- phenixbb - phenix-online.org

error when running phenix_rosetta_refine
by Wei Wang 19 Nov '15

19 Nov '15

Hi, I just experienced an error when using phenix_rosetta_refine. It appeared after "Generating 5 models". I'd appreciate any help on solving this. Generating 5 models on 3 processors... DEBUG dumping error message ERROR: Rosetta exited with status 1 stderr output: Traceback (most recent call last): File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/rosetta/xray_target.py", line 203, in compute_target tfx_r = self.target_functor(compute_gradients=compute_gradients) File "/Applications/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/targets.py", line 247, in __call__ compute_gradients=compute_gradients)) File "/Applications/phenix-1.10.1-2155/modules/cctbx_project/cctbx/xray/target_functors.py", line 58, in __call__ compute_gradients=compute_gradients) RuntimeError: cctbx Internal Error: /Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64-10_9/modules/cctbx_project/cctbx/xray/targets.h(498): CCTBX_ASSERT(f_calc.size() == f_obs.size()) failure. ERROR: error computing X-ray target

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Re: [phenixbb] (no subject)
by Ashok Nayak 18 Nov '15

18 Nov '15

Dear luzuok, The merging job can easily be done in Pymol. 1.Create symmetry molecules (say at 4A radius) -> Select the symmetry related molecules of your choice -> save the selected coordinates of the same or 2.You can also do the same by saving the coordinates of two symmetry related molecules separately and merge in a text file with proper TER records. regards Ashok CSIR-CDRI Lucknow, INDIA On Wed, Nov 18, 2015 at 9:09 PM, Ashok Nayak <ashokgocrackin(a)gmail.com> wrote: > Dear luzuok, > The merging job can easily be done in Pymol. > 1.Create symmetry molecules (say at 4A radius) -> Select the symmetry > related molecules of your choice -> save the selected coordinates of the > same > or > 2.You can also do the same by saving the coordinates of two symmetry > related molecules separately and merge in a text file with proper TER > records. > > regards > Ashok > CSIR-CDRI > Lucknow, INDIA > > On Wed, Nov 18, 2015 at 5:59 PM, luzuok <luzuokun(a)126.com> wrote: > >> Dear Tom, >> I have the same question too. >> Another simple question is that how can I merge two symmetry related >> molecule? Though I can easily expand them by coot. >> >> Best! >> Lu >> >> >> -- >> >> >> Lu Zuokun, Ph.D. Candidate >> College of Life Science, Nankai University >> >> 在 2015-11-18 23:14:48，"Terwilliger, Thomas Charles" <terwilliger(a)lanl.gov> >> 写道： >> >> Hi Ashok, >> >> If you have a PDB file with 2 crystallographically-related copies of your >> molecule, with one called chain A and one called chain B, you can run >> phenix.simple_ncs_from_pdb on your PDB file to find the matrices and >> translations. Let me know if that doesn't do it! >> >> All the best, >> >> Tom T >> >> >> ------------------------------ >> *From:* phenixbb-bounces(a)phenix-online.org < >> phenixbb-bounces(a)phenix-online.org> on behalf of Ashok Nayak < >> ashokgocrackin(a)gmail.com> >> *Sent:* Wednesday, November 18, 2015 7:58 AM >> *To:* phenixbb(a)phenix-online.org >> *Subject:* [phenixbb] (no subject) >> >> Hello Phenix BB, >> Like every amateur crystallographer I could easily generate symmetry >> mates in a given radius in coot, but I wondered always which is the >> crystallographic two fold axis axis(my space group being C2) through which >> the molecule is rotated and translated (if it is) to get the next molecule. >> I tried superpose to find the answer, but could only get the Euler angles >> and transformation matrix and not the axis. Are there any programs where I >> can get to know this, would be grateful to be enlightened for the same >> >> thanks BB in advance >> >> >> >> regards >> >> -- >> Ashok Nayak >> PhD student- >> Molecular and Structural Biology Division >> CSIR-CDRI, Janakipuram Extension >> Lucknow-226031 >> India >> >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > > -- > Ashok > Senior Research Fellow - Dr JV Pratap, Lab No-LSN 008 > Molecular and Structural Biology Division > Central Drug Research Institute, Janakipuram Extension > Lucknow-226031 > India > -- Ashok Senior Research Fellow - Dr JV Pratap, Lab No-LSN 008 Molecular and Structural Biology Division Central Drug Research Institute, Janakipuram Extension Lucknow-226031 India

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(no subject)
by Ashok Nayak 18 Nov '15

18 Nov '15

Hello Phenix BB, Like every amateur crystallographer I could easily generate symmetry mates in a given radius in coot, but I wondered always which is the crystallographic two fold axis axis(my space group being C2) through which the molecule is rotated and translated (if it is) to get the next molecule. I tried superpose to find the answer, but could only get the Euler angles and transformation matrix and not the axis. Are there any programs where I can get to know this, would be grateful to be enlightened for the same thanks BB in advance regards -- Ashok Nayak PhD student- Molecular and Structural Biology Division CSIR-CDRI, Janakipuram Extension Lucknow-226031 India

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phenix 1.10.1-2155 has no kicked map option
by Tarek DawoD 18 Nov '15

18 Nov '15

Dear Phenix developer why i could not see the kick map option under phenix.refine (GUI). i used to use it in the previous version. Kick in phenix 1.9.1692 no Kick in phenix 1.10.1-2155 Best RegardsTDawoD

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Re: [phenixbb] Omit map output map files
by Fischmann, Thierry 16 Nov '15

16 Nov '15

What Pavel describes is how to get a “difference map”. But it is not an “omit map” per the original definition. The omitted part should never have been part of the model during any refinement step before the omit map is calculated. The purpose is to prevent bias. If the model has already been refined with a ligand, then the technique of simulated annealing refinement can be used to remove the bias after removing the ligand. This approximates an “omit map” (still one may argue not a real “omit map”, but close enough). Thierry From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Manoj saxena Sent: Sunday, November 15, 2015 11:20 PM To: Pavel Afonine Cc: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Omit map output map files Thanks Dr. Pavel, This looks simple. regards Manoj On Sun, Nov 15, 2015 at 11:49 PM, Pavel Afonine <pafonine(a)lbl.gov<mailto:[email protected]>> wrote: Hi Manoj, you can do it this way: 1) remove ligand from PDB file; 2) compute mFo-DFc map. This is your ligand-omit map. Some would advise to do a round of refinement between steps 1-2 above in order to remove "memory from the ligand". I'm not convinced this is critical though. Pavel On 11/15/15 12:18, Manoj saxena wrote: Greetings, I would be very grateful if someone can help me to explain in I can get F0-Fc omit maps of a particular ligands using Phenix. I am trying to generate an omit map for the ligands in my protein model using the composite omit map GUI feature of phenix version 1.10.1-2155. I selected my ligands by using atom selection feature under the map options(and in the omit map method I put refine). What map type I should give in the map types input to get the F0-Fc maps. Currently I may getting a map that look like my 2F0-Fc map that I got after my refinement. Also, I have no waters in my model. Can we define areas (boxes) around the ligand to generate omit map of that particular region to get output maps with densities like Fo-Fc maps. So many thanks in advance. Regards Manoj Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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Omit map output map files
by Manoj saxena 15 Nov '15

15 Nov '15

Greetings, I would be very grateful if someone can help me to explain in I can get F0-Fc omit maps of a particular ligands using Phenix. I am trying to generate an omit map for the ligands in my protein model using the composite omit map GUI feature of phenix version 1.10.1-2155. I selected my ligands by using atom selection feature under the map options(and in the omit map method I put refine). What map type I should give in the map types input to get the F0-Fc maps. Currently I may getting a map that look like my 2F0-Fc map that I got after my refinement. Also, I have no waters in my model. Can we define areas (boxes) around the ligand to generate omit map of that particular region to get output maps with densities like Fo-Fc maps. So many thanks in advance. Regards Manoj

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Re: [phenixbb] [ccp4bb] question on mtz file
by Smith Lee 15 Nov '15

15 Nov '15

Dear Ian, The mtz was transformed from a cryo-EM mrc file by phenix.map_to_structure_factors, and it contains both label "F" and "F_ampl". When I do phenix.mtz.dump, the labels include H,K,L,F,PHIF,F_ampl,HLA,HLB,HLC,HLD. Smith On Sunday, November 15, 2015 11:03 PM, Ian Tickle <ianjt05(a)gmail.com> wrote: Hi, I assume what you mean is "what is the difference between the column labelled 'F' and the one labelled 'F_ampl' ?" in your MTZ file. Since MTZ column labels are effectively arbitrary and may be user-specified, that is clearly an impossible question to answer without knowing the history of your MTZ file. The column labelled 'SIGFP' would normally be the standard deviation of the 'FP' column (assuming there is such a column), though there's no absolute requirement that this be the case (it just makes life easier for everyone if it is!), so again it's impossible to say which amplitude column the SIGFP column is related to without knowing the history of your file. Bottom line is: you have not supplied sufficient information to make it possible to answer your question. Cheers -- Ian On 15 November 2015 at 02:27, Smith Lee <00000459ef8548d5-dmarc-request(a)jiscmail.ac.uk> wrote: Dear All, For a mtz file, will you please introduce to me the difference between label "F" and label "F_ampl"? For the label "SIGFP", is it the deviation related to label "F" or label "F_ampl"? Smith

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ionic radius
by Manoj saxena 12 Nov '15

12 Nov '15

Greetings, I was wondering if someone can enlighten me on the issue of how the metal ionic radius are defined in the protein structures. Is there any place in the refinement process where we can define it or it is automatically taken from some library in the phenix background. What is a good resource for knowing the ionic radii, I came across this one in an old blog post http://abulafia.mt.ic.ac.uk/shannon/ is there any other source that is used. Thanks so much in advance Manoj Saxena

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Rigid body refinement
by Rex Palmer 11 Nov '15

11 Nov '15

We have 1.5A resolution data for a heterodimeric protein with linked A and B chains. Phenix MR has produced a promising solution. We would now like to perform an initial refinement using Phenix with the A chain and B chain individually treated as rigid bodies.Is this possible with Phenix and if so how? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4614-3954-7

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wwPDB X-ray validation task force update
by Randy Read 11 Nov '15

11 Nov '15

Dear CCP4 and Phenix BB subscribers, The worldwide PDB X-ray validation task force is being reactivated to consider what updates need to be made to the validation criteria that are reported and the validation reports that are produced when you either deposit a new structure or use the standalone wwPDB validation server. We're already aware of a number of issues. Probably the biggest single issue is improving the validation of ligands, including numerical and visual analysis of fit to density. There's a lot of room for improvement of the validation of carbohydrates. Our agenda also includes discussions on metals, radiation damage and cis-peptides, among other topics. The task force will be meeting this coming Monday and Tuesday, so now would be a good time to provide feedback on the current state of the art and in particular on any aspects that I've left out of that list of the topics we'll be discussing. If you have constructive suggestions on any aspect of X-ray structure validation at the wwPDB, I would be happy to collect any emails I receive and convey them to the rest of the task force. It's also possible to send feedback at any time through the official channel by an email to validation(a)mail.wwpdb.org. * Are there current validation criteria that should be retired in favour of other criteria? * Are there missing criteria that should be added? * Are there ways in which the presentation of the validation results in the report could be clarified? Best wishes, Randy Read ------ 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 Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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mr_rosetta fragment_files by chain
by Perry, Kay H. 10 Nov '15

10 Nov '15

I am trying to run rosetta for a heterodimer with two different chains. I have the following commands, but in some subprocesses, I get the error message: Sorry: Sorry, need 2 fragment files (3 and 9 residues) for rosetta_rebuild I have the following in my script: fragment_files_chain_list=V \ fragment_files_chain_list=A \ fragment_files_3_mer_by_chain="orfx3_03_05.200_v1_3" \ fragment_files_9_mer_by_chain="orfx3_09_05.200_v1_3" \ fragment_files_3_mer_by_chain="orfx1_03_05.200_v1_3" \ fragment_files_9_mer_by_chain="orfx1_09_05.200_v1_3" \ Do I need to have the chain ID in the filename? Kay Kay Perry NE-CAT 9700 S. Cass Ave. Bldg. 436 E007 Argonne, IL 60439 630-252-0692

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error with phenix.refinine
by Maxime Cuypers 08 Nov '15

08 Nov '15

hi, i have the following error refining a neutron structure (no xrays data) with the latest builds (dev and official): it used to work perfectly and now it says: tried many things with my pdb yet to no avail. even archived runs do not work anymore. ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS work free delta data restr 19.38 23.49 4.11 1.665 13.405 32.138 0.039 Traceback (most recent call last): File "/usr/local/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/command_line.py", line 162, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/driver.py", line 1532, in run call_back_handler = call_back_handler).result File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/strategies.py", line 201, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 117, in __init__ self.call(self.adp, "ADP refinement (reciprocal space)") File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 143, in call func(prefix = prefix) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 396, in adp log = self.log) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/adp.py", line 62, in run h_params = h_params) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 232, in __init__ nproc = nproc) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 337, in __init__ result = self.try_weight(weight, print_stats=True) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 427, in try_weight minimized = self.minimize() File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 496, in minimize self.model.set_refine_individual_adp() File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/model.py", line 1523, in set_refine_individual_adp iselection = selection_iso.iselection()) RuntimeError: cctbx Internal Error: /home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/modules/cctbx_project/cctbx/xray/scatterer_flags.h(417): CCTBX_ASSERT(f.use_u_iso()) failure. any clue what is happening? thank you for your help, Maxime Cuypers

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Berkeley Server Downtime Cancelled
by Paul Adams 06 Nov '15

06 Nov '15

Dear Colleagues, I’m pleased to report that the scheduled power outage has been cancelled and will be rescheduled for a future weekend. Cheers, Paul -- Paul Adams Interim Division Director, Molecular Biophysics & Integrated Bioimaging, 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 ] --

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Trends In Initial Crystallization Screening
by Mustafa Koksal 06 Nov '15

06 Nov '15

Dear members of the crystallography community, I would like to assess the tendency/trend in our community to outsource initial crystallization screening experiments. Here, outsourcing refers to sending your protein/DNA/RNA sample to a service provider, who will set up crystallization experiments, take images of crystallization drops at various time points, make images available to you, and, if you require, send you the plate to retrieve any crystals. To do assessment, I prepared a short-answer questionnaire, which contains 10 questions and should take less than 5 minutes to complete. I especially encourage the new PIs and young researchers to complete the questionnaire. Could you please fill out the questionnaire at the following link? https://tr.surveymonkey.com/r/BVNCPVV In case you are unwilling to click links in e-mails, I also included the questions here. Please reply with answers in private to: mustafakoksal(a)iyte.edu.tr Thank you very much for your contribution. Mustafa Questionnaire: 1. Have you outsourced initial crystallization screening experiments in any of your projects before? Yes No 2. If you did, what format and type of experiment you used (choose all that apply)? 96 well/plate 384 well/plate 1536 well/plate Sitting Drop Hanging Drop Microbatch Other (please specify) 3. If you did, what price did you pay per 96-conditions? 4. If you did not, what prevented you from outsourcing (choose all that apply)? It is costly Shipping a sample is hard Privacy concerns I prefer to do it in my lab I do not think it is advantageous I do not have enough sample Other (please specify) 5. Would you be interested in outsourcing initial crystallization screening experiments in future? Yes No 6. If you are interested, which method would you prefer (choose all that apply)? Sitting Drop Hanging Drop Microbatch Counter Diffusion Other (please specify) 7. If you are interested, up to what price would you be willing to pay per 96-conditions? $1 $2 $3 $4 $5 $6 $8 $10 $12 $15 $20 $25 $30 $50 8. If you are interested, what would be your minimum-maximum throughput (# of 96-condition experiments per month)? Note: a 1536-condition experiment is 16 x 96-condition experiments? 1 - 2 2 - 4 4 - 8 8 - 12 12 - 16 16 - 32 32 - 64 32 - 128 More than 128 9. How much sample would you be willing to sacrifice per screening 96-conditions (please specify in micrometers)? 10. Would you consider international shipping of your sample for outsourcing? Do you have any other comments? End of Questions -- Mustafa Koksal Postdoctoral Fellow University of Pennsylvania Department of Chemistry Roy and Diana Vagelos Laboratories Office: 2090 IAST Office Phone: (215) 898-2227 Mobile Phone: (267) 319-6443 Mail Address: 231 S. 34th St, Philadelphia 19104, USA --

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(no subject)
by Nigel Moriarty 05 Nov '15

05 Nov '15

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2016 issue is 18 December 2015 (with some leeway if you are still working on the text, especially as it can be polished over the break). The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. 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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ERRASER Updates
by Caleb Geniesse 05 Nov '15

05 Nov '15

Hi all, My name is Caleb and I am a research programmer in the Das lab who has taken over the maintenance of ERRASER. ERRASER (Enumerative Real-space Refinment ASsisted by Electron-density under Rosetta) is an application for improving RNA crystal structures based on Rosetta and Phenix. While benchmarking the current state of ERRASER, I uncovered some discrepancies in the clash scores and outliers of the resulting models (compared to the original benchmark in Chou FC et al., 2012). Accordingly, I've made some updates to the ERRASER code within Rosetta addressing these issues. *To avoid possible inaccuracies introduced by these bugs,* *all PHENIX-ERRASER users should download/install a weekly build of Rosetta 2015.35 (released Sept. 24, 2015) or later.* For more extensive PHENIX-ERRASER documentation and installation notes, please see: https://www.phenix-online.org/documentation/reference/erraser.html. Please let me know if you have any questions! All the best, Caleb Geniesse

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Berkeley Server Downtime
by Paul Adams 04 Nov '15

04 Nov '15

Dear Colleagues, as part of routine maintenance at our new building there will be a power outage to the Computational Crystallography Initiative server room. As a result several structural biology web services will be offline for a short while. These include: - 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/) The servers will be shutdown at 5pm Pacific time on Friday November 6th. Services should resume by the evening of Sunday November 8th at the latest. During the downtime bug reports and emails requesting help should be queued and received by us once the servers are back online. We greatly appreciate your understanding, and hope that this doesn’t present too much of an inconvenience. Cheers, Paul -- Paul Adams Interim Division Director, Molecular Biophysics & Integrated Bioimaging, 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 ] --

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Modifying restraints for a single glutamate
by Eric Johnson 04 Nov '15

04 Nov '15

Is it possible to modify the restraints for single glutamic acid residue that forms an ester bond with a heme? Formation of the ester bond should lengthen the C - O bond length. Normal restraints distort the geometry of the covalent adduct. Thanks, Eric Johnson

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Installation problem
by Ricardo Padua 03 Nov '15

03 Nov '15

Hi all, I have the error below when trying to install Phenix in Centos6 running in a virtual machine (VMware workstation 12) in Win7 Enterprise. I've searched for this error in ccp4bb, phenixbb and google but nothing came out. Can anyone enlighten me? Best ========================================================================== Phenix Installation version: 1.10.1-2155 machine type: intel-linux-2.6-x86_64 OS version: 2.6.32-573.el6.x86_64 destination: /usr/local/phenix-1.10.1-2155 # of processors: 8 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install() File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 185, in install self.install_from_binary() File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary self.reconfigure(log=log) File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-1.10.1-2155/base/bin/python /usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 127 Ricardo

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Formylmethionine
by mohamed noor 31 Oct '15

31 Oct '15

Dear all I am refining my model (1.8 A) where there is an excess density even after fitting the N-terminal Met. From Edman degradation data, the Met is actually an FME. However, only the density in one chain allows me to confidently place FME, and not for the other chain. The first chain also has a good enough density for me to be able to build all the residues in the protein except the last two at the C-terminus. So, do I model FME for both chains? Thanks. Mohamed

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a question on rotamer restraints
by Smith Lee 31 Oct '15

31 Oct '15

Dear All, When I run phenix.real_space_refine, in the rotamer restraints step I meet the following error message: RuntimeError: rotatable bond atoms CG1-CD (as defined by tardy-tree): no match in rotamer-info.tor_ids Will you please let me know how to overcome this error? Best regards. Smith

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CaBLAM validate - alternative output?
by Oliver Clarke 28 Oct '15

28 Oct '15

Hi all, I really like the idea of CaBLAM validate for model validation at low resolution based on the CA and backbone geometry, but the output is a little limiting - either text or kinemage right now. Would it be possible to create an output format that can easily be visualized (and turned into figures) in chimera, pymol or coot? Maybe a modified version of the input pdb with the CA/peptide outlier status mapped to the B-factor and occupancy columns? Cheers, Oliver.

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Restraining/constraining partial occupancy waters
by David Briggs 27 Oct '15

27 Oct '15

Hi PhenixBB. I have a very minor problem with partial occupancy waters moving out of density during refinement I have 2 structures, one apo structure (~1.3Å), one ligand bound (~1.5Å). The ligand binding site contains a Calcium ion. In the apo form there are 2 waters co-ordinating this Calcium. In the ligand bound form, these waters are replaced by oxygen atoms within the ligand. However, the ligand is only at 0.5 Occupancy as part of the ligand lies on a crystallographic two-fold axis. The ligand itself refines well with occupancy fixed at 0.5, and the Bs are sensible. In the 50% of the molecules which don't co-ordinate ligand, two waters must co-ordinate the calcium ion, and in keeping with this, we see that the electron density around these positions is greater than would be expected for the 50% occupancy ligand. So I added 2 0.5 occupancy waters to the model at these positions. However, when I run phenix.refine (refining XYZ, real space, occupancy, and individual Bs (isotropic for the ligand & waters - for the protein I use anisotropic Bs) these two 'ghost waters' move out of the electron density and their Bs increase massively. *My questions are:* Is there any way to restrain these waters to their apo positions? Is this the correct approach? I had initially thought that reference model restraints might be useful here, but if I understand correctly, reference model restraints cannot be applied to waters - Is this correct? If I cannot restrain the waters to the apo positions, would I be justified in fixing (constraining) them? This seems a little extreme and I am loath to do it, but given the isomorphous apo structure, I do have evidence that in the absence of ligand waters do take up these positions. Can anyone help? Cheers, Dave [image: David Briggs on about.me] David Briggs about.me/david_briggs <http://about.me/david_briggs>

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2nd International Conference on Image Analysis in Three-dimensional Cryo-EM, March 30-April 2 2016
by Cathy Lawson 24 Oct '15

24 Oct '15

Dear Crystallography List Members, I'm forwarding info about this upcoming conference on image analysis in 3D cryoEM on behalf of the organizers. [Also, while I have your attention, a reminder to participate in the ongoing EMDataBank map and model challenges, see http://challenges.emdatabank.org.] <http://challenges.emdatabank.org.]> > We are pleased to announce the 2nd International Conference on Image Analysis in Three-dimensional Cryo-EM, to be held at Granlibakken Conference Center, Lake Tahoe, California from March 30 to April 2, 2016 (http://ncmi.bcm.edu/cryoemsoftware-2016). The 2016 Symposium builds on our very successful previous meeting on the same theme in 2014. > The goal of the Symposium is to discuss state of the art image analysis approaches to tackle challenging biological problems and to identify current limitations and remaining problems in the field as currently practiced. The goal will be for developers in this area, both established as well as students/postdocs to discuss the detailed algorithms and methodologies in this field in greater technical detail than is possible at more general meetings like the GRC. The central premise is that gaining a comprehensive and quantitative understanding of highly sophisticated machines, complexes, and organelles of the cell requires the active, timely and coordinated development of complementary image analysis and data mining algorithm and approaches. We have recruited an outstanding panel of speakers (current agenda provided in the web site). > > > Sessions: > > * Handling Compositional and Conformational Variability > > * High Resolution Subtomogram Averaging and Related Techniques > > * High Resolution Single Particle Analysis > > * Resolution Assessment, Model and Map Validation > > * Data Storage Roundtable > > * Poster Talks > > All session will focus on interactive discussions with plenty of time for questions. We will also have a poster session, and selected posters will be invited to give short-format talks. The early registration deadline for this workshop ends in Jan 2016. Registration details can be found at http://ncmi.bcm.edu/cryoem-software-2016. > > > Dorit Hanein, CHAIR & Steven Ludtke, Co-CHAIR > > ORGANIZING COMMITTEE > > Wah Chiu, Ed Egelman, Ben Hankamer, Masahide Kikkawa, David Mastronade, Pawel Penczek, Henning Stahlberg, Fei Sun, Niels Volkmann >

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Raw data.....
by Jrh 24 Oct '15

24 Oct '15

Good morning Tim, Overnight thoughts: Another aspect that seems to me to be accelerating now is the use of the diffuse scattering in MX structure AND dynamics analysis. There are several really nice papers in the last year. I post this on the Phenixbb because the drive forward on this is linked to Phenix. My point obviously is that this involves the whole diffraction pattern. I recognise that raw diffraction data measured for 'conventional crystal structure analysis', to use a term, may not be ideal but nevertheless these papers show that analysis is developing and so, at the Beamline, if diffuse scattering is evident it seems to me not so burdensome to add a data sweep with stronger exposures and a smaller beam (ie to minimising obscuring the diffuse by the Bragg). Also, just to mention, to add to my last message to you, I could mention specifically the very important initiative taken by Wladek Minor at Virginia within the US Big Data new funding. He already has a portal to 2800 raw data sets. At Utrecht Loes Kroon Batenburg and Toine Schreurs have shown what can be done with personal weblinks to raw data these last three years. And of course the US Structural Genomics centres pioneered much of this too. Greetings, John Emeritus Prof John R Helliwell DSc_Physics FInstP FRSC FRSB Fellow of the ACA Emeritus Member of the British Biochemical Society School of Chemistry, University of Manchester, M13 9PL, UK.

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