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phaser ep_sad zscore
by Bryan Lepore 09 Dec '10

09 Dec '10

dev-601 in phaser ep_sad mode, i tried ZSCORE SOLVED 0 to get more sites output, and i can see a peak of about Z=4 in the stdout, but no peaks are written to the .pdb am i applying ZSCORE wrong here? -Bryan

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reflection outliers detection in phenix.refine
by guanrj＠foxmail.com 08 Dec '10

08 Dec '10

Hi All I have a question regarding reflection outliers detection in phenix.refine: in my input reflection file, there are 24432 reflections, but only 22769 of them were used in refinement. I checked the log file and saw 1663 outliers. (below if from the log) basic_wilson_outliers = 14 extreme_wilson_outliers = 18 beamstop_shadow_outliers = 0 model_based_outliers = 1657 total = 1663 What is the "model_based_outliers"? What causes so many reflections rejected and not used in the refinement? Thanks Rongjin

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Multistart simulated annealing refinement
by Joseph Noel 08 Dec '10

08 Dec '10

Hi All, I'm sure this has already been addressed but is there a way through the PHENIX GUI to carry out multistart simulated annealing refinement either with different starting seeds (velocities) or temperatures automatically or does one have to start a fresh run each time? Thanks! Joe P.S. Similar procedure as described in the PNAS paper: "Multistart simulated annealing refinement of the crystal structure of the 70S ribosome" ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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phenix.fmodel or other utility: calculate HL's as well?
by Francis E Reyes 08 Dec '10

08 Dec '10

I love the phenix cmd line utilities, however is there one that'll calculate HLA/HLB/HLC/HLD given FModel/Phimodel? My expectation is that phenix.fmodel would do this with an option toggle or something. F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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No clash evaluation between symmetry mates in phenix.refine
by Keitaro Yamashita 08 Dec '10

08 Dec '10

Dear Phenix developers, I have a question about phenix.refine. I'm refining complex structure against X-ray diffraction data with packing disorder. (Some domains overlap with their symmetry mates (4-fold), so their occupancies are set to 0.25) So I want phenix.refine to ignore clashes between symmetry mates. Can phenix.refine exclude any interaction between symmetry mates from geometric term in target function: E = E(x-ray) + E(geometry)? Is there any option? Thank you very much in advance, K. Yamashita

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switch off anti-bump restrain
by Agnieszka 08 Dec '10

08 Dec '10

Hi, I have double conformation of my residue. There is a water molecule that interacts with conformation A. In the same time the water is very close to conformation B. During the refinement the water is pushed out. I try to switch off the site refinement of the water and some atoms of conformation b but it didn't work out for me. Do you know how can I switch off the anti-bump restrain of this two guys? Thank you Agnieszka Kiliszek

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ncs restraints
by Timothy Springer 08 Dec '10

08 Dec '10

Hi, I am using NCS restraints for 4 copies of a molecule at 3.05 Å. We are using the standard weights: coordinate_sigma = 0.05 b_factor_weight = 10 and the 4 molecules look identical. What are suggested values for looser restraints? One of my colleagues said that varying them did not make a difference- ncs was still very strict. Is there a way to make them less strict? Thanks, Timothy A. Springer, Ph.D.

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phaser version
by Bryan Lepore 08 Dec '10

08 Dec '10

using dev-596 from source, i see `phenix.phaser --version` is Phaser-2.2.4 (svn ) that's true for dev-601 (Intel binary) also. the phaser wiki says 2.3 is the latest, and to compile it from the phenix distribution. so... wondering how to get phaser 2.3 (before asking questions about ep_sad...) -Bryan

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anyone with a scalepack file with R3 or R32 using rhombohedral axes?
by Ralf W. Grosse-Kunstleve 08 Dec '10

08 Dec '10

I'm looking for a little help from the phenix user community. Does anyone have a scalepack output file with data in space group R3 or R32 using rhombohedral axes, i.e. unit cell parameters a=b=c, alpha=beta=gamma? What is the space group symbol in the file? I'm only interested to know this for files that are the direct output of scalepack. I'd like to verify that this part of the scalepack documentation is actually true: http://www.hkl-xray.com/hkl_web1/hkl/manual_online.pdf Page 139: 146 R3 R3 in hexagonal setting 446 H3 R3 in primitive setting 155 R32 R32 in hexagonal setting 455 H32 R32 in primitive setting If this is actually true, it is the exact opposite of what's used by the PDB. Thanks in advance for feedback. Ralf

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modelling of a novel protein
by intekhab alam 07 Dec '10

07 Dec '10

Hi I am trying to solve the structure of RNA polymerase in complex with its protein primer. The size of protein primer is 70 amino acids which i complexed with the polymerase and collected a data of the complex crysta at 2.3A. The space group is C2 and after Molecular replacemnet with full length polymerase in auto MR i got 3 subunits in ASU. The parameters of MR solution RFZ=71.5 TFZ=41.2 PAK=0 LLG=8812 suggests that the solution is correct. I used autobuild for model building which gave me the model of the polymerase as well as some extra density that i am considering as the other protein. After several round of refinemnt i have R and R free of 27and 32 respectively. My queries: 1. I want to know ,how can i improve my R as well as R free. 2. How can i model other protein as the density is weak and not complete, how can i improve the map of the other protein so that i can b ebale to trace the c-alpha backbone, i was able to model only 10 amino acids so far. Please guide. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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