- phenixbb - phenix-online.org

Number of reflections
by Ana Ramos 29 Apr '15

29 Apr '15

Dear all, I am finishing with the refinement of my structure and I noticed that the number of observed reflections used for refinement 36720 is less than 80 percent of observed reflections for data collection (172551). I am aware that the data collection statistics should be calculated in the same resolution range of refinement. Do you know the reason of this difference? I just followed the instructions from HKL where I indexed and scaled and then used Phenix for MR and refinement. Ana

3 2

on phenix.real_space_refine
by Smith Liu 29 Apr '15

29 Apr '15

Dear All, If with phenix.real_space_refine, I got a model (with PDB), in which there is a fragment containing several residues (not in continuation in the fragment), with side chains not fitting to the corresponding side chain density (or out of the density, but close to the density), which function(s) of phenix.real_space_refine (for example,minimization_global or local_grid_search?) can improve the fitting of the sidechains to the density? I am looking forward to getting your reply. Smith

2 1

Autobuild on parallel
by Kaushik Hatti 29 Apr '15

29 Apr '15

Hi, What is the best way to run Autobuild if I need to run it on hundreds of datasets (through command-line)? I have a single machine with 24 cores and access to a cluster with 128 cores (on parallel; accessible only through PBS script). Each Autobuild job with nproc=4 on a single core machine takes ~12 hours to run (nproc > 4 wouldn't make any difference in the speed of computation?!). However, I read that I could set nproc=10 (or more) and run on parallel ( https://www.phenix-online.org/documentation/reference/autobuild.html#parall…). When I tried the same through PBS script, I got the following error, XXXXXXXXXXXXXX Running up to 1 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running with 1 processors using qsub background=False nproc=20 background=False in ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1.log Traceback (most recent call last): File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 2364, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 4647, in AutoBuild_rebuild_cycle_run always_reuse_model=always_reuse_model) File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 7452, in AutoBuild_build_refine mtz_file=mtz_file,mtz_ref_file=mtz_ref_file) File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 7696, in run_standard_build_in_parallel r.run(out=sys.stdout) File "~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line 294, in run self.start_run(run_file,last=is_last) File "~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line 604, in start_run cmd+" "+self.add_double_quote(run_file,escape_space=False)).raise_if_errors() File "~opt/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 37, in raise_if_errors raise Error(msg) RuntimeError: child process stderr output: command: 'qsub background=False nproc=20 "~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1"' /bin/sh: qsub: command not found XXXXXXXXXXXXXX Please let me know if I can share eff and log files of the run. Please advice, Kaushik -- People living deeply have no fear of death - Anais Nin Caution: I am still the dumbest person I have ever known :-)

3 3

FEM map calculation without model?
by Oliver Clarke 29 Apr '15

29 Apr '15

Hi all, Is there any way to apply the local map sharpening and histogram equalization procedures described as part of the FEM map generation procedure (described in “FEM: feature-enhanced map”, Afonine et al,mActa D71 2015) to an MTZ containing amplitudes and phases only, without a model (e.g. as generated by phenix.map_to_structure_factors)? I would like to see if these different approaches to map modification are useful for improving maps derived from cryoEM. I guess there is no way to do the random map perturbation part of the FEM procedure without a model, but the sharpening and histogram equalization seem like they might be applicable? Best, Oliver.

2 1

Scientist position -- Protein Crystallization at AbbVie, North Chicago
by WEi WEi 29 Apr '15

29 Apr '15

*Scientist II, Structural Biology - Crystallization-1500000257* AbbVie (NYSE:ABBV) is a global, research-based biopharmaceutical company formed in 2013 following separation from Abbott Laboratories. The company's mission is to use its expertise, dedicated people and unique approach to innovation to develop and market advanced therapies that address some of the world's most complex and serious diseases. AbbVie employs approximately 26,000 people worldwide and markets medicines in more than 170 countries. The Structural Biology organization has an exciting opportunity for a Scientist I or Scientist II (depending on experience) to join the Crystallization group to support AbbVie's new collaboration with Calico. The Scientist will conduct biological macromolecule crystallization experiments in support of structure based drug design. The selected candidate must be knowledgeable in protein handling and characterization techniques and possess excellent communication skills. The Scientist will be expected to consistently work on multiple projects in parallel and be able to adjust to rapidly changing priorities. In addition, this individual will be highly self-motivated, able to work independently in their area of expertise and work collaboratively with cross-functional teams. For detail information, please visit the link below and apply online using the Job ID: *1500000257. * https://abbvie.taleo.net/careersection/2/jobsearch.ftl?lang=en Thanks, Wei

1 0

Global real-space refinement
by oleg＠quantumbioinc.com 28 Apr '15

28 Apr '15

I have a question. What does trigger Global real-space refinement ? I never seen it before except one structure I am currently working on. Also I do not see any options that switch on/off "Global real-space refinement " Please advise Oleg

2 1

Automatic linking of glycans doesn't work when hydrogens are added by ReadySet
by Tristan Croll 28 Apr '15

28 Apr '15

Hi, I'm currently using the dev 2000 version of Phenix, and noticed an issue with the automatic linking of N-linked (and presumably O-linked) glycans. If you feed a glycosylated structure sans hydrogens to Phenix and allow ReadySet to add hydrogens prior to refinement, it adds hydrogens as if the glycans are unlinked. Then, the automatic linking script rejects them due to valence issues. Cheers, Tristan

2 2

idealizing structure
by PC 28 Apr '15

28 Apr '15

Is there a way to "idealize" a structure in Phenix? I mean, ideal omega, all residues within allowed regions of Ramachandran maps, no clashes..etc. I know it won't fit the map well but I would like to see what it looks like. Thank you. ____________________________________________________________ FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop! Check it out at http://www.inbox.com/marineaquarium

4 5

Re: [phenixbb] citation
by Sneha Rangarajan 28 Apr '15

28 Apr '15

Hello All, I have a non-Phenix problem- finding shape complementarity! I tried running the script for sc (ccp4) but it doesn't run to completion to give me the sc number. It stops saying "imaginary contain". What does that mean? However there is no error as such. I gave it the pdb that I got after my phenix refinement. Is there something I should be doing first to the pdb after refinement before running sc on it? Here is the script and I am also attaching the pdb. sc XYZIN F7-2_refine_113.pdb <<eof-sc MOLECULE 1 CHAIN A CHAIN B MOLECULE 2 CHAIN C eof-sc Thanks in advance!! Sneha From: Randy Read [mailto:[email protected]] Sent: Tuesday, April 21, 2015 3:42 AM To: Sneha Rangarajan Subject: Re: [phenixbb] citation Dear Sneha, Here's a link to the publication (which is open access): http://scripts.iucr.org/cgi-bin/paper?ba5210. Best wishes, Randy Read On 20 Apr 2015, at 19:02, Sneha Rangarajan <rsneha(a)umd.edu<mailto:[email protected]>> wrote: Hello, What is the correct way to cite Phenix MRage? Thanks, Sneha _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]> ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk<mailto:[email protected]> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk<http://www-structmed.cimr.cam.ac.uk>

1 0

rigid_body refinement
by Irina PROKHOROVA 25 Apr '15

25 Apr '15

Hello, how can i select two chains to be refined as one rigid body? I tried refinement.refine.sites { rigid_body = chain A and chain B } but it did not work. Irina

2 2

on Cutting out density by Phenix
by Smith Liu 23 Apr '15

23 Apr '15

Dear All, I have tried to cut out the density by the Phenix graphical interface with the cutout type as model, but I find in the cut out map, there is more density arond the residues than in the input mtz map, here I mean, take a Lys residue as an example, in the input map, from Calpha there is about 1/2 of the sidechain was surrounded by the density, but in the cutting out map, there is about 2/3 of the sidechain was surrounded by the density. Will you please tell me if I want to get the cutting out density in the model cutout type, how can I have the cutting out density looks exactly or very close to the input density in the input mtz? Smith

2 1

Generating cif file for DNA basepairing in PHENIX
by 李翔 23 Apr '15

23 Apr '15

Hi everyone, I am trying to build some DNA duplex models with different pitches by 3DNA. After changing the pitches from the original duplex model, I refined the duplex in PHENIX with geometry minimization. However, the basepairing get completely distorted. Is there a quick way to generate the cif file for basepairing in PHENIX or are there any other better ways to keep the basepairing restraint during the model refinement? Thank you very much for your kind help! Sincerely, Xiang -- Li Xiang Department of chemistry, University of Michigan Email：lixiang1642(a)gmail.com

3 3

on the convergence of the Phenix refine
by Smith Liu 22 Apr '15

22 Apr '15

Dear All, Suppose I have a refine of 10 cycles, it get stablized from cycle 7. But sometimes I noticed that from the end of the cycle 10 to the end of the whole refinement, the stablization from 7 to cycle 10 can be destroyed a little, which makes me concern whether the final refinement can be regarded as convergent or not. Will you please explain why the stablization from 7 to cycle 10 can be destroyed a little from the end of cycle 10 to the end of the whole refinement? More critically, in the other situation, suppose I have a refine of 10 cycles, it get relatively stablized from cycle 5, from the end of cycle 5 to the end of cycle 10 the Rfree increase very slightly each cycle of the refine, which makes at the end of cycle 10 the Rfree is slightly higher than the Rfree at the start of the whole refinement. But from the end of cylce 10 to the end of the whole refinement, there is a slight decrease of Rfree, which makes the Rfree at the end of the whole refinement slightly lower than Rfree at the start of the whole refinement. It seems to increase the cycles of the refinement would not help further. Will you please explain the above phenomenon and to see whether the refine result can be acceptable, or do you have any suggestions for improvement? Smith

2 1

Off-topic: Hydrogen images
by mohamed noor 22 Apr '15

22 Apr '15

Dear all I will be presenting about protein crystallography to a group of PhD-level physicists and need some images from the community. Would anyone have high-quality images of density maps that show hydrogen atoms at 1. high and ultra-high X-ray resolution (say, about 1.2 A to about 0.5 A) 2. low or medium X-ray resolution (where H atoms are not visible) compared with neutron data (with H). Ideally these images should be from the same protein so that I can show the power of complementary beam source for the diffraction. A side question - what is the community's preference to get deuterated samples? Is it crystal soaking or growing E. coli in deuterium? All contributions will be credited. Thanks.

2 2

citation
by Sneha Rangarajan 21 Apr '15

21 Apr '15

Hello, What is the correct way to cite Phenix MRage? Thanks, Sneha

2 2

Standard settings for map generation in phenix.refine
by Tristan Croll 21 Apr '15

21 Apr '15

Hi all, In the phenix.refine GUI, the default options for the maps auto-generated in Coot include the R-free set in the map coefficients. Is this the best choice? It's fairly natural for the user to immediately inspect/correct their structure using the helpfully-provided Coot window - which, as per a recent discussion thread on this list, can easily lead to over-fitting. I suspect I've been looking at such a case over the last week or so - a mid-3A structure refined in Phenix with an amazingly low Rfree (0.234) and Rfree-Rwork (~0.016), despite clear (albeit non-disastrous) errors in a number of loops, and moderate-poor statistics in structural quality metrics. Tellingly, the Rfree goes up quite substantially upon re-refinement after correcting these issues. If maps generated with the Rfree set included should only ever be used for final display, wouldn't it be better to have them excluded by default? Best regards, Tristan Tristan Croll Lecturer Faculty of Health School of Biomedical Sciences Institute of Health and Biomedical Engineering Queensland University of Technology 60 Musk Ave Kelvin Grove QLD 4059 Australia +61 7 3138 6443 This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.

2 1

on importing CIF structure factors and cutting out density
by Smith Liu 21 Apr '15

21 Apr '15

Dear All, By importing CIF structure factors of the Phenix graphical interface, I converted a CIF file to a mtz file. But when I tried to cutting out the density by Phenix with the converted mtz file, it request the map labels, which the converted mtz file seems does not have. Will you please let me know how to have the issue settles? Smith

2 1

phenix refinement of cryoEM data
by Ali Malay 18 Apr '15

18 Apr '15

Dear all, I am a relative newcomer to Phenix. I have a large multimeric protein structure docked into an electron density map, and I would like to further refine it by rigid-body refinement using Phenix. Is this a realistic strategy? I have made some attempts, first by converting the .mrc map file to .mtz as outlined here: https://www.phenix-online.org/documentation/reference/map_to_structure_fact… <https://www.phenix-online.org/documentation/reference/map_to_structure_fact…> Then I tried to refine using rigid body refinement in Phenix. However, the program quits but doesn’t really tell me why. Here’s the last part of the log file: Number of unique models: 24 Time building chain proxies: 36.85, per 1000 atoms: 0.26 Number of scatterers: 142296 At special positions: 0 Unit cell: (342, 342, 342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 264 16.00 O 27720 8.00 N 25872 7.00 C 88440 6.00 sf(0) = scattering factor at diffraction angle 0. Writing MTZ file: /Users/xxx/Documents/Phenix/TEST/Refine_1/Test_refine_data.mtz Sorry Can anyone give me any ideas as to what went wrong? Also, is there a better way to do this? Thanks very much in advance!! A.M.

2 1

find difference peaks
by Alejandro Virrueta 16 Apr '15

16 Apr '15

Hello, I'm working on a small project, and need some feedback. I am trying to rebuild methionine side-chains by looking at the difference peaks for a given Fo-Fc map. I envision a process as follows: 1. Delete the MET side-chain of a PDB file 2. Refine structure to get Fo-Fc map 3. Get a list of the peak positions relative to the coordinates of the PDB file I used 4. Filter list by keeping peaks near the MET C alpha/beta PDB coordinate. 5. Try to rebuild side-chain after anchoring the sulfur atom (assuming sulfur is located at the highest peak and within some distance to C beta) What functions should I use to achieve step 3? I am also trying to implement this process within the ringer program (phenix/cctbx_project/mmtbx/command_line/ringer.py). If anyone is familiar with this, what commands would work best within this ringer program? i.e. what functions can operate on difference_map (which is sampled by a point using tricubic_interpolation under 'def sample_angle')? I hope this makes some sense to someone. Thanks! Alex

2 1

reflections file editor
by Almudena Ponce Salvatierra 14 Apr '15

14 Apr '15

Dear all, I would like to merge two datasets containing anomalous signal. If have done so earlier for native data within phenix in the reflections editor by selecting the arrays corresponding to FP and SIGFP and then running the program. However when I try to do so for the anomalous datasets it writes FP SIGFP and FP2 SIGFP2 instead or merging them, so it does with the anomalous signal... so I guess I have basically only one file containing two datasets but not a merged dataset. How can I solve it? Would it be possible, on the other hand, to merge a dataset with anomalous signal with a native one? The intention behind is to extend the resolution to the one of the native data. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

3 2

sugar puckering refinement with phenix refine
by Almudena Ponce Salvatierra 14 Apr '15

14 Apr '15

Dear all, does anyone know how phenix.refine deals with the sugar puckering of an RNA or a DNA strand? Does it refine it? Or does it leave it as it was built? Thank you very much in advance. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

2 1

Link NGA and THR
by Cory Brooks 14 Apr '15

14 Apr '15

Hello! I am refining a structure with O-link glycosylation (GalNAc linked to Thr). Phenix seems to remove the link during refinement. Can anyone suggest a solution that will maintain the bond during refinement? Regards, Cory Cory Brooks,Ph.D.

3 2

elbow-readyset
by Tarek DawoD 14 Apr '15

14 Apr '15

Dear All if i have pdb file for CdCl2, how could i generate cif file (to use later in phenix.refine) from that using readyset or elbow or any other tool.i could not find 3 letter could for CdCl2. COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.1 HETATM 1 CD LIG 1 0.994 8.428 20.546 1.00 0.00 Cd HETATM 2 CL1 LIG 1 -0.441 6.507 20.373 1.00 0.00 Cl HETATM 3 CL2 LIG 1 3.190 7.731 21.231 1.00 0.00 Cl END Thank you for Help.regardsTK_DawoD

3 2

Submit your abstract for the ACA Annual meeting in Philadelphia July 25-29, 2015
by Terwilliger, Thomas Charles 14 Apr '15

14 Apr '15

Hi Phenix users! You are invited to the ACA meeting in Philadelphia! Abstracts are still being accepted (see the invitation below). All the best, Tom T Tom Terwilliger Vice President, ACA Abstracts still being accepted ACA 2015 Meeting - July 25-29 Philadelphia, PA Is this email not displaying correctly? View it in your browser<http://us2.campaign-archive2.com/?u=3e43dd9d1724b97d2bc286881&id=0f524b9d2c…>. [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/2a8238a9-d30…] [http://www.amercrystalassn.org/2015-mtg-homepage]<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…> ABSTRACT SUBMISSION DEADLINE IS EXTENDED ACA Annual Meeting • Philadelphia, PA • July 25 - 29, 2015 Submit abstract now to be considered for an oral presentation. Once all the lectures are scheduled, abstracts will continue to be accepted for poster presentations. [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/21952137-733…] Exhibit Show<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…> First-time exhibitors receive 25% discount Discount rates for Not-for profits Corporate Members receive an additional discount Coffee breaks & poster sessions held in the exhibit hall to offer multiple opportunities to reach your target audience Your website linked on the meeting page Free listing in ACA RefleXions and Program & Show Guides Special sponsorships for Exhibitors only [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/d9f63f39-b8b…] Call for Papers:<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…> 40% of talks selected from contributed abstracts No abstract submission fee Lower registration fees for members Sessions for students & young scientists on career directions, reviewer practices & more Full scientific program:www.AmerCrystalAssn.org<http://amercrystalassn.us2.list-manage1.com/track/click?u=3e43dd9d1724b97d2…> [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/961e8c70-86c…] Registration<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…>: Join or pay membership dues and save on Registration fees Corporate Members receive advertising and exhibiting discounts Early bird rates until May 31 Online registration now open<http://amercrystalassn.us2.list-manage2.com/track/click?u=3e43dd9d1724b97d2…> follow on Twitter<Twitter%20Account%20not%20yet%20Authorized> | friend on Facebook | forward to a friend<http://us2.forward-to-friend.com/forward?u=3e43dd9d1724b97d2bc286881&id=0f5…> Copyright © 2014, AmericanCrystallographicAssn. All rights reserved. Our mailing address is: aca(a)hwi.buffalo.edu<mailto:[email protected]> ACA, PO Box 96, Buffalo, NY 14205 [Email Marketing Powered by MailChimp]<http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm…> unsubscribe from this list<http://amercrystalassn.us2.list-manage.com/unsubscribe?u=3e43dd9d1724b97d2b…> | update subscription preferences<http://amercrystalassn.us2.list-manage.com/profile?u=3e43dd9d1724b97d2bc286…>

1 0

pdbtools: how to set the occupancy for an atom selection?
by Alejandro Virrueta 13 Apr '15

13 Apr '15

Hello, I was wondering if someone could show me a way to set the occupancy of a specific set of atoms to 0 using phenix.pdbtools. I noticed here <http://www.phenix-online.org/download/documentation/cci_apps/pdbtools.html#…> that there is no option under modify => occupancies to do an 'atom_selection'. Any help would be appreciated. Cheers, Alex

4 4

Deposition question
by mohamed noor 13 Apr '15

13 Apr '15

Dear all I solved my structure using SAD from heme to 2 A and then did molecular replacement with a dataset diffracting to 1.2 A. Do I deposit only the mtz and pdb file from the last refinement run and report the corresponding statistics in 'Table 1'? Should I specify the experimental f' and f'' values? Thanks.

2 1

expermiental sigma or SIGFP of the mtz file
by Smith Lee 13 Apr '15

13 Apr '15

Dear All, Will you please let me know what is the expermiental sigma or SIGFP of the mtz file? If a mtz file lacks the expermiental sigma or SIGFP, what does it mean? I am looking forward to getting your reply. Smith

3 2

Reference model restraints in real space refinement?
by Oliver Clarke 13 Apr '15

13 Apr '15

Hi all, Is it possible to use reference model restraints at the moment during real space refinement (in phenix.real_space_refine)? I can’t see it in the documentation. On a related note, would it be possible at some point to allow users to set d_max in the phenix.map_to_structure_factors utility? At the moment it seems like the user can set d_min but not d_max - sometimes it is convenient to restrict the low res to 20 or 50Å, rather than the whole box size of an EM-map, which is the default. Best, Oliver.

3 2

Phenix command to align the PDB sequence and input sequence
by Smith Liu 11 Apr '15

11 Apr '15

Dear All, Will you please tell me the Phenix command to align the PDB sequence and input sequence? I am looking forward to getting your reply. Smith

4 4

Error refining with ramachandran restraints
by Oliver Clarke 11 Apr '15

11 Apr '15

Hi all, When I attempt to run a refinement using phenix.refine from the command line, using the parameter “ramachandran_restraints=true”, in the latest nightly build of phenix (dev-2006), I get the following error: ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. Traceback (most recent call last): File "/Applications/phenix-dev-2006/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/command_line.py", line 96, in run master_params=customized_master_params) File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/driver.py", line 272, in __init__ secondary_structure_manager=self.sec_str, AttributeError: refine instance has no attribute 'sec_str' This happens for two different structures, so I don’t think it is a structure-specific thing, and I don’t recall this happening in older builds of phenix. The refinement runs fine if I don’t specify ramachandran restraints. Is there something obvious I am doing wrong? Best, Oliver.

2 2

Autobuild error
by Lau Sze Yi (SIgN) 08 Apr '15

08 Apr '15

Hi, I did an Autobuild run. The Status panel indicated that the run is finished. In the Model building panel the status of run# 5 still says running (See attached screenshot). Is this normal? And when I click on run #4 to Open in Coot, I get an error message indicating that the directory could not be found (see attachment). What is wrong and how can I fix this? I am using version phenix-1.9-1692 on Mac. Regards, Sze Yi Research Fellow Singapore Immunology Network (SigN) 8A Biomedical Grove, #03-06 Immunos, Singapore 138648 DID: +65 6407 0640 Fax: +65 6407 0640

2 1

on reciprocal space refine of the electronic microscopy map by Phenix
by Smith Liu 08 Apr '15

08 Apr '15

Dear All, Recently there are cryo-electronic microscopy papers which refine the reciprocal space of the electronic mcroscopy map by phenix refine. For the electronic mcroscopy map, what does it mean for the reciprocal space? How to get the reciprocal space map from the electronic mcroscopy map? In order to realize this kind of refine in phenx, we only process the xyz coordinates strategy refine in the graphical interface, right? I am looking forward to getting your reply. Smith

2 1

FINAL REMINDER: Neutrons in Structural Biology
by Meilleur, Flora 06 Apr '15

06 Apr '15

6th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 1 - June 5, 2015 Application deadline: April 10, 2015 Detailed information can be found on the workshop web page: https://public.ornl.gov/neutrons/conf/gcnb2015. Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

1 0

Ensemble refinement
by mohamed noor 04 Apr '15

04 Apr '15

Using the FEM map, I managed to remove more bad waters and add instead ions from the crystallization mix. I tried phenix.ensemble_refinement but the Rfactor increased by 2 % (originally 19/22 % from phenix.refine). Before it crashes at the validation point all the time, it prints out the validation summary with 0.53-3.48 % and 1.87-7.22 % Ramachandran outlier (from 0.3 %, supported by density) and a Molprobity score of 1.57-1.92 and 1.82-2.14 depending on pTLS used (original single model score was 2.08). The clashscore in both settings (pTLS=0.6 and 1) are 0. Do I still go by the Rfactor and decide to not use ensemble refinement at all? Thanks.

3 2

Structure with pseudo-NCS translation
by Mark A Saper 04 Apr '15

04 Apr '15

I know that Phaser takes account of NCS translation in the likelihood statistics ( Read, Adams, McCoy (2013) Intensity statistics in the presence of translational non crystallographic symmetry”). Has this also been incorporated into phenix.refine? I have a structure with pseudo NCS translations because of NCS rotational symmetry. One suggestion that I found in the archives, was to explicitly LS target refinement rather than ML. Any comments? Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

4 5

refinement
by Almudena Ponce Salvatierra 02 Apr '15

02 Apr '15

Dear all, I am using Phenix.refine after MR and I have a complete model and data to 2.8 Angstrom resolution. However, for some reason, Phenix does not place any water molecules. Is there a setting I could change in order to see whether this situation changes? What could the reason be? 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

2 1

twinning
by Shun Liu 02 Apr '15

02 Apr '15

Dear all, Recently I have got a data set that diffracts to 1.7 angstrom. Images look good. During data processing I did not find anything that looks strange. However, when I was doing Phaser-MR, I got a warning: “ Intensity moments suggest significant twinning (>5%). Tests based on possible twin laws will be more definitive.” What does this mean? A twinning data set? I still found a solution and refined the model step by step, using the data (20-1.7 angstrom). It seems that the final model and map are acceptable. But R-factors are 0.24/0.28, very high. Does the twin cause the high R-factors? Is there a solution to detwin? Or are the R-factors acceptable for a twinning data set? Any suggestions are appreciated and thanks in advance! Best, Shun

5 10

a question on henix refine
by Smith Liu 01 Apr '15

01 Apr '15

Dear All, For the Phenix refine, the default for the Scattering table in "other options" in the graphical interface is n_gaussian, in which situation to use electron is much better? And how much would be the benefit to use electron instead of n_gaussian? Smith

2 1

Maps
by mohamed noor 01 Apr '15

01 Apr '15

Dear developers What is the difference between MEM and FEM maps? I read the documentation and my understanding is both are supposed to create beautiful maps :) My problem is I have a structure at 1.9 A (a different protein than the one referred to in my previous question), the Rfactor is around 20/22 %, Rms bonds is 0.03 and Rms angles is 1.845. If the bonds/angles get lower, the Rfactor jumps up (same problem as the other structure). Looking in Coot, there are positive and negative density and missing density for the side chains of residues with high B factor. For some reason, phenix.refine keeps on adding water at strange places even at regions that I suspect to be just noise. For this reason, I want to see if the noise is really noise. A second reason is I have density that seem to be too big for a water molecule but waters were placed anyway, so I want to know if these are real positive density. The dataset was obtained from only 50 degrees, SG is P 61 2 2. Including more images brought up the Rmerge to 30-40% and Rfactor being stuck at 30 %. For some reason, I don't find the X-ray statistics from the phenix.model_vs_data logfile but in essence, I have: 28-1.9: 82 % 6 A - infinity: 95 % in the shells (2.25-2.14, 2.14-2.04, 2.04-1.97, 1.97-1.9) my completeness is around 85-62 % and CCwork is at least 70 % and CC1/2 of the dataset is 60 % at the highest resolution shell. Thanks.

2 1

continuously Rfree lower than Rwork
by Smith Liu 31 Mar '15

31 Mar '15

Dear All, If in a Phenix.refine proces, the Rfree continuously lower than Rwork, what does it mean? Smith

4 3

Twinning
by Shun Liu 31 Mar '15

31 Mar '15

Dear all, Recently I have got a data set that diffracts to 1.7 angstrom. Images look good. During data processing I did not find anything that looks strange. However, when I was doing Phaser-MR, I got a warning: “ Intensity moments suggest significant twinning (>5%). Tests based on possible twin laws will be more definitive.” What does this mean? A twin data set? I still found a solution and refined the model step by step, using the data (20-1.7 angstrom). It seems that the final model and map are acceptable. But R-factors are 0.24/0.28, a little high. Does the twin cause the high R-factors? Is there a solution to detwin? Or are the R-factors acceptable for a twin data set? Any suggestions are appreciated and thanks in advance! Best, Shun

1 0

First-Science Discussions for Life-Science Beamlines at NSLS-II: April 21-22, 2015
by Robert Sweet 28 Mar '15

28 Mar '15

We will hold a "First Science at the ABBIX Beamlines" meeting on Tuesday - Wednesday, April 21-22, 2015, pertaining to the National Institutes of Health (NIH)-sponsored "Advanced Beamlines for Biological Investigations with X-rays" (ABBIX) Project. These three state-of-the-art beamlines are now under construction at the National Synchrotron Light Source (NSLS)-II facility at Brookhaven National Laboratory (BNL). Two of the beamlines are for macromolecular crystallography (MX), and the third is for life sciences applications of x-ray scattering. Visit this web site for further information and registration materials: http://workshops.ps.bnl.gov/?w=ABBIXApr2015 Briefly, the MX beamline called FMX - Frontier MX - is optimized to address microbeam applications, and the other called AMX - Highly Automated MX - is optimized for highly automated throughput. The scattering beamline called LIX - High Brightness X-Ray Scattering for Life Sciences - will offer multiple modes of study. The MX beamlines view canted undulator sources, and the scattering beamline views a single undulator, providing world-leading brightness. Current plans are to conclude construction by the end of 2015 and start commissioning then. During the commissioning period, opportunities will arise to perform early experiments before the general user programs of the beamlines commence in 2016, and it is the upcoming meeting's purpose to explore and discuss scientific areas and opportunities on which early operation of the beamlines could capitalize. Note: Registration is required. There is no registration fee. Visit this site to register: http://workshops.ps.bnl.gov/?w=ABBIXApr2015 Those who registered for the original meeting planned for January must re-register for the new occurrence in April. Contributed presentations describing experiments that exploit the capabilities of the ABBIX beamlines will be selected from submitted abstracts. The meeting will consist of both plenary and parallel sessions. The plenary session will begin with presentations on science topics in research fields that the beamlines are designed to address, followed by facility presentations to update the community about the early scientific capabilities at the suite of ABBIX beamlines and, in addition, of the Life Science and Biomedical Technology Research Resource (LSBR), sponsored by the NIH and the Department of Energy Office of Biological and Environmental Research (DOE BER). Two parallel sessions on Tuesday afternoon will focus on MX and x-ray scattering, consisting mainly of presentations that will address specific opportunities in these areas. These will be followed by two more parallel sessions on Wednesday morning, also focusing on MX and x-ray scattering, which will include contributions. If you wish to give a contributed presentation during one of the parallel sessions, please submit an abstract here: http://workshops.ps.bnl.gov/abstracts/default.aspx?w=ABBIXApr2015 The parallel sessions are designed to provide forums to facilitate more detailed discussions about potential first experiments at specific beamlines and the formation of the experiment teams. Specifically, each parallel session group will be charged to accomplish these goals: 1. Identify key research projects and the associated first experiments that may be performed at the suite of ABBIX beamlines, emphasizing those projects that will take advantage of NSLS-II properties and ABBIX beamline capabilities. 2. Facilitate the formation of research teams to generate first experiment proposals for submission. 3. Identify key additional team members in such areas as theory and analysis, ancillary measurements, and specimen preparation, needed to achieve the research goals. Confirmed invited speakers: Karen Allen (Boston Univ), Martin Caffrey (Trinity College Dublin), Seth Darst (Rockefeller Univ), Richard Gillilan (Cornell Univ), Wayne Hendrickson (Columbia Univ), AndrHoelz (California Inst Tech), Huey Huang (Rice Univ), Shenping Liu (Pfizer), Lee Makowski (Northeastern Univ), David Ostrov (Univ of Florida), Rebecca Page (Brown Univ), Anna Marie Pyle (Yale Univ), Christian Riekel (ESRF), Thomas Schneider (EMBL-Hamburg), John Tainer (Scripps Research Inst). We would like two outcomes from this meeting: (a) a concise meeting report outlining how ABBIX beamlines will help to address outstanding problems in life sciences, and (b) a list of potential first experiments along with the corresponding research teams. For more information on the meeting, please contact Sonya Kiss, at skiss(a)bnl.gov. Note: Registration deadline is Tuesday, April 14, 2015. Organizers: Lonny Berman ABBIX Project Manager National Synchrotron Light Source II Brookhaven National Laboratory Sean McSweeney Structural Biology Program Manager Photon Sciences Division Deputy Director National Synchrotron Light Source II

1 0

can mr_rosetta include twin_law?
by Ni, Fengyun 28 Mar '15

28 Mar '15

Hi everyone, When I run phenix.mr_rosetta, I use the following file (twin.eff) to add the twin_law with the keyword: refinement_params=twin.eff. I checked the output that the phenix.refine stage could recognize this file. But the autobuild step can not read this file and give the error information as follows, refinement.twinning { twin_law = "h,-h-k,-l" } Unable to read the parameters file twin.eff. Is there anyway to overcome this issue? Thank you very much in advance! Fengyun

2 1

Refinement
by mohamed noor 26 Mar '15

26 Mar '15

Dear all I have a structure at 1.4 A currently with an Rfactor of 21/26 %. I notice from the plot by cycle that everytime the RMS bonds/angles reduce, the Rfactor increases a few percent. Is there any way of telling phenix.refine to not 'restrain' the model too much? I have already used automatic weighting. Also, RINGER identified a few alternate conformations, so I'm thinking that modeling this might account for a better model. However, as I have an NCS of 4, this can be tedious to do by hand, and AFAIK, phenix.refine does not create new conformations. Is there an alternative? Final question, some residues were flagged as having high B factors but not in all the copies. How do I deal with this? Some background: I initially had problems with refinement being stuck at 30-35 % in SG P 3 2 1 (as suggested by Pointless and Xtriage). However, the beamline scientist suggested that there could've been lattice translocation and that it is actually P 3. Reintegrating seems to have solved the problem. With integrated data up to 1.2 A, I tried cut-off at 1.4, 1.3 and 1.2 A. Together with CC1/2 and refinement results, I chose 1.4 A, but should I cut it a bit lower? Thanks.

2 1

PhD position in Structural Biology in Norway
by Hans-Petter Hersleth 24 Mar '15

24 Mar '15

Dear all, A 3- or 4-year PhD position in Structural Biology / Biophysics / Biochemistry starting August 2015 is available at University of Oslo, Department of Biosciences, Section for Biochemistry and Molecular Biology in the Metalloprotein group. The project is in the field of structural biology, biophysics and biochemistry with an emphasis on protein crystallography and spectroscopy (UV-vis, Raman and EPR) in combination with other biochemical and biophysical methods. The project is dealing with different redox proteins involved in oxygen activation and electron transfer. The focus will be on some enzyme systems like ribonucleotide reductase and nitric oxide synthase, their reaction mechanism and redox activation pathways. More information about the project, position and application procedure is found on the website: http://uio.easycruit.com/vacancy/1352831/96323?iso=no Applicants must hold a Master's degree or equivalent in structural biology, bioinorganic chemistry, biochemistry, biophysics, protein crystallography or related fields. We are seeking a highly motivated candidate that should have skills and experience in working with proteins or bioinorganic molecules. It would be advantageous with hands-on experience within topics like cloning, protein expression, purification, crystallisation, protein crystallography, spectroscopy, bioinorganic chemistry, protein-protein interactions, enzyme kinetics and redox-, radical- and metalloproteins. Candiates without a Master's Degree have until 30 June 2015 to complete the final exam. Application deadline is 13th April 2015 through the website: http://uio.easycruit.com/vacancy/1352831/96323?iso=no For further information please contact: Dr. Hans-Petter Hersleth, (h.p.hersleth(a)ibv.uio.no) ---------------------------------------------------------------------------------------------- Hans-Petter Hersleth, PhD Project Leader, Researcher and Senior Lecturer Department of Biosciences, University of Oslo Section for Biochemistry and Molecular Biology P.O.Box 1066 Blindern, NO-0316 Oslo, Norway Phone: +47 2285 4631 Fax: +47 2285 4726 Mobile: +47 413 33 126 http://www.hersleth.org/ -----------------------------------------------------------------------------------------------

1 0

on Phenix's "Generate "Table 1" for journal"
by Smith Liu 24 Mar '15

24 Mar '15

Dear All, With the Phenix refine PDB and mtz file, I just prepared a "Table 1" for journal with Phenix. Here I find something special, which I hope I can get your advice. First, for the "Total reflections" and "Multiplicity", they are empty (no data given). Wil you please tell me why? Secondly, it writes, "Statistics for the highest-resolution shell are shown in parentheses". Suppose my crystal resolution is 2.5-45.6, then the the highest-resolution value should be 2.5, rather than 45.6, right? In addition, what is the diffrence between highest-resolution shell in the Table 1 and highest-resolution bin in the "Results" of Phenix refine? What is R-merge, R-meas,CC1/2 and CC*? I can get these data from MOSFLM output mtz file. But is my images were processe by HKL, which I have no experience, then how can I get the R-merge, R-meas,CC1/2 and CC*? I am looking forward to getting your reply. Smith

7 6

question related to phenix produced PDB file
by Dialing Pretty 22 Mar '15

22 Mar '15

Dear All, In my Phenix refine produced PDB file, I find in REMARK 3, there is a sentence "PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED): 42.3. Does 42.3 means 42.3%? Is it too high? I am looking forward to getting your reply. Dialing

3 3

error message in phenix refine
by Almudena Ponce Salvatierra 20 Mar '15

20 Mar '15

Hi everyone, I have merged 3 mtz files into one and done successfully Molecular replacement with it. However when I try to refine, I get the following error message: "cctbx error: merge_equivalents_exact: imcompatible flags for hkl (0, 0, 16) (mismatch between Friedel pairs). How can I fix this? Thank you very much 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

2 1

fixing rotamers with coot
by Benoît Masquida 20 Mar '15

20 Mar '15

Dear all, I am using Coot 0.7.2 and phenix 1.9-1692 on Ubuntu 13.10 and I have the following error message when I try to regularize zone, edit Chi angles or fix rotamer outliers. Error message :"Refinement setup failure. Failed to find restraints for : 'residue list' " Apparently a cif dictionary is missing that should be output by phenix to be used by coot. Does anyone has any idea? Thanks in advance. Benoit --

2 1

on Phenix refine
by Smith Liu 20 Mar '15

20 Mar '15

Dear All, Will you please tell me which strategy of Phenix refine is for reciprocal space refinement? In the log, I often see "XYZ individual (reciprocal space)", will you please let me know whether "XYZ individual (reciprocal space)" is caused by "XYZ coordinates" or by "Optimize X-ray/sterochemistry weight"? Smith

4 3