- phenixbb - phenix-online.org

Phenix Autobuild error
by Xiao Lei 24 Jul '15

24 Jul '15

Hi All, I am using Phenix autobuild (version 1.10pre on CentOS) and I failed with an error message (I put it below). My input experimental data (in MTZ format) is 2.5A, with space group C2, and 1 molecule per ASU (No NCS copies), the molecule contains two protein chains and one double-strand DNA (heterodimer protein bound to dsDNA). It seems to me the error is because in my model PDB there are different atoms in DNA with the same name. How can I fix this problem? Error message from phenix.refine: number of groups of duplicate atom labels: 4 total number of affected atoms: 8 group "HETATM 4930 O3' DT C 716 .*. O " "HETATM 5471 O3' DT C 716 .*. O " group "HETATM 4937 C7 DT C 716 .*. C " "HETATM 5472 C7 DT C 716 .*. C " group "HETATM 4950 O3' DG C 717 .*. O " "HETATM 5473 O3' DG C 717 .*. O " group "HETATM 4964 O6 DG C 717 .*. O " "HETATM 5474 O6 DG C 717 .*. O " Refinement failed... Thanks ahead. Xiao

2 1

High B-factors and High Clash Score
by Edwin Lazo 24 Jul '15

24 Jul '15

Hi all, I am refining a structure that diffracted to 3.5 Angstroms and contains 6 monomers in the ASU. It is noteworthy to mention, in certain monomers, half their residues are missing (in other words no density). Initial b-factors after molrep were 118.585, R=0.32, and Rfree=0.40. Initial refinement was done with refmac and: mean b-value=117.344 R=0.31 Rfree=0.40 Refinement with Phenix (phenix-installer-dev-2054-intel-linux-2.6-x86_64-centos5) was performed and the Ramachandran plot was bad: OUTLIERS : 6.52 % ALLOWED : 13.67 % FAVORED : 79.82 % ROTAMER OUTLIERS : 7.18 % CBETA DEVIATIONS : 8 And final R=0.38 and Rfree=0.41. I then improved Ramachandran plot in coot and follow Pavel's suggestion: / - add H atoms: />>/ />>/ phenix.reduce model.pdb > model_H.pdb />>/ />>/ - then run a quick geometry regularization:*(**T**his part I**did in coot. phenix.**pdb**tools model_H.pdb --geom and phenix.pdbt**ools model_H.pdb --geometry**-**restraints do not work)* />>/ />>/ phenix.pdbtools model_H.pdb --geom />>/ />>/ - then strip off H: />>/ />>/ phenix.reduce -trim model_H_regularized.pdb > start.pdb />>/ />>/ - then run refinement using NCS and Ramachandran plot restraints: />>/ />>/ phenix.refine start.pdb def_data.mtz main.ncs=true --overwrite />>/ output.prefix=def2 main.number_of_mac=5 ramachandran_restraints=true />>/ rama_potential=emsley strategy=individual_sites+**individual_adp />>/ />>/ - then take outcome of previous refinement and run the same refinement />>/ plus weights optimization: />>/ />>/ phenix.refine def2_001.pdb def_data.mtz main.ncs=true --overwrite />>/ output.prefix=def3 main.number_of_mac=5 ramachandran_restraints=true />>/ rama_potential=emsley strategy=individual_sites+**individual_adp />>/ optimize_xyz=true nproc=6 /My current stats are as follows: Final R=0.35 Final Rfree=0.38 ALL-ATOM CLASHSCORE : 173.74 RAMACHANDRAN PLOT: OUTLIERS : 2.27 % ALLOWED : 4.61 % FAVORED : 93.13 % ROTAMER OUTLIERS : 36.26 % CBETA DEVIATIONS : 6 Wilson B-Value: 108.4 Mean B-value: 108.997 I am unsure how to proceed from here. I am planning on removing some side chains which have no density and then refining with Rama. restraints. I can also send my mtz and pdb if that would help. The stats when I processed the data are as follows from xia2 -3d (xds, xscale): High resolution limit 3.50 15.65 3.50 Low resolution limit 109.96 109.96 3.59 Completeness 94.1 90.5 91.5 Multiplicity 4.8 5.1 3.2 I/sigma 11.3 26.5 2.4 Rmerge 0.118 0.068 0.458 Rmeas(I) 0.144 0.080 0.605 Rmeas(I+/-) 0.144 0.083 0.584 Rpim(I) 0.062 0.036 0.311 Rpim(I+/-) 0.081 0.047 0.358 CC half 0.992 0.994 0.791 Wilson B factor 90.052 Anomalous completeness 86.9 93.6 71.3 Anomalous multiplicity 2.4 3.0 1.8 Anomalous correlation -0.262 -0.440 -0.052 Anomalous slope 1.005 0.000 0.000 Total observations 169836 2234 7765 Total unique 35071 442 2464 Assuming spacegroup: P 21 21 21 Unit cell: 73.010 180.780 219.910 90.000 90.000 90.000 Any help would greatly be appreciated, -- Edwin Lazo Scientific Associate Life Science and Biomedical Technology Research Resource National Synchrotron Light Source II Building 745 Upton, NY 11973 Office:(631)344-7247 Fax:(631)344-5059

2 1

Posting to List
by Courtney Daczkowski 24 Jul '15

24 Jul '15

I would like to be able to post questions to all users. Thank you for your time, Courtney -- Courtney Marie Daczkowski ------------------------------------------------- PhD in Pharmacutical and Biomedical Science University of Georgia 2019 ------------------------------------------------- Masters in Biology Georgia Southern University 2014 ------------------------------------------------- Bachelors of Science James Madison University 2011

2 1

Phenix GUI big reporting
by Nigel Moriarty 23 Jul '15

23 Jul '15

Folks One of the features of the Phenix GUI is the bug reporting which allows a user to send a program traceback. This allows the developers to zero in on the line that causes the problem but it is much easier if we have the inputs. This is why we ask that you include you email se we can work with you to resolve the problem ASAP. One of the weaknesses of the current system is that it relies on the user typing their email address correctly. If it is incorrect, we are sending replies that bounce. This happens occasionally and it's almost impossible to track the user down. We can also only assume, given that this misstyped user is sending in more reports, that he is getting frustrated. To that end, I'm naming names. If you typed in jwaning(a)umich.edu please contact us or fix the email in your preferences. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

1 0

Announcing the 2015 EMDataBank Map Challenge
by Cathy Lawson 23 Jul '15

23 Jul '15

Dear PhenixBB List Members, EMDataBank/Unified Data Resource for 3DEM is pleased to announce the 2015 Map Challenge. All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors. Seven benchmark raw image datasets have been selected for the challenge. Six are selected from recently described single 3D electron microscopy single particle structure determinations with image data collected as multi-frame movies; one is based on simulated (in silico) images. Challengers are sought to create single particle reconstructions from the targets, and then to upload their results with associated details. Assessors are sought to participate in evaluating submitted reconstructions. Registration is now open for all interested participants. Challengers may submit maps between August and December. Before submissions open, all are encouraged to provide feedback on submission requirements. An open assessment period will commence in early 2016. To learn more about this challenge and to register, please visit http://challenges.emdatabank.org and click on "MAP CHALLENGE" in the menu bar. The map challenge is the first of two community-wide challenges being sponsored by EMDataBank this year to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model. The second challenge, focused on creating coordinate models from 3DEM maps, will be announced later this year. Sincerely, Cathy Lawson on behalf of the EMDataBank Team and the Map Challenge Committee emdatabank.org www.facebook.com/emdatabank3dem

1 0

Short contact with symmetry mate
by Ashok Nayak 22 Jul '15

22 Jul '15

Dear Phenix BB, I am refining a helical bundle structure where I have been obtaining an invariant short contact (close to 2A) at a Glu residue with Lys of symmetry related molecule of one helix of the bundle. I had been using Rigid body, TLS, occupancy and Indv ADP for the refinement (which gave the best Rfree values). If I include coordinate refinement the short contact seems to be gone rather with higher Rfree values. I ll appreciate some suggestions regarding this. Thank you in advance. Ashok Nayak CSIR-CDRI Lucknow, India

2 1

NIH Request for Information about Technology Development
by Paul Adams 22 Jul '15

22 Jul '15

Dear Colleagues, my apologies for the slightly off-topic and US-centric posting, but I felt this was of sufficient interest to the structural biology community at large. The NIH, specifically the National Institute of General Medical Sciences, is in the process of considering how best to support the development of biomedical technologies, and access to those technologies. They have issued a request for information: http://grants.nih.gov/grants/guide/notice-files/NOT-GM-15-118.html This covers a very broad range of biomedical activities, including the development of new hardware and software for techniques such as NMR, crystallography, SAXS, and cryo-EM. It also includes the provision of technologies through facilities such as synchrotrons and other national research centers. For those of us in the US this provides an excellent, and rare, opportunity for researchers to voice their thoughts about how important technology development and national facilities are to the success of structural biology research. Please note that the deadline for response is August 7th. Cheers, Paul -- 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 33, Room 347 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 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

1 0

histidine flip in refinement
by Joel Tyndall 22 Jul '15

22 Jul '15

Hi all, We are trying to optimise a histidine interaction where NE2 would ideally make a hydrogen bond with an adjacent tyrosine hydroxyl. The starting point contains the hydrogen bond. However upon refinement the ring flips (chi2 x 180 degrees) to place the CE1 adjacent to the tyrosine hydroxyl. Is it possible to stop this as I see no reason why phenix.refine would want to do this Regards Joel _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

5 8

Newest phenix version for Unix cluster
by Xiao Lei 20 Jul '15

20 Jul '15

Hi All, I'd like to download the newest phenix version ( 1.10pre-2104 July13th2015 nightly build) and install it on HPC cluster (Unix system). Is CentOS 5 ok for my purpose? It seems for a 64bit linux this is the only download option: 64-bit Linux (Intel/AMD) Kernel 2.6 (64-bit; CentOS 5) [ download command-line installer ] Thanks ahead. Xiao

1 0

Re: [phenixbb] pdb LINK record lost after phenix refine in GUI
by Pavel Afonine 16 Jul '15

16 Jul '15

Hi Lu, could it be that you define a conflicting restraint? On one hand you want that O-C bond to be 1.44A (that's what I see on your picture), on the other hand you want that H to be reasonable distance apart from O (and not 1.14A). I would guess if you want to define that bond you nee to delete H first. Could this explain what you observe? Pavel On 7/16/15 18:38, luzuok wrote: > Dear Pavel, > Thank you for your explanation. > After adding the bond restrain and refinement, the position of the > hydrogen from the bonded atom of the ligand seems not reasonable. This > hydrogen is too close to the other bonded atom. I can even see this H > atom links to two atom. > It seems that the riding H of C23 cannot see the OG neighbouring > to it. > > Best wishes! > Lu > > > -- > 卢作焜 > 南开大学新生物站A202 > > Lu Zuokun, Ph.D. Candidate > College of Life Science, Nankai University > > At 2015-07-16 23:07:49, "Pavel Afonine" <pafonine(a)lbl.gov > <mailto:[email protected]>> wrote: > > Hi Lu, > > seeing the link in graphics and actually having bond defined in > refinement are two different things. Refinement uses standard > restraints and those you define on top of that. Visualization > tools use standard bonding patterns to show you the bonds (and > sometimes also use distance based connectivity, such as Pymol). > Visualization tools are unlikely to guess anything on top of that. > > So if you want to have specific bond in refinement, then tell > refinement program to add it (and checking .geo file is not a bad > idea to verify that it was actually added). Seeing that bond on > graphics is a different story and it is outside the scope of > Phenix refinement. Check documentation of visualization program > you use to learn what's required to see what you want to see. > > Pavel > > On 7/16/15 00:54, luzuok wrote: >> >> Dear Pavel and Nigel, >> >> I can see: >> >> bond pdb=" OG SER A 265 " >> pdb=" C23 AIX A 700 " >> ideal model delta sigma weight residual >> 1.330 1.339 -0.009 2.00e-01 2.50e+01 2.16e-03 >> >> I think this bond is what I want. >> >> If I want to _see_ this bond in graphical tool, like coot or >> pymol, Do I have to add a link record in PDB? >> >> You are right Nigel, I made a mistake of python and Phenix version. >> >> Best withes! >> Lu >> >> -- >> >> Lu Zuokun, Ph.D. Candidate >> College of Life Science, Nankai University >> >> 在 2015-07-16 14:21:24，"Pavel Afonine" <pafonine(a)lbl.gov> 写道： >> >> All connectivity information is in .geo file: check it to see >> if the bind in question is present there. >> phenix.refine does not read/write LINK records given that all >> info is in .geo file, and input (custom) linking is specified >> via custom bonds using atom selection syntax (or clicking in >> the GUI). >> >> Pavel >> >> On 7/15/15 18:04, luzuok wrote: >>> Dear all, >>> Although Custom geometry restrains was added (see log). >>> After phenix refine, the link record was lost and there seem >>> no bond between this two atoms (1.44 angstrom). >>> Do you think this is a real bond? How to maintain this record? >>> Any comment is appreciated! >>> Best regards! >>> >>> Data resolution: 2.4 >>> Phenix version:v2.7 >>> >>> phenix refine log: >>> ======================== Summary of geometry restraints >>> ======================= >>> >>> Number of disulfides: simple=1, symmetry=0 >>> Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS >>> A 484 " distance=2.04 >>> Custom bonds: >>> bond: >>> atom 1: "ATOM 1205 OG SER A 265 .*. O " >>> atom 2: "HETATM 3413 C23 AIX A 700 .*. C " >>> symmetry operation: x,y,z >>> distance_model: 1.339 >>> distance_ideal: 1.330 >>> ideal - model: -0.009 >>> slack: 0.000 >>> delta_slack: -0.009 >>> sigma: 0.2000 >>> Total number of custom bonds: 1 >>> Time building geometry restraints manager: 0.20 seconds >>> >>> pdb file LINK record: >>> LINK OG SER A 265 C23 AIX A 700 >>> 1555 1555 >>> >>> >>> -- >>> >>> Lu Zuokun, Ph.D. Candidate >>> College of Life Science, Nankai University >>> >>> >>> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> Unsubscribe:[email protected] >> >> >> > > >

2 2