January 2017 - phenixbb - phenix-online.org

on use of pdbtools
by Smith Liu 20 Jan '17

20 Jan '17

Dear All, Can you show me how to use the phenix pdbtools to get the mate pdb of the original input pdb?Take the phenix pdbtools graphical interface for example, I think after I load the original pdb, I should click "options" and then click "Coordinates". Suppose my original PDB was X, Y, Z, and I want to get the mate PDB -X +Y, -X ,1/3 +Z, then how should I input the "Switch rotamers", "Translate", and "Rotate" for this specific example? Does it has anything to do with "Euler angle convention"? I am looking forward to getting a reply from you. Smith

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polder vs fem vs composite omit map vs maximum entropy
by Murpholino Peligro 20 Jan '17

20 Jan '17

So I got a MR solution and maybe a dozen residues are not clearly defined (most of them in the surface) I used to compute the feature enhanced map but now I can see there are a lot of options in phenix->maps. Which one is better for me? (~130 residues, 1.5 A resolution, ~ 90% complete) Probably I should try them all, and compare them visually in coot with appropiate sigmas (taken from maps-> map comparison) (is that a good workflow? what you guys do?) ...but some of the maps take a lot of time to compute. So any help will be appreciated. Thanks

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AutoSol invalid MTZ column_types error
by Stan Yoo 19 Jan '17

19 Jan '17

Hello, I am getting an error message "Invalid MTZ column_types for the given miller_array." while I try to do AutoSol. The last line in the log is "Adding array ['N(+)', 'N(-)'] to output file with type II". Do you have any suggestion how to fix this error? Thanks

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phaser.labin not respected
by Murpholino Peligro 19 Jan '17

19 Jan '17

When I do in the terminal: phenix.phaser phaser.hklin="out.mtz" phaser.labin="F(+),SIGF(+),F(-),SIGF(-),merged" phaser.model="prot.pdb" phaser.mol_weight=14400 phaser.model_rmsd=0.3 my log file says it is using F and SIGF: LABIN F = F SIGF = SIGF Why it does not respect the labels provided? or..Am I doing something wrong. PS MR is successful Thanks

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help with Histidine flip in phenix refinement
by Vikram Dalal 19 Jan '17

19 Jan '17

Hi all, I have 4 Mn (2 Mn in each chain) in my protein structure. One Mn has 1 cordination with water, 1 cordination with His and 4 cordination with Asp. I model build the His in coot. Even this His is in bond range with Mn. But, when i refine this model in phenix. This His again flip other side (N terminal which has to cordinate with Mn goes to other direction). I am facing this problem only with His of A chain only while N of His of B chain are towards Mn only. Is there any option in pehnix refinment where we can exclude a specific residue or atom in refinment??

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Phenix.refine Restraints: replicating refmac external restaints
by Elliot Nelson 19 Jan '17

19 Jan '17

Hi All, Looking to generate restraints for phenix.refine that are similiar/equivalent to external restraints in REFMAC. From over viewing the documentation i feel the correct way to do this is to generate bond restraints, i.e: Equivalent of: exte dist first chain A resi 38 atom C alte A second chain A resi 38 atom C alte B value 0.0 sigma 0.02 type 1 would be : refinment.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain A and resid 38 and altloc A and name C atom_selection_2 = chain A and resid 38 and altloc B and name C symmetry_operation = None distance_ideal = 0.0 sigma = 0.02 slack = None } } If this is incorrect: Am i missing another way to create external restraint functionality in phenix, or am I making a more fundamental misunderstanding of how restraints are handled in both programs? Thanks in advance Elliot Nelson

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QuantumBio Release: XModeScore & DivCon Discovery Suite v7.1
by Lance Westerhoff 16 Jan '17

16 Jan '17

Hello All- I trust everyone had a nice holiday break and a Happy New Year! Today, we are excited to kick the new year off with a new release of our QM/MM refinement and analysis plugin for the Phenix platform. The full announcement, along with links to the details and licensing information, is available at this URL: http://www.quantumbioinc.com/news/show/DDS-012017 Thanks to our many users - academic, industrial, and government - who have provided feedback and support for this effort. This plugin, available within the DivCon Discovery Suite version 7.1, has a number of significant improvements applicable to users of Phenix including: * QM/MM X-ray Refinement Standard: Version 7.1 represents a complete overhaul of our MM and QM/MM implementation for improved stability, performance, and usability. Our fully automated QM/MM implementation has now come out of "beta" status and it is ready for production use. The implementation also supports truncated residues, multiple regions, and integrated ligand atom typing. * Application: Fragment Based Drug Design: Phenix/DivCon coupled with the novel, our patent pending XModeScore tool has been applied to several key areas including protomer/tautomer determination, binding mode selection, crystal water positioning, and now even fragment-based screening. We have provided a tutorial of MOE-based fragment docking coupled with XModeScore-based selection. * New Structure/Chemistry Analyses: The question we often hear from new users is how one can evaluate the performance of QM and QM/MM X-ray refinement vs. more conventional methods. We have now packaged several before/after analyses within refinement including Clash Scores (using phenix.molprobity); Strain, Interaction Energies, and ZDD (using DivCon); and GBVI/WSA dG binding score prediction (using MOE - as available). * New Feature [beta] - Protonation: Fast, integrated protonation and hydrogen bond network optimization is a perpetual problem in the field (especially in X-ray crystallography). This method uses a combination of dead end elimination and graph theory along with crystallographic symmetry and density - as available - to quickly and accurately determine the correct protonation states of bound ligands, active sites, waters, and protein/DNA/RNA. If you are interested in using or evaluating our linear scaling, quantum mechanics software in your drug discovery efforts or if you would like to schedule an on-line or on-site meeting to discuss the technology, please email sales(a)quantumbioinc.com and let us know. And as with last year, we are waiving the license free for non-profit, academic users as per academic license agreement. Our academic, commercial, consulting, and evaluation licenses are available on-line (most for electronic signature): http://www.quantumbioinc.com/products/software_licensing Have a great 2017! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909 This message and any attachments are solely for the intended recipient and should be considered confidential. If you are not the intended recipient, please immediately and permanently delete.

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Berkeley Server Downtime (1/13 - 1/14)
by Billy Poon 15 Jan '17

15 Jan '17

Dear all, On Friday, January 13, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available the next day (1/14) by 6:00 pm Pacific at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Calculation of bond lengths, angles and torsion angle for large number of proteins
by Ashraya Ravikumar 11 Jan '17

11 Jan '17

Hi All, I would like to calculate all the bond lengths, bond angles and main chain torsion angles for a large set of proteins, in PDB format. Could you please let me know which module/command in phenix is suitable for this task? Regards, Ashraya

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Re: [phenixbb] Modified DNA residue
by Pavel Afonine 11 Jan '17

11 Jan '17

Hi Melissa, we need to have a closer look to understand what's happening... Could you please send us these PDB file: - original (before modifications); - file after modifications; - file after refinement; - cif file. Pavel On 1/11/17 14:15, Melissa Ford wrote: > I'm having working on modeling a sulfur on the phosphate backbone of > DNA in replace of one of the oxygens and have encountered some > restraint problems. I've successfully managed to replace the oxygen > with a sulfur in the proper geometry in a pdb, generate a cif file for > the modified residue (adenosine 5'-phosphorothioate), and run an > initial refinement. Upon that refinement, a few errors occur. First, > since the phosphate bound to the sulfur is the first atom of the > modified residue the angle between the O3' (of the neighboring > residue) - P- S is not recognized and forced into an unfavorable > geometry. When trying to add that additional angle to the cif file, I > get an error. Aditionally, the change causes Phenix to not recognize > the chirality of the C3' that the phosphate is bonded to and forces > the ribose into a planar conformation. I am sure there is something I > am missing that allows phenix to recognize this new residue as a > modified nucleotide so that it knows these restraints. Any insight on > this would be great. Thank you!

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