- phenixbb - phenix-online.org

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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