- phenixbb - phenix-online.org

mmCIF file must contain at least one data block
by Ursula Schulze-Gahmen 18 Dec '15

18 Dec '15

I am getting this thie error message mmCIF file must contain at least one data block when trying to run readyset or phenixrefine I cannot find anything wrong wqith my input files. What is the problem? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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remove old phenix version but keep the processed data
by Xiao Lei 17 Dec '15

17 Dec '15

Hi Phenixbb member, As I updated Phenix version on my Macbook pro (OS X 10.10), I found the newer version phenix did not automatically replace the old versions. Is there a way to remove the old version Phenix safely and only keep the newer version, but at the same time keep the processed data (data from phenix refine and xtriage)? Thanks ahead. Xiao

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ML with Twinning?
by Keller, Jacob 16 Dec '15

16 Dec '15

Is Phenix able yet to use the ML target function with twinned data? Is it in the works? All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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differences in refinement stats between phenix-dev-2219 and -1.9-1692
by Ezequiel Noguera 16 Dec '15

16 Dec '15

Thank you very much, Pavel. I don't save H's when I modify the model in coot (the input PDB file that I sent you was the output from coot). I did the refinement again, now in version 2247, without NCS. I got the same results, higher R factors and RMS deviations for the newer version. I got better results when I used "update waters" (both in Rfactors and RMS). Below, I list the statistics for refinement without updating waters. Significant differences remain. Could it be any difference in settings of default parameters between versions? version: dev-2247 Start: r_work = 0.1687 r_free = 0.2011 bonds = 0.046 angles = 1.321 Final: r_work = 0.1753 r_free = 0.2040 bonds = 0.030 angles = 0.593 version: 1.9-1692 Start: r_work = 0.1651 r_free = 0.2018 bonds = 0.013 angles = 1.409 Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011 angles = 1.321

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Re: [phenixbb] -differences in refinement stats between phenix-dev-2219 and -1.9-1692
by Pavel Afonine 13 Dec '15

13 Dec '15

Hi Ezequiel, just to make it clear: torsion-angle NCS, Optimize X-ray/stereo weight are *not* the default settings, therefore you did customize the refinement parameters. At this resolution (1.3A) you do not need to use NCS restraints. Also, you say you used "Automatically add H's" however the PDB file you sent me does not contain any H atoms. Furthermore, the PDB file header says H are present: REMARK MODEL CONTENT. REMARK ELEMENT ATOM RECORD COUNT OCCUPANCY SUM REMARK C 1275 1047.00 *REMARK H 2029 1649.00 * REMARK O 559 488.50 REMARK N 315 263.00 REMARK S 6 6.00 REMARK Cu 4 2.89 REMARK TOTAL 4188 3456.39 So overall this make an impression that something has gone wrong. Way forward: 1) Take the file you sent me; 2) Add H atoms: phenix.reduce model_no_h.pdb > model_with_h.pdb 3) Use new file with H atoms added to run refinement. The only setting different from defaults should be "Optimize X-ray/stereo weight". Perhaps you can also enable automated water update. I just did all this myself and got nicely refined model with Final: r_work = 0.1624 r_free = 0.1939 bonds = 0.010 angles = 1.030 Corresponding PDB and MTZ are sent in a separate email that goes to you only (off mailing list). Pavel On 12/6/15 07:59, Ezequiel Noguera wrote: > Hi Pavel, thank you very much for your help. I attach the data. I > didn´t customize parameters. The refinement stategy of the last job > was: XYZ coords, Real-space, Individual B-factors, torsion-angle NCS, > Optimize X-ray/stereo wght and X-ray/ADP wght, Automatically add H's > and correct N/Q/H errors. > > > Hi Ezequiel, > > deviations are not unexpected in general but not that large as you > report, so I wonder what's going on.. Could you please send me input > data and model files, as well as any ligand files you used. If you > customized some parameters, telling what were those would be helpful too. > > Please send all files off-list to my email directly. > > Thanks, > Pavel > > >> Hello, I'm working in a refinement that I started some time ago. I >> noted that repeating the same refinement task using a newer version >> of phenix, the refinement statistics Before and After refinement are >> different from values of the old version (I used "restore job" from >> the Job history to repeat the same task in the two versions installed >> in the same PC). Any explanation? I'm worried about the rms >> deviation. Thanks in advance. >> >> new version: >> R-work: start=0.1697, final=0.1761 >> R-free: start=0.2011, final=0.2053 >> Bonds: start=0.046, final=0.029 >> Angles: start=1.321, final= 0.631 >> >> old version: >> R-work: start=0.1651, final=0.1657 >> R-free: start=0.2018, final=0.2009 >> Bonds: start=0.013, final=0.013 >> Angles: start=1.409, final= 1.411

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autosolve density modification question
by Scott Horowitz 10 Dec '15

10 Dec '15

Hi, a quick question: if when running autosolve on SAD data, if I set the parameter build = false, will that disable all model building, including any model building that would be a part of the density modification process? I'm especially curious about the case if build = false, but mask_type = histograms. I am currently assuming that the histogram matching does not use model building as part of it, and would like to know if this interpretation is correct. Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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Phenix dev-2247 fails to start
by Chen Zhao 07 Dec '15

07 Dec '15

Dear developers, I am now having some troubles initiating the most updated nightly built dev-2247. I have to use this version because it is supposed to have a bug fixed based on my bug report in November. My machine is running Debian 7 with kernel version 3.2.0-4-amd64. And the pheinx installation file I downloaded is the 64 bit linux version for CentOS 5. The symptom is that after I called phenix from a terminal window, there is an error message saying "local 'en_GB' cannot be set" (which is always the case and which does not seem to matter). After that, phenix GUI did not start at all, but ps command shows two python2.7 processes running. Running phenix from command line seems to work fine. Before switching to this version I was running the stable version 1.10.1-2155, and have no problem. Is there any simple fix? If not, I will probably just stick to the command line version for the moment. Thanks a lot, Chen

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differences in refinement stats between phenix-dev-2219 and -1.9-1692
by Ezequiel Noguera 06 Dec '15

06 Dec '15

Hello, I'm working in a refinement that I started some time ago. I noted that repeating the same refinement task using a newer version of phenix, the refinement statistics Before and After refinement are different from values of the old version (I used "restore job" from the Job history to repeat the same task in the two versions installed in the same PC). Any explanation? I'm worried about the rms deviation. Thanks in advance. new version:R-work: start=0.1697, final=0.1761R-free: start=0.2011, final=0.2053Bonds: start=0.046, final=0.029Angles: start=1.321, final= 0.631 old version:R-work: start=0.1651, final=0.1657R-free: start=0.2018, final=0.2009Bonds: start=0.013, final=0.013Angles: start=1.409, final= 1.411

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Trends In Initial Crystallization Screening (Reminder)
by Mustafa Koksal 30 Nov '15

30 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. 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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lose the jobs history when update/install phenix new version
by caio reis 26 Nov '15

26 Nov '15

Hi, my name is Caio, I do Ph.D in biomolecular physics at University of Sao Paulo, Brazil, and I am writing to know if anyone knows if I'm gonna lose my job history in Phenix, if I update my version to the newest one. I work with many proteins and structures (MR, autobuild, phenix.refine, etc), so as I can better manage my jobs and archives using and consulting my job history in Phenix interface. I also want to know, if I can use de openmp without having to compile phenix again...because I don't want to lose my job history (in case it can be lost when Phenix is updated/installed again/compiled). Thank you in advance.

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RapiData 2016
by Smith, Clyde 26 Nov '15

26 Nov '15

The 2016 RapiData Course on Data Collection and Structure Solution will take place at the Stanford Synchrotron Radiation Lightsource (SSRL) from April 24-29 2016. The aim of the course is to educate and train scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on sample preparation, data collection and reduction, phasing and complementary methods. For a more complete description of the course goals and format see http://smb.slac.stanford.edu/rapidata-2016/about.html The deadline for applications is January 4th 2016. To apply follow this link: http://smb.slac.stanford.edu/rapidata-2016/registration.html Several scholarships are available from the International Union of Crystallography to cover partial travel and subsistence for Latin-American students, postdocs and junior faculty. Additional funds may be also be awarded to other participants without restrictions on a per need basis. The instructions to apply for these scholarships can be found in the application page. RapiData 2016 will take place immediately after Crystallization: Focus on Micro and Nano Crystals and High Throughput Methods (April 19-22 2016), also at SSRL. Together, the two courses will cover most aspects of crystal structure determination and we encourage participation in both. For information about the Crystallization course see http://smb.slac.stanford.edu/news/cryst_focus_on/cryst_focus_on_2016/ or contact the organizers: Vivian Stojanoff (vivian.stojanoff(a)gmail.com) or Silvia Russi (srussi(a)slac.stanford.edu) The Organizing Committee of RapiData 2016 shall observe the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist which would prevent the participation of bona fide scientists. Ana Gonzalez and Clyde Smith

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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 19 Nov '15

19 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 19 Nov '15

19 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 17 Nov '15

17 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 16 Nov '15

16 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 13 Nov '15

13 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 12 Nov '15

12 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 05 Nov '15

05 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 05 Nov '15

05 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 04 Nov '15

04 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

2 1

Formylmethionine
by mohamed noor 01 Nov '15

01 Nov '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

4 4

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.

1 0

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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Positions at the NKI - Amsterdam
by Anastassis Perrakis 24 Oct '15

24 Oct '15

Dear all, Three positions are available in the group of Anastassis (Tassos) Perrakis at the Netherlands Cancer Institute. We are looking for: 1. A post-doctoral scientist to work on the European Horizon2020 project iNEXT (http://www.inext-eu.org <http://www.inext-eu.org/>), on collaborative research activities aiming to develop, establish and apply biophysical methodologies for enabling ligand and fragment-based inhibitor discovery (in collaboration with the teams of Jose-Antonio Marquez at EMBL-Grenoble and Frank von Delft at Diamond) and for studying macromolecular interactions in vitro and in vivo (in collaboration with the group of Jan Ellenberg at Heidelberg). The research theme for applying and testing these technologies will be in the area of mitotic kinases and in particular on the study of their regulatory/localisation domains (see Hiruma et al, Science 2015 and Nijenhuis et al, J Cell Biol 2013). 2. A scientific programmer to help further develop our ProteinCCD Java application (http://xtal.nki.nl/ccd <http://xtal.nki.nl/ccd>, Mooij et al, Nucleic Acids Res 2009) and the PDB_REDO web server (http://xtal.nki.nl/pdb_redo <http://xtal.nki.nl/pdb_redo>; Joosten et al, IUCrJ 2014), and deploy them in virtual research environments and cloud-based systems, within the WestLife Horizon2020 e-Infrastructures project. The candidate should also help maintain and further develop the (C++) code behind the PDB_REDO rebuilding applications (Joosten et al, Bioinformatics 2011; Joosten et al Acta Crystallogr D 2012). 3. A scientist with a background on Cheminformatics or (Structural) Bioinformatics, to develop further the PDB_REDO pipeline (see above) to handle automated ligand and fragment placement, refinement and validation pipelines, and to pro-actively participate in the scientific and technical development of PDB_REDO. The Netherlands Cancer Institute (http://www.nki.nl <http://www.nki.nl/>) is a center of excellence with a high standard of biological research and an interactive international atmosphere. It is located in Amsterdam, with all its cultural amenities, close to the Schiphol airport. The group of Tassos Perrakis, which also hosts the team of Robbie Joosten working in the PDB_REDO project, is closely associated with the neighbouring group of Titia Sixma. Both groups have an interest in structural studies coupled to functional analysis, combined with activities in method development for structural biology. Our department also hosts the "Protein Facility" with equipment that includes high throughput crystallisation and crystal visualisation robotics, an X-ray facility, Biacore surface plasmon resonance, isothermal titration calorimetry (ITC), microscale thermophoresis, thermal shift analysis, multi-angle laser light scattering (MALLS), versatile systems for fluorescence based equilibrium and transient state kinetics analysis (a versatile plate reader and stopped-flow), and operational facilities for E.coli, insect cells and mammalian cells based protein expression and purification. Computational facilities are locally available. The groups also share equipment and office space, and together with the group of Thijn Brummelkamp create a lively and highly interactive research environment. Applicants should write an e-mail including a CV, a short letter of motivation and names and addresses of scientists willing to provide a reference to a.perrakis(a)nki.nl <mailto:[email protected]>. Tassos Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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Re: [phenixbb] [ccp4bb] Tantalum anomalous signal of a low-resolution SAD dataset with lattice-translocation disorder
by Christian Roth 21 Oct '15

21 Oct '15

Hi, difficult to say why it doesn't work. Generally as mentioned already automatic model buildíng will most likely fail at this resolution. However why do you think your sites are wrong? Ta-cluster are regular compounds and the sites should fit with the geometry of the cluster at least. Anyway, molecular replacement using anomalous differences and the cluster as search model might work in that case as well, if direct experimental phasing fails. Cheers Christian Am 21.10.2015 um 05:19 schrieb Shun Liu: > Dear CCP4 colleagues, > > We are working on a Ta6Br14 cluster-SAD dataset (4.3 angstroms) with lattice-translocation disorder (with a total Rmerge of 0.16). Both SHELXC and Xtriage gave the similar positive result about the anomalous signal (See below). > > ------------------------------------------------------------------------------------------------- > Resl. Inf. 9.58 7.61 6.65 6.04 5.61 5.27 5.01 4.79 4.61 4.45 4.31 > N(data) 1427 1410 1410 1409 1385 1452 1367 1399 1367 1395 1385 > <I/sig> 76.3 52.1 26.7 13.7 8.7 6.1 5.1 5.0 3.9 2.7 1.8 > %Complete 98.8 99.9 100.0 99.9 100.0 100.0 100.0 99.9 99.7 99.6 95.8 > <d"/sig> 11.67 9.67 6.12 3.73 2.50 1.59 1.21 0.99 0.84 0.79 0.68 > ------------------------------------------------------------------------------------------------ > unused: - 49.7669 [ 0/29 ] > bin 1: 49.7669 - 9.2629 [3086/3100] 0.8212 > bin 2: 9.2629 - 7.3599 [3031/3031] 0.7689 > bin 3: 7.3599 - 6.4318 [3073/3073] 0.5380 > bin 4: 6.4318 - 5.8447 [3071/3075] 0.2933 > bin 5: 5.8447 - 5.4263 [3054/3054] 0.1230 > bin 6: 5.4263 - 5.1067 [3070/3071] 0.0363 > bin 7: 5.1067 - 4.8512 [3038/3039] 0.0126 > bin 8: 4.8512 - 4.6402 [3028/3048] 0.0074 > bin 9: 4.6402 - 4.4617 [2955/3037] 0.0021 > bin 10: 4.4617 - 4.3078 [2730/3059] 0.0000 > unused: 4.3078 - [ 0/0 ] > -------------------------------------------------------------------------------------------------- > The Tantalum sites and the initial map seem ambiguous, with which automatic model-building failed. > I am wondering whether the lattice-translocation disorder of the dataset impacts the reliability of the anomalous signal, tantalum sites and the initial map. If it does, how can we decrease its impact? If it doesn't, is it possible to find the accurate Ta sites and generate an interpretable map suitable for model-building with this dataset? (After all, it has been reported that Ta sites can be found at 6A resolution.) > > Any suggestion and comment will be highly appreciated! > > Best, > Shun >

1 0

Tantalum anomalous signal of a low-resolution SAD dataset with lattice-translocation disorder
by Shun Liu 21 Oct '15

21 Oct '15

Dear Phenix colleagues, We are working on a Ta6Br14 cluster-SAD dataset (4.3 angstroms) with lattice-translocation disorder (with a total Rmerge of 0.16). Both SHELXC and Xtriage gave the similar positive result about the anomalous signal (See below). ------------------------------------------------------------------------------------------------- Resl. Inf. 9.58 7.61 6.65 6.04 5.61 5.27 5.01 4.79 4.61 4.45 4.31 N(data) 1427 1410 1410 1409 1385 1452 1367 1399 1367 1395 1385 <I/sig> 76.3 52.1 26.7 13.7 8.7 6.1 5.1 5.0 3.9 2.7 1.8 %Complete 98.8 99.9 100.0 99.9 100.0 100.0 100.0 99.9 99.7 99.6 95.8 <d"/sig> 11.67 9.67 6.12 3.73 2.50 1.59 1.21 0.99 0.84 0.79 0.68 ------------------------------------------------------------------------------------------------ unused: - 49.7669 [ 0/29 ] bin 1: 49.7669 - 9.2629 [3086/3100] 0.8212 bin 2: 9.2629 - 7.3599 [3031/3031] 0.7689 bin 3: 7.3599 - 6.4318 [3073/3073] 0.5380 bin 4: 6.4318 - 5.8447 [3071/3075] 0.2933 bin 5: 5.8447 - 5.4263 [3054/3054] 0.1230 bin 6: 5.4263 - 5.1067 [3070/3071] 0.0363 bin 7: 5.1067 - 4.8512 [3038/3039] 0.0126 bin 8: 4.8512 - 4.6402 [3028/3048] 0.0074 bin 9: 4.6402 - 4.4617 [2955/3037] 0.0021 bin 10: 4.4617 - 4.3078 [2730/3059] 0.0000 unused: 4.3078 - [ 0/0 ] -------------------------------------------------------------------------------------------------- However, the tantalum sites we found and the initial map seem ambiguous, with which automatic model-building failed. I am wondering whether the lattice-translocation disorder of the dataset impacts the reliability of the anomalous signal, tantalum sites and the initial map. If it does, how can we decrease its impact? If it doesn't, is it possible to find the accurate Ta sites and generate an interpretable map suitable for model-building with this dataset? (After all, it has been reported that Ta sites can be found at 6A resolution.) Any suggestion and comment will be highly appreciated! Best, Shun

5 4

Queueing system commands for parallel Phenix/Rosetta jobs
by Yonglin Hu 21 Oct '15

21 Oct '15

Hello All, We have setup a cluster with several executing nodes and we would like to run our Phenix/Rosetta molecular replacement jobs on the cluster. In the Job Control screen, I put "qsub -q all.q -o $HOME/log1 -e $HOME/log1" as command to use to run multiple jobs. But I am not sure what I should use for "queueing system commands". We are using SGE as the queueing system on our cluster. Any help would be greatly appreciated! Yonglin Hu

2 1

on cif file
by Smith Lee 20 Oct '15

20 Oct '15

Dear All, My protein containing the ADP-AlF3-Mg. In the protein ADP-AlF3-Mg should be very close to each other so that they look like the ATP binding with the Mg. I have prepared the ADP.cif and the ALF3.cif, and have merged the 2 cif files with elbow.join_cif_files. However when I run phenix.real_space_refine with the merged cif file, there was a tendency that ADP, ALF3 and Mg separated from each other based on the map density, which seems did not comply with the prior knowledge on that ADP-AlF3-Mg should occupies the space of ATP-MG. Will you please advice how to have ADP-AlF3-Mg occupies the space of ATP-MG rather than separated by the refine? Best regards. Smith

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Re: [phenixbb] How to convert XDS_ASCII.HKL to MTZ
by Whitley, Matthew J 19 Oct '15

19 Oct '15

Hi Murpholino, I’m not sure if your Phenix commands are correct, but you might try using the program that comes natively with XDS for converting between file formats. That program is XDSCONV. (As a side note, I think that some of the XDSCONV functions require CCP4 to be installed, so if you don’t have CCP4 installed you might need to stick to converting with Phenix.) You can find step by step instructions for generating an MTZ file from XDS output under the “Typical Use” heading here: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv More info about XDSCONV: http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xdsconv_parameter… Good luck! Matthew On Oct 19, 2015, at 12:16 PM, <phenixbb-request(a)phenix-online.org> <phenixbb-request(a)phenix-online.org> wrote: > > Message: 5 > Date: Mon, 19 Oct 2015 11:16:17 -0500 > From: Murpholino Peligro <murpholinox(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] How to convert XDS_ASCII.HKL to MTZ > Message-ID: > <CAMdBu0Uejh0k+Wih1KaF+c=FRJ3fKg+LhQrfuGhUs1tJ8x8HwQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Just want to be sure. > I want to generate the mtz file for refinement. The last step of XDS leaves > me with intensities and space group 89. So I need > > phenix.reflection_file_converter --generate-r-free-flags > --write-mtz-amplitudes --mtz_root_label=FOBS --mtz=d01.mtz > --change-to-space-group=96 XDS_ASCII.HKL > > Is this right? > > Thanks again >

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How to convert XDS_ASCII.HKL to MTZ
by Murpholino Peligro 19 Oct '15

19 Oct '15

Just want to be sure. I want to generate the mtz file for refinement. The last step of XDS leaves me with intensities and space group 89. So I need phenix.reflection_file_converter --generate-r-free-flags --write-mtz-amplitudes --mtz_root_label=FOBS --mtz=d01.mtz --change-to-space-group=96 XDS_ASCII.HKL Is this right? Thanks again

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refinement of coordinated ions
by Irina PROKHOROVA 18 Oct '15

18 Oct '15

Hello, I have many Osmium ions in my structure. They have 6 coordinated ammonium groups and I would like to refine the B-factors for them: one B-factor for Os in each residue and one B-factor for all 6 ammonium groups in each residue. For this I have chosen *group_adp with following syntax adp { group_adp_refinement_mode = one_adp_group_per_residue \ two_adp_groups_per_residue *group_selection group = chain O and element Os group = chain O and element N } I wanted to refine only B-factor for Osmiums in this refinement. To avoid the bias from previously refined values of B-factor I presetted B-factors for all Osmiums to 50. As a result I got the change of B-factors for all residues in the model to the same value (which probably means that all model was refined as one group) and R-free increased from 0.25 to 0.34. What should be the correct syntax for this refinement? Should I also refine ions coordinates for a good refinement of B-factors? Irina

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Fw: on phenix.real_space_refine
by Smith Lee 18 Oct '15

18 Oct '15

Dear Pavel, On Oct 9, 2015 I have e-mailed to you my experience with 1.9-1692 and version 1.10 (and 1.10.1) on phenix.real_space_refine. Today I just completed another protein phenix.real_space_refine. For the following comparison runs, the initial model same, the map same, all 5 macro_cycles default run. For version 1.10.1, the results were as following, Map CC (whole unit cell)： 0.672Map CC （around atoms）： 0.761rmsd （bonds): 0.01rmsd (angles): 1.55All-atom clahscore: 39.27Ramachandran outlier: 0.98%Ramachandran allowed: 12.71%Ramachandran favoured: 86.31%Rotamer outliers: 0.91%C-beta deviations: 0 For version 1.9-1692, the results were as following, Map CC (whole unit cell)： 0.645Map CC （around atoms）： 0.687rmsd （bonds): 0.0071rmsd (angles): 1.15All-atom clahscore:16.88Ramachandran outlier: 2.00%Ramachandran allowed: 6.23%Ramachandran favoured: 91.77%Rotamer outliers: 0.05%C-beta deviations: 0 For the version 1.10.1 phenix.real_space_refine, the most unacceptable was on the clashscore, the whole refine process seems did not care on the clashcore refine at all. I am looking forward to getting an explanation from you on the causes of the difference for phenix.real_space_refine for the 2 versions, and the possible strategy we can take to eliminate the difference to get the acceptable results. Best regards. Smith On Friday, October 9, 2015 12:52 AM, Smith Lee <smith_lee123(a)yahoo.com> wrote: Dear Pavel， As I have told you, I have tried phenix.real_space_refine for 2 protein with version 1.9-1692 and version 1.10 (and 1.10.1) for many times, with cif or without cif, with or without annealing. The general feedback was that the version 1.9-1692 was much much better for the final analysis of the PDB given at the end of the run of the phenix.real_space_refine. Especially for clashing score, version 1.9-1692 can gave acceptable results (below 20 or around 20), but the clashing score given by the above 2 new versions of phenix.real_space_refine was very high (around 50 or 100). For C-beta deviations, the output by 1.9-1692 was also much better Before I have tried the other nightly built versions of phenix.real_space_ refine between version 1.9-1692 and version 1.10 (and 1.10.1) , all I gave acceptable output analysis (something like the Molprobity analysis at the end of the run). Thus may I ask the reason you have version 1.10 (and 1.10.1) phenix.real_space_refine was because you have realized that the result given by version 1.9-1692 was too satisfactory? One direct concern of me was that you have recommended not to use the old version phenix. But I cannot get the satisfactory result with the new version phenix.real_space_refine. The other concern of me was that, I have noticed there were publications In Nature and Science which wrote they use phenix.real_space_refine to got the results in Nature and Science. The Phenix they used should be the versions earlier than version 1.10. Considering what I mentioned above, the Nature and Science results may be not so correct, if new version of phenix was considered as much better than the old version. Thus am I the only user who communicated with you on the high clashing score given by the new version of phenix？Can you give some comments on what I mentioned above on the high clashing score given by the new version phenix.real_spac_refine? Best regards. Smith

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Visualise NCS operators
by Morris, Kyle 16 Oct '15

16 Oct '15

Dear Phenix community, After running $ phenix.find_ncs what would be the best way to visualise the operators found and detailed in the *.ncs_spec file superimposed on the map used in the search? Thanks for your help! Best wishes, Kyle

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Postdoctoral Position in Structural Biology at ICR, London, UK
by Sebastian Guettler 16 Oct '15

16 Oct '15

Dear PHENIX Community, Please see below for details of a postdoctoral position in our team. Best wishes, Sebastian Guettler Postdoctoral Position in Protein Biochemistry / Structural Biology / Electron Microscopy We seek to appoint a Postdoctoral Training Fellow to the research team led by Dr Sebastian Guettler in the Divisions of Structural and Cancer Biology at The Institute of Cancer Research in London, UK. The position is funded by Cancer Research UK. The successful applicant will undertake biochemical, structural and functional studies on members of the ADP-ribosyltransferase (or “PARP”) family of proteins and macromolecular complexes containing PARPs. Our goal is to gain insight into the control and cellular roles of these enzymes with a specific interest in ADP-ribosyltransferase-dependent signalling processes linked to cancer. Applicants should possess a PhD in a biological science such as biochemistry or molecular biology. Experience with recombinant DNA techniques, high-quality protein expression and purification, protein characterisation, structural biology, as well as some experience in structural electron microscopy are essential. Appointment will be on a Fixed Term Contract for 3 years in the first instance. The full salary scale is in the range from £29,517 to £42,187 p.a. inclusive. Starting salary will be based on previous postdoctoral experience. To apply, please submit your CV and covering letter online. Please include the names and addresses of two referees. For further details and instructions on how to apply, please refer to our online vacancy and recruitment site at http://www.icr.ac.uk/jobsearch, quoting job reference number 1494999 for this position. While applications need to be placed via our online system, informal inquiries can be sent to Dr Sebastian Guettler at sebastian.guettler(a)icr.ac.uk<mailto:[email protected]>. Please do not submit your formal application by email! Summary: Closing Date of vacancy: 31 Oct 2015 Type of Contract: Fixed Term, Postdoctoral Training Fellow Length of Contract: 3 years Salary Range: £29,517 p.a - £42,187 p.a. inclusive (full salary scale) Work Location: London Research in the Divisions of Structural and Cancer Biology focuses on the functional, biochemical, and structural characterisation of cellular processes relevant to cancer and cancer therapy. The Division of Structural Biology has managed state-of-the-art facilities for protein crystallography (crystallisation robots, Bruker Microstar and CCD detector), cryo-electron microscopy (FEI Tecnai F20 and T12), and protein production with expertise in multi-subunit expression (insect cell, yeast and bacterial expression, including a 60-litre fermentor). The Division is also well-equipped with instrumentation for biophysical analysis (e.g. ITC, fluorescence, multi-angle light scattering). The Division of Cancer Biology provides a state-of-the-art infrastructure for mammalian cell culture, imaging, mammalian genetics, chemical biology and proteomics. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Local B-factor for a ligand
by Karchevskaya, Anastasia 15 Oct '15

15 Oct '15

Dear Phenix users, Can you, please, clarify, how can I get local B factor for the residues around the ligand. 1) I saw this reply in an archive: http://www.phenix-online.org/pipermail/phenixbb/2011-March/016819.html 2) But it doesn't suit me, because, for instance in this case: http://www.rcsb.org/pdb/explore/explore.do?structureId=4RUP the interacting residues are: http://www.rcsb.org/pdb/images/H97:4RUP_psv_v_500.png 302, 265, 175, 423 can be fitted into a sequence, but I don't need everything in between them 3) There is also another option: http://www.ebi.ac.uk/thornton-srv/databases/PDBsum/ru/4rup/grow.out I can extract interactions from here and make a request to Phenix. If so, can I request the b-factor just for one exact amino acid? Thank you in advance, Anastasia

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peaks and holes for a difference map
by Murpholino Peligro 15 Oct '15

15 Oct '15

Hi. Is there a way to load a pdb and a difference map (ccp4 format) in phenix, command line is better, and then get something like the "validate->difference map peak" analysis (as in coot)..? Thanks

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MRC map as molecular replacement model
by Acharya, Priyamvada (NIH/VRC) [C] 15 Oct '15

15 Oct '15

Hi all, I want to use an MRC map obtained by low resolution EM reconstruction, as molecular replacement model in Phaser. I serached the phenixbb archives and learned that I should us phenix.map_to_structure_factors to convert the map file to mtz so it can be input into Phaser. When I do that I get an error "Sorry: Map must have origin at (0,0,0): recenter the map and try again". I have two questions? 1) What tool should I use to recenter the map and 2) Is there a better way to do this? Thanks in advance for your replies. Best regards, Priyamvada

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