December 2014 - phenixbb - phenix-online.org

number of alternate conformations allowed
by Scott Horowitz 18 Dec '14

18 Dec '14

Hi all, Does anyone happen to know the upper limit on the number of alternate conformations that phenix.refine can handle at once for a residue? From playing around with it, it seems that phenix.refine recognizes both letters and numbers in that position, but not a pound sign, so that would suggest it could at least handle 36, so long as I don't crash my computer trying that many. Is this correct, from anyone's experience/knowledge? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

2 1

how to use phenix.angle command?
by 李翔 16 Dec '14

16 Dec '14

Hi, I am trying to measure the angle between two DNA duplex domains. I used phenix.angle command for calculation. However, I get a wrong answer. Can anyone talk a little bit more details on this command please? I used a single strand DNA from each duplex to calculate the angle which I thought it might be working since it is calculating the axis. Thanks for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

2 1

Reliable twinning fraction estimation
by Xiao Lei 11 Dec '14

11 Dec '14

Dear All, I have a x-ray dataset of a protein-DNA complex to 2.8 A resolution with space group P312 checked by phenix xtriage for twinning. The estimated twin fraction from the output of xtriage is: 0.115 (Britton analysis); 0.119 (H test) and 0.022 (maximum likelihood method). However, the L-test graph in xtriage shows my observed data almost perfectly overlay with theoretical perfect twin data. In addition, when I tried to use phenix to do refinement with twin law -h,-k,l, the log file shows my twin fraction estimation is 0.49, which is very high and much bigger than Britton analysis and H test estimation. As far as my understanding is that if a twin fraction is lower than 15%, I still have hope to solve the structure (molecular replacement in this case) with reasonable R value, but if the twin fraction is 0.49, which is almost a perfect twin, which makes detwin impossible and refinement will stall at high R values (in my case, R free start: 0.4199; R work start: 0.4121; and R free final: 0.4038 and R work final: 0.3640 after running phenix refinement with twin law -h, -k, l). My question: which twin fraction estimation is more reliable? is my data almost perfectly twined? I attached the graphs of L test, Britton analysis and twin estimation from phenix xtriage and part of log file from phenix refine here. Many thanks in advance. Xiao

3 6

Autobuild with "build semet residues"
by Todd Jason Green 11 Dec '14

11 Dec '14

Hello all- I have been trying to use autobuild with a semet dataset. I have checked the "build semet residues" option in the autobuild gui. At some point after the composite build, the error below is generated and the final model has been stripped of all semethionines. I am using phenix version 1.8.4-1496 on a macbook. I have now downloaded the new version. But can someone expand on my problem. My input sequence and model pdb contain Methionine but I expected the rebuild process to alter them. Should I change the one letter code for semet from m to something else. -Todd . . . . Final composite model # 1 : AutoBuild_run_11_/MULTIPLE_MODELS/model.pdb_1 Final composite mtz # 1 : AutoBuild_run_11_/MULTIPLE_MODELS/resolve_composite_map.mtz_1 AutoBuild_combine_iter AutoBuild Run 11 Wed Dec 10 14:51:18 2014 AutoBuild_combine AutoBuild Run 11 Wed Dec 10 14:51:18 2014 Done with combine finished AutoBuild Run 11 Wed Dec 10 14:51:18 2014 Finishing AutoBuild Run 11 Facts written to AutoBuild_run_11_/AutoBuild_Facts.dat Warnings: Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_: NOTE: The following residues (and similar residues) from AutoBuild_run_5_/overall_ortho_best_bchain_molrep1_refmac1_semettomet_ed.pdb are not PROTEIN or do not match the sequence and will not be part of the building process : MSE B33, MSE B45, MSE B59, MSE B63, MSE B68, MSE B194, MSE B201, MSE B210, MSE B216, MSE B256, MSE B266, MSE B308, MSE A33, MSE A45, MSE A59, MSE A63, MSE A68, MSE A194, MSE A201, MSE A210, MSE A216, MSE A256, MSE A266, MSE A308, MSE C33, MSE C45, MSE C59, MSE C63, MSE C68, MSE C194, MSE C201, MSE C210, MSE C216, MSE C256, MSE C266, MSE C308, MSE D33, MSE D45, MSE D59, MSE D63, MSE D68, MSE D194, MSE D201, MSE D210, MSE D216, MSE D256, MSE D266, MSE D308, Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_: Warning: some residues not rebuilt successfully on cycle 2: Chain 'A': 32, 44, 200, 217- 221, 280- 299, 314- 323, Chain 'C': 22- 32, 39- 44, 148- 152, 163- 167, 188- 193, 211- 215, 217- 221, 334- 336, Chain 'B': 32, 44, 118- 122, 193, 227- 231, 309- 318, Chain 'D': 12- 32, 34- 44, 46- 50, 143- 147, 158- 162, 188- 193, 334- 336 Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_: Warning: some residues not rebuilt successfully on cycle 3: Chain 'A': 32, 39- 44, 193, 217- 226, 280- 294, Chain 'C': 22- 32, 34- 44, 46- 55, 153- 162, 193, 200, 211- 215, 217- 221, 242- 246, 324- 336, Chain 'B': 32, 44, 118- 122, 193, 262- 265, 319- 323, Chain 'D': 17- 32, 34- 44, 46- 50, 143- 162, 188- 193, 200, 334- 336

2 1

Rigid body refinement at low resolution
by Jianghai Zhu 10 Dec '14

10 Dec '14

Hi all, I recently solved a complex structure at 8 Å. There are 3 molecules per asymmetric unit and each complex contains 8 domains. I was trying to do rigid body refinement in phenix.refine. However, all the rigid body refinement gave me worse Rfree, even at ultra-low resolution, and phenix.refine reversed the result to the original model. Anyway to make this rigid body refinement more stable? Is there a dampen factor in phenix.refine so that the program only moves a domain at a fraction of what it wants to, e.g. 1/2, 1/3… ? Thanks. Best, —Jianghai

3 2

Not Updating Waters
by Ryan Henry Gumpper 10 Dec '14

10 Dec '14

Hi all, I am having an issue during refinement when using Phenix Refine. Every time I try to "update waters" it does not place or update the waters. My structure is 2.72 A. Is the resolution not good enough for this feature? If anyone has ideas, or if I need to supply more information, I would be happy to oblige as I am fairly new to the field and still learning. Thank you in advance!

2 1

Ramachandran maps
by PC 10 Dec '14

10 Dec '14

Hi guys, Sorry for the repost in COOT/CCP4/PHENIX. It is possible on of the users in one of these communities might know the answer I was wondering if there is a small script I can use to generate the outline of the allowed regions of Ramachandran map on to which I can superimpose my coordinates phi and psi? Something like what appears in COOT->Validate->Ramachandran Plot. How does one generate such images for publications? Thank you, Patrick ____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth

2 1

Challenging Mol.Rep. Problem
by Mo Wong 10 Dec '14

10 Dec '14

Hi all, I’m stuck on a rather complex molecular replacement problem. The crystals are of an antigen-Fab complex totaling ~67 kDa (waiting to confirm using PAGE gel). They diffract to ~3.5A at the synchrotron and process in C2 with dimensions 220x130x230 and beta at 103 so it looks like there are round 9to12-ish copies in the ASU. The overall Rmerge is high at ~25% with I/sig cutoff ~2 and redundancy of 5; however, at 4.5A this drops to ~15%. Furthermore, processing in P1 gives similar Rmerge values too. Self-Patterson doesn’t suggest translational symmetry, but the self-rotation function (SRF) suggests high NCS (see below/attached). I’m hoping the SRF might be helpful in trying to confirm/dismiss C2 is the likely space group, and perhaps suggest a logical assembly with the ASU (I see strong 2-fold and 3-fold NCS operators suggesting to me dimeric trimers or vice versa - however, I’ve never had to really analyze SRFs in the absence of a mol. rep. solution so my interpretation could be wrong). Anyway, any help to bringing a molecular replacement solution closer to reality would be appreciated. Thanks! [image: Inline image 1]

1 0

Re: [phenixbb] [ccp4bb] MR_ROSETTA
by Terwilliger, Thomas Charles 10 Dec '14

10 Dec '14

Hi Bashir, It is probably something very small to fix...can you send me the result of doing this: echo $PHENIX_ROSETTA_PATH echo $ROSETTA3_DB/ ls $PHENIX_ROSETTA_PATH//main/source/bin/mr_protocol* On my machine I get: [terwills-MacBook-Air:~] terwill% echo $PHENIX_ROSETTA_PATH /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle [terwills-MacBook-Air:~] terwill% echo $ROSETTA3_DB/ /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle/main/database/ [terwills-MacBook-Air:~] terwill% ls $PHENIX_ROSETTA_PATH//main/source/bin/mr_protocol* /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle//main/source/bin/mr_protocols.macosclangrelease /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle//main/source/bin/mr_protocols.python.macosclangrelease All the best, Tom T Could some body explain why I am getting the error message when running MR-Rosetta. Message is " Sorry cannot locate a binary starting with mr_protocol.default' in the directory /home/phenix/rosetta_2014.34.57213_bundle/main/source/bin I just download it and locate it in the preferences, wizard and then path to Rosetta. Thanks Bashir -- Muhammad Bashir Khan ************************************************** Department of Biochemistry University of Alberta, Canada Canada

1 0

how to use a dimer as a search model by MRage
by fukamitka＠chugai-pharm.co.jp 09 Dec '14

09 Dec '14

Dear all, I have a dataset, there are 4 or 5 copies of two different hetero dimers (i.e. 4 different chains) in au, and I'd like to use the dimers as search models. I ran phenix.MRage with a phil file below, and it searched each chains separately, as expected. In this case, I want to search dimerA (containing chain1 and 2) and dimerB (chain3 and 4) as 2 search templates, but I couldn't find how to specify a dimer as a component. Using dimer.pdb and dimer.seq caused an error (sequence file can't contain multiple sequence). How do I write an input file? Regards, ------------------------- composition { count = 5 component { sequence = dimerA-chain1.seq stoichiometry = 1 template { pdb = dimerA-chain1.pdb } } component { sequence = dimerA-chain2.seq stoichiometry = 1 template { pdb = dimerA-chain2.pdb } } component { sequence = dimerB-chain3.seq stoichiometry = 1 template { pdb = dimerB-chain3.pdb } } component { sequence = dimerB-chain4.seq stoichiometry = 1 template { pdb = dimerB-chain4.pdb } } } ------------------------- ----- Takaaki Fukami (mailto:[email protected]) Discovery Research Dept. (Biostructure Gr.) Chugai Pharmaceutical Co.,Ltd.

2 3