve the research goals. Confirmed invited speakers: Karen Allen (Boston Univ), Martin Caffrey (Trinity College Dublin), Seth Darst (Rockefeller Univ), Richard Gillilan (Cornell Univ), Wayne Hendrickson (Columbia Univ), AndrHoelz (California Inst Tech), Huey Huang (Rice Univ), Shenping Liu (Pfizer), Lee Makowski (Northeastern Univ), David Ostrov (Univ of Florida), Rebecca Page (Brown Univ), Anna Marie Pyle (Yale Univ), Christian Riekel (ESRF), Thomas Schneider (EMBL-Hamburg), John Tainer (Scripps Research Inst). We would like two outcomes from this meeting: (a) a concise meeting report outlining how ABBIX beamlines will help to address outstanding problems in life sciences, and (b) a list of potential first experiments along with the corresponding research teams. For more information on the meeting, please contact Sonya Kiss, at skiss(a)bnl.gov. Note: Registration deadline is Tuesday, April 14, 2015. Organizers: Lonny Berman ABBIX Project Manager National Synchrotron Light Source II Brookhaven National Laboratory Sean McSweeney Structural Biology Program Manager Photon Sciences Division Deputy Director National Synchrotron Light Source II

1 0

can mr_rosetta include twin_law?
by Ni, Fengyun 27 Mar '15

27 Mar '15

Hi everyone, When I run phenix.mr_rosetta, I use the following file (twin.eff) to add the twin_law with the keyword: refinement_params=twin.eff. I checked the output that the phenix.refine stage could recognize this file. But the autobuild step can not read this file and give the error information as follows, refinement.twinning { twin_law = "h,-h-k,-l" } Unable to read the parameters file twin.eff. Is there anyway to overcome this issue? Thank you very much in advance! Fengyun

2 1