July 2015 - phenixbb - phenix-online.org

weird problem with autosol
by Almudena Ponce Salvatierra 28 Jul '15

28 Jul '15

Dear all, I give autosol a list of HA sites generated with SHARP, an mtz file and the sequence of my protein and I get the following: "Invalid MTZ column_types for the given miller_array." DO you know if this is a bug? Or something else? my mtz contains all the relevant columns, so I don't understand why I get such a message. 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

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Covalent Linker
by Courtney Daczkowski 27 Jul '15

27 Jul '15

We are currently trying to build a model that has a nonstandard ligand that is covalently bonded to two peptide chains. We've placed the ligand and linked it using Coot, but phenix.refine keeps removing the links. We generated the restraints using Elbow and wrote the .edits file using phenix.link_edits, but phenix.refine is still removing the links. We also tried turning on automatic ligand linking in phenix.refine, but that didn't work either. Any advice? Thanks. Courtney

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Parameters of a metal ion do not change during refinement
by Ezequiel Noguera 27 Jul '15

27 Jul '15

I added a Cu(II) ion in a blob of density using Coot (this metal is used in crystallization solution). When I refined using phenix, I noted that occupancy does not change from the arbitrary value that I set in Coot, and negative density remains when refinement is complete. When I manually adjust occupancy to 0.3, phenix changes it to 0.29, and no negative density is seen, however B-factor does not move from my arbitrary setting of 30 in Coot. I worry if something is wrong in my refinement strategy. I thank any suggestion.Some additional information: my mtz is merged F's, resolution is 1.3 A, refinement strategy includes XYZ coordinates, Occupancies and Individual B-factors. Ezequiel

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on refine related to b-factor
by Smith Liu 25 Jul '15

25 Jul '15

Suppose a 500-aa protein crystal structure has a flexible loop of 30 aas, and the loop fragment has a relatively high b-factor (above 100) in comparison with the whole protein b-factor. Is any refine strategy we can refine so that the b-factor of that loop fragment will be decreased? Smith

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Phenix Autobuild error
by Xiao Lei 25 Jul '15

25 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

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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

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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

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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

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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

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Short contact with symmetry mate
by Ashok Nayak 23 Jul '15

23 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

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