- phenixbb - phenix-online.org

how not to refine residue X?
by Murpholino Peligro 19 Jan '16

19 Jan '16

Hi. How to tell phenix.refine to leave residue X during refinement? I already tried in the .eff >>> strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous sites { individual = not (chain A and resid 97) <<< But resid 97 is being moved to another position. I am using phenix.refine_1.10.1-2155 Thanks

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phenix.sort_heteroatoms produced duplicated residue number
by luzuok 12 Jan '16

12 Jan '16

Dear phenixbb, When I use phenix.sort_hetero_atoms to resort my pdb, there are duplicated residue number of water and aa in the output pdb. Is this a bug? As there are many number gaps water, how can I fix it? Best wishes! Lu -- 卢作焜南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University

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pdbtools model_statistics: average B-factors
by wtempel 11 Jan '16

11 Jan '16

Hello, are the mean B-factors in the "ADP statistics" table occupancy-weighted, or perhaps weighted in any other way? If so, please could you provide the formula. Thank you. Wolfram Tempel

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phenix.refine with reference model
by Falk, Sebastian 08 Jan '16

08 Jan '16

Hi! I am currently building a 3.3 A structure of a large protein. I do have a reference model at much better resolution that has 58% sequence identity and 77% similarity. The structures are quite similar, there are only a few regions with insertions. However, phenix.refine does ‘accept’ the reference model and thus creates no torsion restraints. I also tried to run ProSmart in CCP4 but there the cut-off for the reference model is 75% sequence identity. I could not find any threshold for phenix.refine though. I am happy for any suggestion or tip how to include the reference model even though the sequence identity is not as high. Thank a lot. Sebastian Sebastian Falk Max-Planck-Institute for Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany sfalk(a)biochem.mpg.de

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Generate sequence files of homodimer protein or double strand DNA for phaser MR
by Alex Lee 08 Jan '16

08 Jan '16

Dear Phenixbb members, I am using Phaser MR for solving a homodimer DNA binding protein with dsDNA complex structure. I'd like to use sequence file rather then molecular weight in the component definition of ASU. As there are solved homodimer protein structures (amino acid identity 100%) on PDB, I can download seq file (fasta form) from PDB webpage, but the seq file is only for one protein chain. I also tried online tools like "make sequence from PDB file" (http://swift.cmbi.ru.nl/servers/html/soupir.html), when I put the protein dimer bound to dsDNA pdb into the online tool, the outtput pir sequence file only shows a single protein chain and dna which dose not seems like two strands, rather then just put two 23base dna together for a 46 base length single strand DNA. I am asking is there a way to generate sequence file for a homodimer and dsDNA? or I have to generate sequence file for each chain separately (there will be four sequence files in this case, two protein chains and two dna chains)? Thanks. Alex Alex

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coot generate symmetry mates like pymol
by Xiao Lei 08 Jan '16

08 Jan '16

Hi Phenixbb members, 1. Is there a function in coot which can generate symmetry mates like pymol (action--> generate symmetry mates)? I know in coot there is a "Draw---> Cell&Symmetry" function, but it seems the display results could not display my crystal packing like pymol. 2. In pymol, is there a button which just display structure in one unit cell? Thanks. Xiao

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unwanted N/Q/H flipping in PHENIX.REFINE
by Bernhard Loll 05 Jan '16

05 Jan '16

Dear all, I am currently refining a 1.9 A structure with PHENIX 1.10.1-2155. The problem I am facing is the following: Running the Molprobity server, it suggests me to correct a couple of N/Q/H flips. I perform the flips re-run PHENIX.REFINE with “Automatically correct N/Q/H errors” not ticked. The log file confirms the selection with nqh_flips = False. Nevertheless PHENIX.REFINE again flips these residues and the output PDB file has all previously flipped residues “re-flipped” in comparison to the input PDB file. I am very confident that the automatically flips performed by PHENIX.REFINE (REDEUCE) are wrong, since I have two metal binding sites. Why PHENIX.REFINE rotates side chains by 180 degree even though nqh_flips were set to false? Any help is appreciated. Cheers, Bernhard Dr. Bernhard Loll Freie Universitaet Berlin Fachbereich Biologie, Chemie, Pharmazie Institut fuer Chemie und Biochemie AG Strukturbiochemie Takustr. 6 D-14195 Berlin Germany Phone: +49 (0) 30 838-57348 Fax: +49 (0) 30 838-454936 Email: loll(a)chemie.fu-berlin.de Homepage: http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/

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Project info lost after a disk crash
by hli 04 Jan '16

04 Jan '16

Hi, The hard drive of our major Linux computer crashed recently. After installing a new disk and recovering all the data in the damaged disk I lost all the project information in PHENIX GUI home page. I noticed that under .phenix directory there are files like project_db.pkl, but do not know how to retrieve the old project info into the GUI. Thanks in advance for your help. Huiying Dept. MB&B UC Irvine

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Re: [phenixbb] Modifications for Ca-binding site
by Nigel Moriarty 30 Dec '15

30 Dec '15

Jacob Once again Boaz is leading you in the correct direction. You did send me a *.metals.edits file. You just need to change the ideal distances in this file. On another point, I ran a refinement with your inputs and the values don't seem a long way off. However, I'd wait for Pavel to take a look because the density around the Calcium ion itself seems unusual. 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 On Wed, Dec 30, 2015 at 6:27 AM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > Hi Jacob, > > My guess is that answer (or hint) is here (taken from this link : > https://www.phenix-online.org/documentation/faqs/refine.html#targets-and-re…): > > > *I have ions very close to water molecules/protein atoms, and > phenix.refine keeps tring to move them apart. How can I prevent this?* > > Use phenix.ready_set or *phenix.metal_coordination* to generate custom > bond (and optionally, bond angle) restraints, which will be output to a > parameter file ending in ".edits". If you are using the PHENIX GUI, there > is a toolbar button for ReadySet in the phenix.refine interface, which will > automatically load the output files for use in phenix.refine. > > I have not used it myself but I assume that the sigmas for the restraints > would be in the *.edits files that you'll generate. > > Hope this helps. > > Boaz > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of Life > Sciences Ben-Gurion University of the > Negev Beer-Sheva > 84105 > Israel > E-mail: > bshaanan(a)bgu.ac.il <bshaanan(a)bgu.ac.il> Phone: 972-8-647-2220 Skype: > boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > ------------------------------ > *From:* Keller, Jacob [kellerj(a)janelia.hhmi.org] > *Sent:* Wednesday, December 30, 2015 4:09 PM > *To:* Nigel Moriarty > *Cc:* בעז שאנן; phenixbb(a)phenix-online.org > *Subject:* RE: [phenixbb] Modifications for Ca-binding site > > How does one change the ideal bond length/sigma in Phenix? > > > > JPK > > > > *From:* Nigel Moriarty [mailto:[email protected]] > *Sent:* Tuesday, December 29, 2015 10:12 AM > *To:* Keller, Jacob > *Cc:* Boaz Shaanan; phenixbb(a)phenix-online.org > *Subject:* Re: [phenixbb] Modifications for Ca-binding site > > > > Jacob > > > > Boaz has some sage advice. I recommend not excluding the Ca-O coordination > but changing the ideal to better reflect the distances in your files. > > > > PS I'd also like the PDB files, directly, so as not to put noise on the > list. > > > 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 > > > > On Tue, Dec 29, 2015 at 5:49 AM, Keller, Jacob <kellerj(a)janelia.hhmi.org> > wrote: > > Well, I think it's more of a data-vs-geometry battle, with the geometry > dragging in the side chains towards the calciums, and the data pulling them > out. When I real-space refine them in Coot, some of the Ca-O distances are > pretty different from the "ideal" values. Maybe I could just exclude them > from xyz refinement in Phenix after making sure they're correct in Coot? > I'll give that a shot. > > Kol tuv, > > Jacob > > > > > > -----Original Message----- > From: Boaz Shaanan [mailto:[email protected]] > Sent: Tuesday, December 29, 2015 7:52 AM > To: Keller, Jacob; phenixbb(a)phenix-online.org > Subject: RE: Modifications for Ca-binding site > > Hi Jacob, > > Sucking-up neighboring residues into the Calcium (or other heavier atoms) > density is a known issue. Turning-off the Ca-O or other distance restraints > around the Calcium is the last thing you want to do, in my experience. > You'd better check those distance restraints and verify that they're > compatible with the distances in other (preferably high resolution, of > course) structures with calcium binding sites similar to yours and then > make sure they're given the appropriate weight during refinement. That's my > view but Pavel will give you more advices I'm sure. > > Cheers, > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: phenixbb-bounces(a)phenix-online.org [ > phenixbb-bounces(a)phenix-online.org] on behalf of Keller, Jacob [ > kellerj(a)janelia.hhmi.org] > Sent: Tuesday, December 29, 2015 4:44 AM > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Modifications for Ca-binding site > > I am getting a lot of problems with my calcium binding sites--there is > clear density for the calciums and the protein side chains, but Phenix > keeps sucking the side chains out of their density towards the calciums and > also the calciums show some positive difference density, perhaps due to > too-high b-factors (or potentially partial occupancy by Na?). I think what > might work best is to turn off the Ca-O bond length restraints somehow, but > don't see where/how to do that. I tried releasing them from geometrical > restraints, but that made things worse, since things went haywire in the > sidechains themselves. > > Is it possible to make Phenix ignore the Ca-O bond distance restraints? > > JPK > > ******************************************* > Jacob Pearson Keller, PhD > Looger Lab/HHMI Janelia Research Campus > 19700 Helix Dr, Ashburn, VA 20147 > email: kellerj(a)janelia.hhmi.org > ******************************************* > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > >

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Modifications for Ca-binding site
by Keller, Jacob 30 Dec '15

30 Dec '15

I am getting a lot of problems with my calcium binding sites--there is clear density for the calciums and the protein side chains, but Phenix keeps sucking the side chains out of their density towards the calciums and also the calciums show some positive difference density, perhaps due to too-high b-factors (or potentially partial occupancy by Na?). I think what might work best is to turn off the Ca-O bond length restraints somehow, but don't see where/how to do that. I tried releasing them from geometrical restraints, but that made things worse, since things went haywire in the sidechains themselves. Is it possible to make Phenix ignore the Ca-O bond distance restraints? JPK ******************************************* 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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RSRZ in Phenix?
by Keller, Jacob 30 Dec '15

30 Dec '15

Dear Crystallographers, Is there any place in Phenix where RSRZ or a similar measure is shown? 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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Coot add DNA base or mutate DNA base
by Xiao Lei 25 Dec '15

25 Dec '15

Hi All, I'm using coot to build DNA, when I click "add residue" to one end of DNA, coot automatically add an "A" base to it, but I'd like to add "G" base, is it a way to mutate the A base to G base, I know coot can mutate amino acid residue, is is a way to mutate DNA residue in coot GUI? Thanks ahead. Xiao

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Trouble refining following molecular replacement
by Tyler Liban 22 Dec '15

22 Dec '15

Hello all, We are currently working with a dataset for a trimeric protein complex at 3A that is giving us some issues. The space group seems to be P21 ( 59.5, 61.6, 99.6 , 90, 98, 90) and the Mathews coefficient (2.6) suggests 2 copies of this 35kDa complex in the ASU. We are using a homolog as the search model that is 80% identical, and Phaser is able to find 2 molecules in P21 when searching in the same point group and gives good TFZ scores (TFZ = 9 or 10). However, these solutions do not refine well following Phaser (Rfree ~.50), and after removing parts of the model that look incorrect the Rfree still stays between .46 and .50. We ran the data through Xtraige and saw no signs of twinning based on the L-test, and the Patterson map has one small off-origin peak that is only 5%, indicating that there is no significant pseudotranslation. We have also tried finding MR solutions in P1, but haven’t had much luck. Any ideas on where to go from here would be greatly appreciated. Tyler

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command line for reflection file editor
by Zheng Zhou 22 Dec '15

22 Dec '15

Dear phenix experts, How do I combine Rfree from one dataset with the new dataset under command line? I can do this using reflect file editor GUI easily. But I tried to look up the documentation for phenix.reflection_file_converter and could not find a solution. I am trying to write a script to handle several datasets scaled from HKL2000. I could do this easily in ccp4, but looks like Ctruncate's French&Wilson made the completeness worse than scale.log. Thanks for your help in advance. Best, Zheng

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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 15 Dec '15

15 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 25 Nov '15

25 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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