- phenixbb - phenix-online.org

Merging Already-Scaled MTZs
by Keller, Jacob 20 Apr '16

20 Apr '16

Dear Crystallographers, I guess it is bad practice to merge/scale already-merged/scaled mtz's, but I have a special reason for wanting to do so. Does anyone know how this can be done in Phenix? The reason is, if you're interested, that I want to detwin several different datasets to varying degrees, then merge them. JPK ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

2 1

Autobuild
by Sam Tang 20 Apr '16

20 Apr '16

Dear colleagues I have recently downloaded a Windows GUI version of Phenix 1.10.1-2155. When I used AutoBuild these few days it keeps turning out the following errors: Job 1 failed: child process stderr output: command: ['phenix.autobuild', 'C:\\Users\\pcshaw\\Desktop\\NPAproc\\B13_proc\\AutoBuild_run_4_\\TEMP0\\PARAMS_1.eff', 'write_run_directory_to_file="C:\\Users\\pcshaw\\Desktop\\NPAproc\\B13_proc\\AutoBuild_run_4_\\TEMP0\\INFO_FILE_1"'] Traceback (most recent call last): File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\build\..\modules\phenix\phenix/command_line\autobuild.py", line 228, in <module> run_autobuild=run_autobuild(args=sys.argv[1:]) File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 564, in __init__ self.RunWizard() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 2372, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 4626, in AutoBuild_rebuild_cycle_run refine_2fofc=refine_2fofc) File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 5500, in AutoBuild_resolve_with_model hklout=hklout,labin=labin) UnboundLocalError: local variable 'labin' referenced before assignment Could I please enquire if these are due to mis-setting of parameters or in fact problems related to my recent installation? Yet another question on my mind is, is AutoMR still supported in this Windows version? I can now no longer find it in the GUI while it used to be there in the 1.7 Mac version. Kind regards Sam Biochemistry Programme, School of Life Sciences, CUHK

2 1

phenix output graphs
by Christian Roth 19 Apr '16

19 Apr '16

Hi Phenix-Team, there are some nice graphs produced for example after refinement. If I want to save such a graph (B-Factor histogram) as jpg or so, is that possible or do I have to save the values and redraw it outside phenix? The only plot I oculd save was the B-Fac plot per residue, which wouldn't be helpful in that case. Thanks for some insight. Cheers Christian

1 0

questions/problems with tls_as_xyz routines
by David A Case 19 Apr '16

19 Apr '16

I'm trying to use tls_as_xyz, but having some problems. 1. In the paper describing this, Urzhumtsev et al, Acta Cryst D71:1668, 2015, there seems to be something wrong with Section 6.2, which describes results on PDB entry "1dqv", syanptotagmin III. The description says that there are two copies of the molecule in the asymmetric unit, and the resolution is 2.5 Ang. However, the file with this code in the RCSB (which is indeed syanptotagmin III) has one molecule per asymmetric unit, a single chain of 296 amino acids, rather than two chains of 97 amino acids, as in Tables 2 and 3 of the paper cited above; the resolution is 3.2 Ang. And it doesn't look anything like the picture of "1dqv" in Fig. 3a. So something looks wrong; does anyone know what system Section 6.2 is using? 2. I'm asking the above because I'm having trouble with my own applications, and was hoping to check that I could reproduce the results in the paper. Apropos of that, is there a test case or example for tls_as_xyz in the phenix distribution? [I'm not all that familiar with phenix, so apologies if I've missed the easy way to find this.] 3. Here is a summary of what is not working for me. (I don't expect anyone to debug this on such little information, but thought that someone on the list might have done some similar calculation.) a. I took a small domain (residues 6-61 from GB3, PDB code 2IGD), and used Ethan Merrit's lsq_tls_fit to obtain a set of TLS tensors that best fit the deposited ADP's. The statisitcs are pretty good, indicating (not surprisingly) that motions in this domain are well characterized as a rigid body--which is why I chose this system. I just used the CA atoms for this initial study. b. I used phenix.tls_as_xyz to compute an ensemble from the TLS matrices obtained in step a. c. I then computed ADP's from the ensemble, using tools from cpptraj in Amber, (or our own codes, which give the same results). But the extracted isotropic B factors (and the anisotropic components) are much larger than the input ones. So, the ensemble is giving me what I expected: a sampling of structures whose fluctuations arise from the input TLS matrices. I've done a fair amount of due diligence in trying to track down errors on my end, but I could be making a mistake on any one of the steps above. Or, I could be mis-interpreting what I should expect to get from the tls_as_xyz procedure. I'd be happy to share details off-line with any one who might volunteer to help. ...thanks...dave case

2 2

Application deadline is this week: CCP4/APS crystallographic school, June 21 - 29, 2016
by Sanishvili, Ruslan 18 Apr '16

18 Apr '16

Dear Colleagues, Deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. If you have a crystallographic problem you cannot resolve independently, this school is for you. From our past experience, the majority of participants bring with them the crystallographic problems and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed at http://www.ccp4.ac.uk/schools/APS-school/publications.php This school will cover popular packages such as CCP4, PHENIX, SHELX and much, much more: http://www.ccp4.ac.uk/schools/APS-2016/program.php Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found at: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Wednesday, March 23, 2016 10:26 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] Reminder, CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, This is a reminder that the application deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. The school will take place from June 21 through June 29, 2016 at the Advanced Photon Source, Argonne National Laboratory, near Chicago. All aspects of macromolecular crystallography from data collection to structure refinement and validation, as well as functional assessment, will be covered. Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. >From our past experience, the majority of participants bring with them the crystallographic problems they cannot resolve independently and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed here: http://www.ccp4.ac.uk/schools/APS-school/publications.php Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found here: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Tuesday, February 23, 2016 7:48 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

1 0

Re: [phenixbb] Data processing: exhaustive search?
by Kay Diederichs 17 Apr '16

17 Apr '16

Hi Kaushik, there is no need for, and no sense in, an exhaustive search of data processing parameter space, because its dimensionality is way too high to achieve anything useful. The programs MOSFLM and XDS have undergone decades of development, and their processing defaults are carefully chosen. It is rather the user of the programs who is in charge to correctly interpret the output (which requires reading of their documentation, and some experience), and to make meaningful adjustments to (usually very) few parameters. Speaking for XDS, I recommend to read XDSwiki articles (there are tutorials and example data sets, and lots of explanations) and a book chapter that I recently wrote (#131 at http://cms.uni-konstanz.de/strucbio/diederichs-group/publications ). If you use the generate_XDS.INP script from XDSwiki, and follow the paper and the "Optimization" article, you will get good data from XDS. (There are other scripts, like autoPROC, xia2, xdsme and so on, which usually also give good results but I don't know them well.) In particular, in case of XDS there is usually no need to fiddle around with "box size, spot separation, tolerance and other parameters". The fact that you seem to try and optimize Rmerge suggests to me that you are trading precision for accuracy. Too many people still do this, but it is a legacy of the past. "Trying a combination of better frames over poorer frames" is most likely _not_ going to improve your merged intensities - this is another unfortunate and very common misunderstanding (see references 113 and 130). I hope this helps you to get better data. Kay On 16.04.2016 21:18, phenixbb-request(a)phenix-online.org wrote: > Message: 6 > Date: Sun, 17 Apr 2016 00:48:31 +0530 > From: Kaushik Hatti <hskaushik(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Data processing: exhaustive search? > Message-ID: > <CAGMFGb=B9s-j4yXmRx8_M7NPndf86puviiY9QMg=EAqaWr9thw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I have a data set diffracted to 2.7A collected at 1.54 wavelength. The data > is not of great quality with very close spots, ellipsoid spots in certain > regions of the frames and spot overlaps. Also certain frames are poorer > than rest. The crystal could not be reproduced. > > The best R merge (overall) I have achieved so far is 17% with 85% > completeness and 3 I/SigI processed in P4 space group. I feel it's possible > to process it better by identifying right values for box size, spot > separation, tolerance and other parameters. I am also suspecting a higher > symmetry space group. I believe, trying a combination of better frames > over poorer ones with improve merging statistics. > > I have so far tried processing in iMosflm and XDS. Is there a tool which > could search exhaustively trying different values for parameters and > suggest the combination which provide best merging statistics? > > Sorry if this question is not relevant in this group. > Any pointers/suggestions would be gratefully helpful. > > Thanks in advance, > Regards, > Kaushik > Molecular Biophysics Unit, > Indian Institute of Science, > Bangalore, India. -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz

2 1

Data processing: exhaustive search?
by Kaushik Hatti 16 Apr '16

16 Apr '16

Hello, I have a data set diffracted to 2.7A collected at 1.54 wavelength. The data is not of great quality with very close spots, ellipsoid spots in certain regions of the frames and spot overlaps. Also certain frames are poorer than rest. The crystal could not be reproduced. The best R merge (overall) I have achieved so far is 17% with 85% completeness and 3 I/SigI processed in P4 space group. I feel it's possible to process it better by identifying right values for box size, spot separation, tolerance and other parameters. I am also suspecting a higher symmetry space group. I believe, trying a combination of better frames over poorer ones with improve merging statistics. I have so far tried processing in iMosflm and XDS. Is there a tool which could search exhaustively trying different values for parameters and suggest the combination which provide best merging statistics? Sorry if this question is not relevant in this group. Any pointers/suggestions would be gratefully helpful. Thanks in advance, Regards, Kaushik Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

1 0

Re: [phenixbb] Hardward phenix.refine
by Kay Diederichs 13 Apr '16

13 Apr '16

Colin, check out the first option in the FAQ at https://www.phenix-online.org/documentation/faqs/refine.html A core i7 and a Xeon of the same generation are equally fast if their frequency is the same. The main differences are that - Xeon E3 supports ECC memory (most core i* don't) - Xeon E5 supports Dual-CPU (core i* is just one) - Xeon E7 supports multi-CPU and is very expensive - most Xeons don't have built-in graphics whereas most core i* do There are many other small differences but most of them irrelevant; inspect the Wikipedia pages! Xeons won't be faster with phenix.refine; a core i7 already has enough cores - to increase their usage you'll have to recompile as per the FAQ. HTH, Kay > > Message: 1 > Date: Mon, 11 Apr 2016 07:56:39 +0000 > From: Colin Levy <C.Levy(a)manchester.ac.uk> > To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Hardward phenix.refine > Message-ID: <773C4580-FA01-4246-86E9-2D73AFD98421(a)manchester.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > Having read the FAQ regarding hardware I have a few ideas but would greatly appreciate any input from the community or developers. > > Would anyone like to suggest the best configuration of hardware for running phenix.refine? I mainly operate in OSX but have no issue with switching operating system if I can get a faster setup. My current thoughts are either something running a 4GHz Quad core i7 or an alternative would be a 3.7GHz Quad-Core Intel Xeon E5 (iMac v Mac Pro) or equivalent Linux builds. > > I know that the i7 is reasonably fast as I have this setup in a different machine and phenix.refine runs reasonably quickly but as ever I would like it to be faster. Budget is not unlimited by any means but I would be interested in learning what an optimal setup might look like. > > Many thanks, > > Colin > > > Manchester > Protein > Structure > Facility > > Dr. Colin W. Levy > MIB G034 > Tel. 0161 275 5090 > Mob.07786 197 554 > c.levy(a)manchester.ac.uk<mailto:[email protected]> > > Manchester Institute of Biotechnology | University of Manchester | 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN

3 2

Re: [phenixbb] Phenix Xtriage label error
by Alex Lee 12 Apr '16

12 Apr '16

Hi Dorothee and Billy, Thank you for your information! I have both I, SIGI and IPR, SIGIPR labels in my unmerged MTZ (I checked this with ViewHKL). But it seems the Xtriage only offers choices to merged mtz. I tried to choose I,SIGI, Merged option (even though my mtz is unmerged), the Xtriage output shows "anomalous flag false" and I did not get any additional anomalous information from the report. On Tue, Apr 12, 2016 at 12:16 PM, Dorothee Liebschner <dcliebschner(a)lbl.gov> wrote: > Hi Alex, > > What data labels are in the file pointless_xxx.mtz? > You can check with > > phenix.mtz.dump pointless_xxx.mtz > The output should list the available labels. > (you should see the labels also in hklview) > > You cannot leave the data labels choice blank in xtriage, as you have two > data choices in your file, so you need to tell the program which ones to > use. > > Apart from xtriage, it is always helpful to check the anomalous signal > reported in various log files from your data processing steps, such as > aimless.log and also from mosflm (I am not familiar to mosflm but I guess > it outputs also some info about anomalous signal?). > > Best wishes, > > Dorothee > > > > > > On Tue, Apr 12, 2016 at 11:08 AM, Alex Lee <alexlee198609(a)gmail.com> > wrote: > >> Dear Phenixbb members, >> >> I have a data-set of a 8 kDa protein crystal around 2.5A resolution. The >> protein crystal was soaked in potassium iodine before collecting data using >> in-house beam (1.54A wavelength). As I expected some anomalous signal from >> the iodine ion from the crystal, after I use Imosflm to index, integrate >> and scale the data (space group P3). I got four output .mtz files: >> pointless_XXX.mtz; aimless_xxx.mtz; ctruncate_xxx.mtz; >> ctruncate_xxx-unique.mtz. After I check with viewHKL, I found the only >> unmerged mtz data is pointless_XXX.mtz, the other three mtz files are >> merged. >> >> The next step I tried to use Phenix Xtriage (Linux version 1.10.1) to >> check my mtz data for anomalous completeness, I thought in this step my mtz >> should be unmerged type to see the anomalous signal, so I chose >> "pointless_xxx.mtz" as Xtriage input, but for the data labels in the >> Xtriage GUI panel, I can only have two choices of "I, SIGI, Merged" and >> "IPR, SIGIPR, Merged", it seems I do not have a choice of an unmerged mtz >> label. I decide to leave this choice blank by choosing data labels"---". >> After I click "run", Xtriage gave an error "please select labels for input >> data". >> >> Any input on this issue? >> >> Thanks in advance. >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > >

3 2

Phenix Xtriage label error
by Alex Lee 12 Apr '16

12 Apr '16

Dear Phenixbb members, I have a data-set of a 8 kDa protein crystal around 2.5A resolution. The protein crystal was soaked in potassium iodine before collecting data using in-house beam (1.54A wavelength). As I expected some anomalous signal from the iodine ion from the crystal, after I use Imosflm to index, integrate and scale the data (space group P3). I got four output .mtz files: pointless_XXX.mtz; aimless_xxx.mtz; ctruncate_xxx.mtz; ctruncate_xxx-unique.mtz. After I check with viewHKL, I found the only unmerged mtz data is pointless_XXX.mtz, the other three mtz files are merged. The next step I tried to use Phenix Xtriage (Linux version 1.10.1) to check my mtz data for anomalous completeness, I thought in this step my mtz should be unmerged type to see the anomalous signal, so I chose "pointless_xxx.mtz" as Xtriage input, but for the data labels in the Xtriage GUI panel, I can only have two choices of "I, SIGI, Merged" and "IPR, SIGIPR, Merged", it seems I do not have a choice of an unmerged mtz label. I decide to leave this choice blank by choosing data labels"---". After I click "run", Xtriage gave an error "please select labels for input data". Any input on this issue? Thanks in advance.

3 4

Hardward phenix.refine
by Colin Levy 11 Apr '16

11 Apr '16

Dear all, Having read the FAQ regarding hardware I have a few ideas but would greatly appreciate any input from the community or developers. Would anyone like to suggest the best configuration of hardware for running phenix.refine? I mainly operate in OSX but have no issue with switching operating system if I can get a faster setup. My current thoughts are either something running a 4GHz Quad core i7 or an alternative would be a 3.7GHz Quad-Core Intel Xeon E5 (iMac v Mac Pro) or equivalent Linux builds. I know that the i7 is reasonably fast as I have this setup in a different machine and phenix.refine runs reasonably quickly but as ever I would like it to be faster. Budget is not unlimited by any means but I would be interested in learning what an optimal setup might look like. Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk<mailto:[email protected]> Manchester Institute of Biotechnology | University of Manchester | 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN [cid:[email protected]]<https://www.facebook.com/MIB2006/?ref=aymt_homepage_panel>[cid:[email protected]]<https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…>[cid:[email protected]]<https://www.linkedin.com/company/manchester-institute-of-biotechnology?trk=…>[cid:[email protected]]<https://twitter.com/?lang=en-gb&lang=en-gb>[cid:[email protected]]<https://www.youtube.com/channel/UCCBV8zDxk4L9yOEcujvSFNw> <https://www.youtube.com/channel/UCCBV8zDxk4L9yOEcujvSFNw><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…>

2 1

Call for targets for CASP12 - Critical Assessment of Protein Structure Prediction
by Torsten Schwede 08 Apr '16

08 Apr '16

Dear colleagues, The CASP experiment is looking for prediction targets: Novel folds, membrane proteins, protein complexes and multimers, comparative modeling targets. As many of you know, the CASP community experiments have been running once every two years since 1994, collecting information on soon to be solved structures from the experimental community, and passing on sequence data to the structure modeling community so that blind predictions of structure can be collected and assessed. Over that period CASP has seen enormous progress in the quality of modeled structures, but many problems remain, and further testing of prediction methods is imperative for advancing the field. CASP organizers collect target information for a three month season every two years, and in that period we can acquire around 100 targets, sufficient to evaluate the state of the art for most types of modeling. For those of you who have not provided targets to CASP before, the procedure is simple - there is a web page for submitting targets, and a very experienced staff to deal with any queries. We don't need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. We need all sorts of targets and in general everything that has low coverage by the templates (<70% of the sequence length) and relatively low sequence identity to the best template (<50% ) will be appreciated. In particular, we are interested in: 1. Novel folds and membrane protein targets. Last round we observed some interesting methods developments for contact prediction and ab initio modeling, and it is important to be able to decisively evaluate their effectiveness this CASP again. 2. Protein complexes and multimers. Since the last edition of CASP, the assessment of structure prediction methods has stronger emphasis on evaluating the accuracy of quaternary structure prediction. Both oligomeric targets and complexes are of interest for the experiment. 3. A diversity of comparative modeling targets. Cases where there is fairly high sequence identity (30-50%) between the target structure and an available template are valuable for testing the degree to which model accuracy can approach that of experiment, particularly in functionally critical regions. Cases with lower sequence identity to template, right down to undetectable, are valuable for testing the ability of the methods to detect remote homologs, to overcome challenging alignment difficulties, to make use of multiple templates, and to build regions of the structure not obviously available from a template. The time table is similar to previous CASPs: The prediction season opens at the beginning of May, and will run until the end of July. We are releasing targets continuously throughout that period, as evenly spaced as possible, aiming for about 100 targets altogether. Each target will be available for prediction for a period of three weeks. For cases where longer periods are possible, these targets may be used to test refinement and data-assisted methods. It is of course important that there not be any kind of public release of the experimental structure (including things like pictures on web pages or abstracts) until after the predictions for that target are closed. As many of you know, it's fairly simple, with just two things to bear in mind. First, because of the timing framework, there needs to be at least a month between the submission date and any release of the structure. Second, we ideally need the experimental co-ordinates by the beginning of August and definitely by the end of August, so that the predictions can be assessed. At that point, they can be kept confidential if necessary, though we would like to provide them to predictors of your structure at the beginning of November at the latest, so that can see how well they have done. Participants would also usually like to be able to show slides and discuss their predictions at the meeting at the beginning of December. So, if you are currently working on an interesting protein structure suitable as prediction target for CASP , we would be most grateful if you would inform us via the target entry page: http://www.predictioncenter.org/casp12/targets_submission.cgi After CASP prediction season is over we usually publish a paper on the experimentalists' insights into the most interesting targets (see below). 2015: Some of the most interesting CASP11 targets through the eyes of their authors. Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. Proteins. 2015 Oct 16. doi: 10.1002/prot.24942. [Epub ahead of print]. PMID: 26473983. 2014: Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. Proteins. 2014 Feb;82 Suppl 2:26-42. doi: 10.1002/prot.24489. Erratum in: Proteins. 2015 Jun;83(6):1198. PMID: 24318984. 2011: Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. Proteins. 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. Epub 2011 Oct 21. PMID: 22020785. Thanks, CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel, Switzerland Anna Tramontano, University of Rome, Italy Get in touch: casp(a)predictioncenter.org<mailto:[email protected]> More information: http://www.predictioncenter.org/casp12/index.cgi Submit a target: http://www.predictioncenter.org/casp12/targets_submission.cgi

1 0

Position available with Phaser team at University of Cambridge
by Randy Read 06 Apr '16

06 Apr '16

I’d like to draw your attention to an opening that we have for someone to join the team developing Phaser. The ideal person would have experience with C++ and/or Python, graphical interfaces, and knowledge of how macromolecular structures are solved and validated, but it would also be good to hear from people who only tick some of those boxes. Full details of the position and the application process are given on the jobs.ac.uk website: http://www.jobs.ac.uk/job/ANJ468/research-associate/. I’m happy to answer any informal enquiries about the position. 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

1 0

Modeller- homology modelling
by Shilpa Janarthanan 03 Apr '16

03 Apr '16

Hello, Has anyone encountered this error while running Modeller for doing Homology modelling "Sequence mismatch between alignment and pdb"? If yes, how did you solve it? I checked, there is no mismatch between sequence(both fasta and pdb) and alignment. Thank you. -- Shilpa J Bioinformatics Dept., SASTRA University.

1 0

Finding the transcript
by Shilpa Janarthanan 02 Apr '16

02 Apr '16

Hello, Can you tell me, on what basis should I find the exact transcript (mRNA) sequence for a given protein sequence, in NCBI -Gene? Thank you. -- Shilpa J Bioinformatics Dept., SASTRA University.

1 0

The Hitchhiker’s Guide to the Biomolecular Galaxy symposium - May 11-12th 2016
by Noinaj, Nicholas 02 Apr '16

02 Apr '16

Dear PHENIXbb, I would like to bring to your attention our upcoming symposium (May 11-12) hosted here at Purdue University for students and postdocs. There will also be a Career Session on May 10th for students and postdocs only. More information is listed below and can also be accessed on our website: Symposium Website: https://purduegalaxy.science.purdue.edu/ Symposium Flyer: https://purduegalaxy.science.purdue.edu/images/2016/hg2bg_logo_Flyer_new.jpg Registration (including breakfast and lunch for both days and a T-shirt!) and abstract submission are completely FREE! And now, we are offering at least 10 travel grants (up to $150 each) for students and postdocs who are within driving distance of Purdue. Please forward this to anyone you think might be interested. Thanks in advance! Cheers, Nick Nicholas Noinaj 240 S. Martin Jischke Dr. Hockmeyer Building of Structural Biology, Rm 333 Dept. of Biological Sciences, Purdue Univ. West Lafayette, IN 47907 765-496-0061 (office) 765-496-0059 (wetlab) nnoinaj(a)purdue.edu ++++++++ Greetings all from Purdue! We would like to cordially invite you, your colleagues, students, postdocs and staff to our upcoming symposium hosted here at Purdue University, West Lafayette campus. The name of the symposium is: The Hitchhiker’s Guide to the Biomolecular Galaxy symposium May 11-12, 2016 ARMS 1010, Purdue University The symposium will highlight research from students and postdocs from neighboring institutions and from many departments here at Purdue including Biological Sciences, Medicinal Chemistry and Molecular Pharmacology, Chemistry, Biochemistry, and Physics and Astronomy. The keynote speaker will be Dr. Peter Kwong from NIAID/NIH who will talk about his work on ‘Multi-dimensional searching and the coordinates of effective HIV-1 and RSV vaccines’. In addition to the keynote address, the symposium will include six scientific sessions covering the following topics: Disease, Pathogenesis and Therapeutics; Biosynthesis and Catalysis; Biophysical Methods and Emerging Techniques; Macromolecular Assemblies and Complexes; and Disorder and Conformational Plasticity. There will also be opportunities for discussion and interactions during catered breaks, a poster session, and a reception. And back by popular demand, a Career Session will also be hosted on the evening of May 10th at the Lafayette Brewing Company for students and postdocs and will include a panel representing industry, academia, and government. Registration and abstract submission are both FREE. Undergraduates, graduates, and postdocs are encouraged to submit abstracts for poster or oral presentations. Prizes for best posters (undergrad ($100), grad ($150), and postdoc($150)) and oral presentations (grad ($200) and postdoc ($200)) will also be awarded at the close of the symposium. REGISTER NOW for the HG2BG symposium!!! The deadline is quickly approaching!!! Click link below to Register (Abstract submission NOT required!): https://purdue.qualtrics.com/jfe/form/SV_eeZ2HT409liD27z Just LOOK at ALL the FREE stuff you get with registration: Just a 1-click, 1-minute process FREE registration fees! FREE abstracts submission! FREE attendance to the Career Session which includes food and drinks at Lafayette Brewing Company! FREE HG2BG symposium T-shirt! FREE chance to win either a poster/oral presentation prize ($100-$200 each)! FREE food and drinks at the poster presentations/reception! FREE breakfast for both days of the symposium! FREE lunch for both days of the symposium! FREE travel grants for up to $150 each for registrants from neighboring institutions (10 available)! FREE attendance to all poster and oral presentations, including talk by Peter Kwong! We look forward to your participation and another successful symposium! On behalf of the organizing committee: Satarupa Bhaduri (Biological Sciences) Chen Chen (Medicinal Chemistry and Molecular Pharmacology) Samantha Lee (Biochemistry) Ngango Yvon Rugema (Chemistry) Phillip Rushton (Biological Sciences/ PULSe) Valentyn Stadnytskyi (Physics and Astronomy) Dr. Nicholas Noinaj (Faculty advisor; Biological Sciences) A special thanks to our corporate sponsors: Millipore(Jim Henderson) Carl Zeiss Microscopy LLC (Sam Byerly) Molecular Dimensions (Issa Isaac) Qiagen (Andrew Fritts) Rigaku (Angela Criswell) TTP Labtech (Melanie Adams) Anatrace (Ed Pryor) Hinds Instruments (Connie Wimmer) Beckman Coulter (Jona Kristo) Mitegen (Ben Apker) Fisher Scientific (Keven Peterson) Sigma Aldrich (Rick Belcher)

1 0

phenix.AmberPrep
by Liu, Jing-Yuan 01 Apr '16

01 Apr '16

Dear PHENIX Developers, I would like to perform phenix.refine using amber gradient. I installed AmberTools 15 and the newest version of Phenix by following the instruction found here http://www.phenix-online.org/documentation/reference/amber.html.<http://www.phenix-online.org/documentation/reference/amber.html> However, when I ran"phenix.AmberPrep", it complains "phenix.AmberPrep not found". In dead, I cannot find any binary named "phenix.AmberPrep". However, it looks to me that phenix is installed OK and so does AmberTools 15. I checked each step of my installation, I could not find anywhere is wrong. Can you please help me out? Thank you! Sincerely, Jing-Yuan

2 1

Tautomer/protomer plugin for Phenix
by Lance Westerhoff 01 Apr '16

01 Apr '16

Hello All- A paper from our group just came out in ActaD which I think fellow phenix users should find interesting. The paper details a new module we have available which uses our QM/MM-based Phenix plugin to correctly refine and determine tautomer/protomer, rotamer, flip state, and binding mode using X-ray data and refinement. The paper is available for free, Open Access on ActaD’s website: http://scripts.iucr.org/cgi-bin/paper?S2059798316002837 If you would like to give it a try, please let me know. The software is available for free for pure non-profit academic research and for a reasonable fee for commercial/industrial efforts. For more information, please visit our product site: http://www.quantumbioinc.com/products/phenix_divcon Or fill out one of our on-line license agreements to gain access: http://www.quantumbioinc.com/products/software_licensing Thank you for your time and have a good weekend! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

1 0

Berkeley Server Downtime (3/30/2016)
by Billy Poon 30 Mar '16

30 Mar '16

Dear all, On Wednesday, March 30, our servers will be shutdown starting at 7:00 am Pacific for scheduled maintenance in our server room. This will affect, - 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/) We expect that the servers will be available by 5 pm Pacific at the latest. Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

1 1

autosol error
by Schnicker, Nicholas J 30 Mar '16

30 Mar '16

Hi, I have tried using Autosol through the Phenix GUI and it starts to run and then crashes with the following error. I could use some help figuring out what I need to do to fix this? Your help is appreciated! Thanks Nick AssertionError : Traceback (most recent call last): File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/wizards/AutoSol.py", line 3492, in AutoSol_scale_and_analyze_mad verbose="") File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/run_solve.py", line 499, in __init__ raise AssertionError,error AssertionError: None of the solve versions worked Traceback: File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/cctbx_project/libtbx/thread_utils.py", line 236, in run return_value = self._target(self._args, self._kwargs, self._c) File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/cctbx_project/libtbx/runtime_utils.py", line 95, in __call__ result = self.target() File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/cctbx_project/libtbx/runtime_utils.py", line 74, in __call__ result = self.run() File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/wizards/runtime.py", line 36, in run run_wizard = wizard_cmdline(args=list(self.args)) File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/wizard_command_line.py", line 564, in __init__ self.RunWizard() File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line

1 0

Selenocysteine
by Shilpa Janarthanan 30 Mar '16

30 Mar '16

Hello, How to add an unnatural amino acid (say OCS) at a position in the sequence and view it in PyMol, provided the protein structure (PDB file) is given? Is it correct to make changes in the PDB file itself, if Yes, then how should I do it? Thank you. -- Shilpa J Bioinformatics Dept., SASTRA University.

3 2

symmetry rejected as inconsistent by model_vs_data
by wtempel 30 Mar '16

30 Mar '16

Hello, phenix.model_vs_data_1.10.1-2155, along with printing to stderr: Sorry: Crystal symmetry mismatch between different files. prints these, and only these, lines to stdout: x251682_scaled3.mtz (36.692, 53.798, 108.063, 90, 84.258, 90) P 1 21 1 readySet.pdb (36.69, 53.8, 108.06, 90, 84.26, 90) P 1 21 1 Is this related to this code <http://cci.lbl.gov/cctbx_docs/cctbx/cctbx.crystal.html#cctbx.crystal.symmet…> ? Can I force phenix.model_vs_data to omit this isomorphism check and “run” with the reflection dimensions? Thank you. Wolfram

3 6

BSR2016: 12th International Conference on Biology and Synchrotron Radiation
by Thomas Eriksson 29 Mar '16

29 Mar '16

The 12th International Conference on Biology and Synchrotron Radiation will be hosted by the SLAC National Accelerator Laboratory - August 21-24, 2016. The objective of the conference is to bring together the community of biologists and scientists involved in the methodological developments on synchrotron and X-ray laser sources to discuss the novel possibilities of these sources and to promote their applications to challenging biological problems. The scientific program for the 2016 BSR covers applications of diffraction, spectroscopy and imaging methods applied to the structural and time-resolved studies of biological macromolecules, complexes and cellular and sub-cellular structures. There will be a $500 early registration fee ($350 for students). To take advantage of the early fees, registration must be complete by June 30th. Full information about the meeting, scientific program, registration and abstract submission forms can be found at the conference web site: https://conf-slac.stanford.edu/bsr-2016/content/biology-and-synchrotron-rad… Ana -- ------------------------------------------- Ana Gonzalez <ana(a)slac.stanford.edu> Staff Scientist Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Road, MS 99 Menlo Park CA 94025 Phone: (650) 926 8682 Fax: (650) 926 3292 -------------------------------------------

1 0

how to generate a set of alternative conformations ?
by cedric bauvois 29 Mar '16

29 Mar '16

Dear all, Is there a way with phenix, in a badly defined electron density area, to generate a set of different alternative conformations for a small protein fragment ? Thanks a lot in advance Cedric Bauvois

2 1

iNEXT / X-rays (and more) notes
by Anastassis Perrakis 24 Mar '16

24 Mar '16

Dear all, I want to bring to everybody’s attention a few things about iNEXT Synchrotron Access proposals, as they seem to surface up often. - “BAG” proposals are possible, but only when under a common translational scientific theme; not simply based on lab proximity. - iNEXT funds complete projects, both beam time and travel; arguing that "we have beamtime, just give us travel money” will likely get your proposal rejected. - Please be clear to state that you have crystals and/or justify what the SAXS experiments are answering. Please keep in mind a specific difference from past schemes: you do not need to submit a separate proposal to the synchrotron site to get beam time! A successful iNEXT application will be received by the site(s) you apply for, and only safety data will be requested and a technical review will be done based on the existing application. We are looking forward receiving your applications for high-end synchrotron data collection, but also for : 1. Structural Audit (including crystallisation trials and SAXS: please advertise to your biochemistry colleagues!) 2. Macromolecular Interactions (Biophysics for quantitative characterising) 3. Cryo-EM sample optimisation (if you have negative stain images) 4. High-end NMR data collection 5. High-resolution EM (if you have good cryo conditions, and also for tomography and CLEM) … and more modalities to come soon! http://www.inext-eu.org/access/ <http://www.inext-eu.org/access/> On behalf of the iNEXT team, Tassos

1 0

.Trash_UID error message
by Michael Weyand 23 Mar '16

23 Mar '16

Dear experts, our Phenix installation suffers on a nasty error message concerning permission problems on /data/.Trash_UID (/data is our mount point of a NFS share) when deleting a certain job from the history. Of course, no user has write access to the top folder / mount point! And I know that is might be an OS problem with NFS mounted disks (well known for Ubuntu systems). But we have an openSuSE with KDE, not GNOME. I also checked the Phenix preferences for an option, but was not successful. Is there any way to get rid of this message or better to say not deleting to .Trash folder? Thanks in advance, Michael

1 0

Reminder, CCP4 crystallographic summer school at the APS, June 21 - 29, 2016
by Sanishvili, Ruslan 23 Mar '16

23 Mar '16

Dear Colleagues, This is a reminder that the application deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. The school will take place from June 21 through June 29, 2016 at the Advanced Photon Source, Argonne National Laboratory, near Chicago. All aspects of macromolecular crystallography from data collection to structure refinement and validation, as well as functional assessment, will be covered. Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. >From our past experience, the majority of participants bring with them the crystallographic problems they cannot resolve independently and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed here: http://www.ccp4.ac.uk/schools/APS-school/publications.php Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found here: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Tuesday, February 23, 2016 7:48 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

1 0

The 2016 Diffraction Methods in Structural Biology Gordon Research Conference
by Edward Snell 22 Mar '16

22 Mar '16

Dear All, This is not Phenix related but we do see a lot of representation from Phenix developers and users at this conference. The 2016 Diffraction Methods in Structural Biology Gordon Research Conference (GRC) will be held at Bates College in Maine from July 17,to July 22nd 2016 - immediately before the American Crystallography Association Annual Meeting. The theme of this year's conference is "Probing the Structure and Dynamics of Macromolecules" and the conference celebrates its 40 year anniversary. Current details are available at https://www.grc.org/programs.aspx?id=11655. Program details are below, it promises to be an exciting. Arwen Pearson (co-chair) and I would like to invite you to consider attending the conference. Topics to be covered include new instruments and opportunities on the horizon, methods to improve maps and models, complementary approaches, resolving dynamics, the interplay between XFEL and synchrotron, new diffraction developments, and structure beyond Bragg diffraction. Many of the worlds experts in these areas will be at the meeting and we encourage the participation of every level of expertise to cross-pollinate the field. We will also have an opportunity for selected poster presenters to present talks at the meeting. Applications for the conference are now being accepted and will continue to be accepted until we are full. >From a personal perspective this is probably one of the best meetings for those interested in the nuts and bolts of diffraction methods. It is also a unique opportunity to meet many of the key members of the field. It is a friendly and productive conference, and an exciting one in terms of getting a preview of the future. We encourage you to attend, take part in great science, and also interact in a less formal social and sometimes sporting atmosphere. This will also be the second year that a related Gordon Research Seminar (GRS) is run. This is a meeting organized for and by post-docs and graduate students. Drs. Rike Mueller-Werkmeister and Bradely Hintze are organizing this with details at https://www.grc.org/programs.aspx?id=16486. We strongly encourage laboratories with an interest in Diffraction Methods in Structural Biology to support their students in attending both the GRS and the GRC with the GRS serving as a useful introduction to the larger conference. We are still raising funds for the GRS and GRC, in particular to enable younger scientists to attend. We are grateful and thank those who have supported us so far, and also those that are in the process of doing so. We are actively looking for further sponsorship. Summer is a full time for meetings but this is going to be a very worthwhile one. Please pass this onto interested colleagues. Thanks, Eddie and Arwen Sunday 17th of July Keynote Session: Structure and Dynamics Discussion Leader: Elspeth Garman (University of Oxford, United Kingdom) * Carrie Wilmot (University of Minnesota, USA) MauG Catalysis: A Tale of Ferryl Heme, Radicals and Long-Distance Hopping * Joseph Ferrara (Rigaku Americas Corporation, USA) A special talk to look back over 40 years of this GRC and describe the developments in the field since the first Diffraction Methods Meeting. Monday 18th July New Instruments and Opportunities Discussion Leader: Sean McSweeny (NSLS-II, USA) * Armin Wagner (Diamond Light Source, United Kingdom) In-Vacuum Long-Wavelength Crystallography - First Results * Matthew Bowler (Synchrotron Crystallography Group, France) Fully Automatic Characterization and Data Collection: A New Tool for Structural Biologist * Marjolein Thunnissen (MAX IV Laboratory, Sweden) Possibilities for Structural and Dynamical Studies on Proteins at MAX IV * Esko Oskanen (European Spallation Source, Sweden) Structural Biology with Neutrons - Opportunities at the European Spallation Source * William Graves (Arizona State University) Electron Diffraction as a Method to Produce a Tabletop XFEL Improving Maps and Models Discussion Leader: Airlie McCoy (University of Cambridge, United Kingdom) * Elspeth Garman (University of Oxford, United Kingdom) Unambiguous Metal Identification and Accurate Stoichiometric Measurements in Proteins * Frank Von Delft (Structural Genomics Consortium, United Kingdom) PANDDA: A Multi-Dataset Method for Electron Density Signal Extraction of Superposed States such as Low-Occupancy Ligands * James Fraser (University of California, San Francisco, USA) Birth of the Cool: Multitemperature X-Ray Crystallography to Reveal Protein Conformational Heterogeneity * Paul Adams (Lawrence Berkeley Laboratory, USA) New Tools for Interpretation of Cryo-EM Maps Tuesday 19th of July Structural Biology Requires Multiple Methods Discussion Leader: Nozomi Ando (Princeton University, USA) * Allison Edwards (Bragg Institute, Australia) Neutron Diffraction from Protein Crystals * Neil Ranson (University of Leeds, United Kingdom) Experiences and Results Using the New Direct Electron Detectors for CryoEM * Saikrishnan Kayarat (Indian Institute of Science Education and Research, India) Mechanism of a Motor-Driven Endonuclease: Combining Structural and Single-Molecule Approaches * Nikolai Skrynnikov (Purdue University) Motions of Protein Molecules Within the Crystalline Lattice * Sarah Bowman (MIT) What Can Spectroscopic Techniques Tell You About Your Crystal Dynamically Resolved Methods Discussion Leader: Carrie Wilmot (University of Minnesota, USA) * Thomas Barends (Max-Planck Institute for Medical Research, Germany) Ultrafast Functional Motions in Myoglobin Probed by Serial Femtosecond Crystallography * Henrike Muller-Werkmeister (University of Toronto, Canada) Time-Resolved S(F)X Studies with a Fixed Target * Gergely Katona (University of Gothenburg, Sweden) An Interleaved Data Recording Method for Studying the Non-Thermal Effect of Terahertz Radiation on Protein Crystals * Petra Fromme (Arizona State University, USA) Time-Resolved Femtosecond Crystallography: Towards Molecular Movies of Biomolecules 'In Action' Wednesday 20th July Hybridization of Synchrotron and XFEL Approaches Discussion Leader: Aina Cohen (SSRL, USA) * Elizabeth Baxter (SLAC National Accelerator Laboratory, USA) Alternative Methods for High Throughput Data Collection * Manfred Burghammer (ESRF, France) Recent Developments in Serial Micro-/Nano-Beam Diffraction X-Ray Techniques at ID13, ESRF * Helen Ginn (University of Oxford, United Kingdom) Development of Methods in XFEL Analysis * Thomas White (CFEL, Germany) Advances in Data Processing for Serial Femtosecond Crystallography * Allen Orville (Diamond Light Source, UK) Dynamic Structural Biology: Awakened and Enabled by New Sources and Complementary Methods Developments in Diffraction Methods Discussion Leader: Nadia Zatsepin (Arizona State University) * Isabel Uson (ICREA and the Spanish Research Council, Spain) Arcimboldo on Tour * Kartik Ayyer (CFEL, Germany) Coherent Diffractive Imaging as a Structure Determination Tool for Disordered Crystals * Andrea Thorne (MRC Laboratory of Molecular Biology, United Kingdom) Developments in Diffraction Data Analysis Thursday 21st July Selected Poster Presentations: New Cool Methods and Hot New Structures Discussion Leader: James Fraser (University of California, San Francisco, USA) Nine posters selected from the meeting for presentation. Structural and Dynamical Information Beyond Bragg Discussion Leader: James Holton (Advanced Light Source, USA) * Michael Wall (Los Alamos National Laboratory, USA) Probing Protein Structural Dynamics Using Diffuse X-Ray Scattering * Robert Rambo (Diamond Light Source Ltd, United Kingdom) A Real-Space Modelling Algorithm for SAXS Using Information Theory and Computational Geometry * Nozomi Ando (Princeton University, USA) Untangling Protein Allostery Edward Snell Ph.D. CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Heisenberg was probably here!

1 0

Denver ACA meeting abstract and travel award deadline March 31!
by Terwilliger, Thomas Charles 22 Mar '16

22 Mar '16

Hi Phenix users! It's time to sign up for the Denver ACA meeting! The meeting will be held Friday, July 22nd - Tuesday, July 26th, 2016 in Denver, Colorado. The abstract and travel award deadline is March 31. You can go to: http://www.amercrystalassn.org/ to register and apply for Young Scientist Travel awards! The transactions symposium will highlight Structural Dynamics across the disciplines represented by the ACA. The rest of the meeting will reflect the wide reach of crystallographic research with sessions on sources, methods, and results. These include opportunities from new and improved instrumentation, single/multiple crystal, powder and solution methods, and hot structural results. There will be sessions highlighting those results requiring complementary techniques including cryo-electromicroscopy. Invited speakers include this year's awardees: Jason Benedict (Etter Award), Axel Brunger (Trueblood Award), Elspeth Garman (Fankuchen Award) and Benno Schoenborn (Bau Award). The meeting will include a strong educational component forearly career scientists with specific talks designed to introduce research areas in addition to presenting results. Related evening sessions include amixer, career fair, career development, and diversity in the laboratory.The conference will end with a closing banquet and the award of poster prizes for the best presentations. DEADLINES: Abstract - March 31 Young Scientist Travel Grant - March 31 Early Registration - May 31 Hotel Reservations - June 28 All the best, Tom T Tom Terwilliger 2016 ACA President

1 0

Error when using phenix.pdbtoos to show model statistics
by luzuok 18 Mar '16

18 Mar '16

Dear developers, Following http://www.phenix-online.org/download/documentation/cci_apps/pdbtools.html When typing phenix.pdbtools Mymodel.pdb --show-adp-statistics I got the following error: pdbtools.py: error: no such option: --show-adp-statistics Does this option belong to old version of pdbtools? My Phenix version is 1.10. 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

2 2

Set up phenix and rosetta for phenix.rosetta_refine
by Yonglin Hu 17 Mar '16

17 Mar '16

Hello List, I would like to perform phenix.rosetta_refine on a structure. I understand that to use this program, I need to set up phenix and rosetta installations separated from those used in MR_Rosetta. I installed the most recent phenix and rosetta and followed the online documents, but when I tried to run "rosetta.build_phenix_interface", the program failed immediately with the following error messages: False scons: Reading SConscript files ... Running versioning script ... fatal: Not a git repository (or any of the parent directories): .git Done. (0.0 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/usr/local/rosetta-refine/rosetta/main/source/SConstruct", line 172: main() File "/usr/local/rosetta-refine/rosetta/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/usr/local/rosetta-refine/rosetta/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/usr/local/rosetta-refine/phenix-dev-2328/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd) These messages are not very informative and I don't know what to do next. Any help will be greatly appreciated. Yonglin Hu

2 2

on b-factor refine
by Smith Liu 15 Mar '16

15 Mar '16

Dear All, I just read a paper on phenix refine, which contains content "B-factor refinement (two groups per residue) ". Here the "two groups per residue" should be accomplished by the phenix command line rather than the GUI, right? And if right, will you please let me know the command for "two groups per residue" for B-factor refine? Smith

2 1

Real space difference maps?
by Oliver Clarke 15 Mar '16

15 Mar '16

Hello, is there any possibility of (or current plan for) including the capacity in a future PHENIX release to calculate a residual map automatically after phenix.real_space refine, (i.e. simulating a map from the model incorporating corrections for B-factor variation and calculating a difference map with the experimental map)? This would be very convenient when building into EM maps. Cheers, Oli

2 5

Postdoc position available at LBNL
by Peter Zwart 14 Mar '16

14 Mar '16

Berkeley Lab's Molecular Biophysics and Integrated Bioimaging Division is looking for a Computational Biologist to work on the development of computational and experimental methodologies for Fluctuation X-ray Scattering (FXS; *http://bit.ly/1W6SONZ* <http://bit.ly/1W6SONZ>) and associated biophysical techniques, such as SAXS/WAXS and Single Particle diffraction. The candidate will be involved in the development and expansion of the underlying theory of FXS, either as a standalone technique or in a hybrid capacity, and will aid in its practical deployment. For details, have a look here: https://lbl.taleo.net/careersection/jobdetail.ftl?job=82189&lang=en#.Vubva0… Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Staff Scientist Berkeley Center for Structural Biology, Science lead Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CAMERA: http://camera.lbl.gov/ -----------------------------------------------------------------

1 0

phenix autosol
by Vandna Kukshal 13 Mar '16

13 Mar '16

Hi , I am solving a structure using selenium SAD using autosol. Autosol gave me nice solution but many loop and side chain density is missing. autosol gave me many different output MTZ files . for building further in coot which MTZ file i should use and for refinement in phenix refinement which MTZ file i should use . I tried doing refinement with .sca file it gave me increase Rfree afte single cycle of refinement . thanks for your suggestions. -- Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110

2 3

Feature request: multi-stage refinement protocols from the GUI?
by Tristan Croll 11 Mar '16

11 Mar '16

Hi all, I'm personally a big fan of the Phenix GUI, in particular for its automated record keeping for different runs. One thing I really wish it had, though, is the option to define more complex refinement scenarios as a single run. An example of what I'm talking about is the following protocol that has been working very well for me on a 3.6 Å strucutre: - ~6 rounds of refinement of TLS, a single group B-factor and occupancies (the latter for a very small set of residues, mostly low-occupancy lead ions) with positions fixed - ~8 rounds of TLS and individual B-factor refinement, still with positions fixed and with no further occupancy refinement - ~8 rounds of TLS, B-factor and position refinement with torsion-angle restraints to the starting model - ~8 rounds of position refinement with no restraints other than standard stereochemistry and metal bonds. I know that all of this could be scripted quite easily from the command line, but it would be fantastic to be able to queue up such a protocol as a single continuous job in the GUI. Best regards, Tristan

5 8

Re: [phenixbb] Fluorescence group of eYFP
by miyatake 09 Mar '16

09 Mar '16

Hello, now I found a solution like below; 1) make links using " Extensions > Modeling > Make Link " in Coot 2) Do Ready_Set using the PDB file, and you'll get cif and link.edits files 3) Delete all the lines which contain OXT in the cif file. 4) Involve the cif and link.edits files to the Phenix.refine job It will work well for the CR2 containing GFP proteins. Best, Miyatake On Tue, 08 Mar 2016 15:00:29 -0800 André Hoelz <hoelz(a)caltech.edu> wrote: > Have you found a solution that works now? I have noticed the same problem that the OXT atom is incorporated and no bond is formed. I would be grateful if you share your a solution. > > Sent from my BlackBerry 10 smartphone. > Original Message > From: miyatake > Sent: Monday, March 7, 2016 11:07 PM > To: Pavel Afonine > Cc: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Fluorescence group of eYFP > > Dear Pavel, > > Thank you for your e-mail. > > The bonds I want to connect are between CR2 and amino acids like below; > > C PHE A 64 N1 CR2 A 66 > C3 CR2 A 66 N LEU A 68 > > so I made links by the "make link" of Coot. > > Then I made .cif file by the Ready_Set, but I noticed > it always contained OTX terminator atom of CR2, so the CR2 connections > to the next amino acids were something wrong after refinement if I used the cif > as it was. > > Thus I deleted OTX in the cif file, and then in turn it went well. > > I wonder why the cif file contained OTX, is it something a bug? > > Thank you for your attention. > > Miyatake > > > > On Mon, 7 Mar 2016 08:40:21 -0800 > Pavel Afonine <pafonine(a)lbl.gov> wrote: > > > Hi Miyatake, > > > > could you please send me (and copy to Nigel) the PDB file (and any > > ligand CIF files you use) and tell what bonds you are expecting to have > > and that brake as result of refinement. > > > > Thanks, > > Pavel > > > > On 3/7/16 03:40, miyatake wrote: > > > Dear all, > > > > > > I'm trying to a mutant of eYFP, which has fluorescence group, > > > CR2. > > > > > > During the refinement, however, the bonds between the CR2 and other amino acids > > > were cleaved even I added the cif file created by the ReadySet. > > > > > > > > > Would some one give me suggestions to solve the problem? > > > > > > Miyatake > > > > > > _______________________________________________ > > > 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

1 0

Re: [phenixbb] 7th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 08 Mar '16

08 Mar '16

Second announcement 7th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. May 16 - May 20, 2016 Detailed information can be found on the workshop web page: https://conference.sns.gov/event/15 Application deadline: April 1, 2016 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 1, 2016. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

1 0

Wrong stereochemical restraint of Hyp
by YANG HAI 07 Mar '16

07 Mar '16

Dear Phenix Developers, I was refining a structure containing L-hydroproline (HYP) and it looks like that the dictionary for HYP in Phenix has the wrong stereochemical restraint. I modeled as L-hydroxylproline (trans) but the phenix.refine always flipped the hydroxyl group and ended up as L-allo-hydroxylproline (cis). I created a .cif file and the issue is resolved, but it would be nice if the restraint can be fixed in the next version of Phenix. Thanks a lot Yang Hai Department of Chemistry, University of Pennsylvnia

2 1

Constrained groups for occupancy refinment
by Jan Abendroth 07 Mar '16

07 Mar '16

Hi all, I have a case where a residue is in two alternative conformations for chain A and chain B. This residue (Arg 62) happens to be close to its NCS mate, such that only conformations A for both chains or only conformations B can take place at the same time. I tried to follow guidance from the CNG newsletter 2015/07 and set up the constrained groups as shown below. However, the refinement crashes with an AtomSelectionError. Any ideas what I could have done differently? Cheers, Jan refinement { refine { occupancies { constrained_group { selection = chain A and resseq 62 and altloc A or \ chain B and resseq 62 and altloc A or selection = chain A and resseq 62 and altloc B or \ chain B and resseq 62 and altloc B or } } } } -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

2 3

Phenix omit maps
by wtempel 04 Mar '16

04 Mar '16

Hello all, is the output of phenix.maps with maps.omit.selection=(resname LIG) equivalent to removal of LIG atoms from coordinates and subsequent map calculation with an empty maps.omit.selection? What, if any, measures of bias removal are applied in the process of map calculation, absent any explicit efforts by the user to modify coordinates? Thank you, Wolfram Tempel

2 1

iNEXT
by Anastassis Perrakis 03 Mar '16

03 Mar '16

Dear all, iNEXT is a Horizon2020 project aiming to allow international users transnational access to infrastructures for Structural Biology, with an emphasis on new users, and a focus on translational research projects in biomedicine, biotechnology and biomaterials. http://www.inext-eu.org For the first time, iNEXT offers coordinated access to NMR, EM, X-ray crystallography and biophysical methods. There are specific access routes for expert users and new users, and for the different techniques. These are becoming gradually available as the project proceeds, and you should expect regular updates. For now you can apply for access to some of the planned modalities, namely: Structural Audit: mail-in your protein sample for quality analysis including stability, dispersity, crystallisation and SAXS Cryo-EM sample optimisation: to move from negative stain to cryo-EM Macromolecular interactions: for accessing biophysical equipment and expertise to quantify macromolecular interactions Synchrotron data: for access to some of the best beamlines in Europe High-field NMR: or access to some of the most powerful NMR machines in Europe High-resolution EM: : for access to some of the best microscopes in Europe For more details please see: http://www.inext-eu.org/access/ with best regards from the iNEXT team, 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

1 0

Remove distant restraint between two atoms
by Blankenfeldt, Wulf 03 Mar '16

03 Mar '16

Dear all, I would like to unrestrain the distance between two atoms in a ligand – how can I do this? I found instructions for writing a remove_restraints_selections.params file in the phenix.refine manual, but it does not seem to address bond distances. Thank you in advance, Wulf ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" 50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50 Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

2 1

Rwork Rfree gap by bust and phenix
by Zheng Zhou 03 Mar '16

03 Mar '16

Dear phenix experts, I have sent the question to the buster discussion board one week ago. I think I'd better consult this problem on the active phenix discussion board. I recently solved a P1 crystal structure, 6 fold NCS at 1.6 angstrom resolution. I used lattice symmetry to generate test set in phenix. The phenix.refine gave me Rwork/Rfree = 0.1828/0.2081. There are pieces of positive and negative density for the compounds. So I tried buster refinement with autoncs, TLS. The density for the compounds are much improved, no obvious positive density. However, It generated Rwork/Rfree = 0.1801/0.1912. I also find similar R factor examples at the similar resolution in the buster wiki: https://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExample4chawa… Would the small gap between Rwrok and Rfree be an issue? I have not deposited buster refined PDB yet, would this acceptable? Any reference to help if any reviewer questions about the small gap? Thanks for your advice in advance. Best, Zheng

1 0

Re: [phenixbb] phenix.elbow with GAMESS
by Dyda 01 Mar '16

01 Mar '16

Dear Nigel, I agree, but pdb is what I have. I should think that the quality of the input should not impact whether .cif is output or not. The end of .gam: COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ CR 24.0 0.1912339815 -0.0759848760 -0.0714344444 O 8.0 2.3234578345 -0.2357845497 -0.1508067587 O 8.0 -0.7105232282 0.0098034893 1.8036685126 O 8.0 1.2076867850 -0.3346443692 -1.7335283981 O 8.0 -0.5260639033 1.7906968578 0.3539796904 O 8.0 0.9068338690 -1.9599479901 -0.6296444533 O 8.0 -1.9397708185 -0.1141525894 0.1891144601 C 6.0 2.8515146213 -0.0055174102 1.1989521238 C 6.0 1.9707450903 -0.6979131843 2.5449414024 C 6.0 0.4359449408 -0.0451724719 2.8465226464 C 6.0 3.0118766316 1.4363395032 1.6481146467 C 6.0 -0.0653144611 0.1564048347 4.4949200023 C 6.0 0.6249516515 0.4233319450 -2.8992641137 C 6.0 0.1643384668 2.4470081023 -2.2535061934 C 6.0 -0.9128640701 2.5088690737 -0.8469830060 C 6.0 1.5743374229 0.5462852223 -3.8500329514 C 6.0 -1.2118325877 3.9283584299 -0.4940679455 C 6.0 -0.1968029455 -3.0386081819 -0.8007813286 C 6.0 -1.6882650231 -2.4665688184 -1.2935287464 C 6.0 -2.6276161825 -1.2806785380 -0.2996777905 C 6.0 -0.3391479898 -3.6453123923 0.6022767778 C 6.0 -4.1453203443 -1.5862494692 0.1854244826 H 1.0 3.8553615186 -0.4420315035 1.2332199192 H 1.0 2.2818981212 -1.6647647766 3.1911897462 H 1.0 1.9667722755 1.9810594320 1.6970399031 H 1.0 3.6823942975 1.6618943249 2.5365171626 H 1.0 3.6238703905 1.9113333115 0.7438740891 H 1.0 0.8971167594 0.4695270592 5.1329947121 H 1.0 -0.6645891831 1.2206664940 4.5846682936 H 1.0 -0.6246971002 -0.6219821332 4.8583146656 H 1.0 -0.2487681929 -0.1134304045 -3.2439960069 H 1.0 1.1860397915 3.0186834522 -2.1641816248 H 1.0 -0.3750591440 2.8925729326 -3.2804399647 H 1.0 -1.9371292026 2.0739333624 -1.0806155814 H 1.0 1.9496290579 -0.6216286700 -4.2730835081 H 1.0 2.4497745286 1.0199721671 -3.6228827183 H 1.0 1.0277269687 0.9853088788 -4.8324755816 H 1.0 -1.6488875565 4.5338413808 -1.4704889855 H 1.0 -1.7951603842 3.9656768136 0.3514485986 H 1.0 -0.2983062508 4.5239905524 -0.4318350930 H 1.0 0.1219656972 -3.8775516930 -1.5693737575 H 1.0 -2.2141859609 -2.6816187114 -2.2405875656 H 1.0 0.7133579392 -3.9124935444 1.0380228614 H 1.0 -0.7783653014 -2.9666445248 1.3120392457 H 1.0 -0.9150821609 -4.6238970562 0.5814496583 H 1.0 -4.2320258907 -2.8021018481 0.2370382406 H 1.0 -4.7833967302 -1.1881592471 -0.7055025179 H 1.0 -4.4126745266 -1.1246420328 1.0220077683 ******************** 1 ELECTRON INTEGRALS ******************** ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 0.1 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 100.00% ------------- GUESS OPTIONS ------------- GUESS =HUCKEL NORB = 0 NORDER= 0 MIX = F PRTMO = F PUNMO = F TOLZ = 1.0E-08 TOLE = 1.0E-05 SYMDEN= F PURIFY= F INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE. HUCKEL GUESS REQUIRES 649929 WORDS. SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH SET(S). 94 ORBITALS ARE OCCUPIED ( 30 CORE ORBITALS). 31=A 32=A 33=A 34=A 35=A 36=A 37=A 38=A 39=A 40=A 41=A 42=A 43=A 44=A 45=A 46=A 47=A 48=A 49=A 50=A 51=A 52=A 53=A 54=A 55=A 56=A 57=A 58=A 59=A 60=A 61=A 62=A 63=A 64=A 65=A 66=A 67=A 68=A 69=A 70=A 71=A 72=A 73=A 74=A 75=A 76=A 77=A 78=A 79=A 80=A 81=A 82=A 83=A 84=A 85=A 86=A 87=A 88=A 89=A 90=A 91=A 92=A 93=A 94=A 95=A 96=A 97=A 98=A 99=A 100=A 101=A 102=A 103=A 104=A ...... END OF INITIAL ORBITAL SELECTION ...... CPU 0: STEP CPU TIME= 0.24 TOTAL CPU TIME= 0.3 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.4 SECONDS, CPU UTILIZATION IS 86.49% ---------------------- AO INTEGRAL TECHNOLOGY ---------------------- S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR). S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE). S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5, ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER). S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY). -------------------- 2 ELECTRON INTEGRALS -------------------- DIRECT SCF METHOD SKIPS INTEGRAL STORAGE ON DISK. DIRECT TRANSFORMATION SKIPS AO INTEGRAL STORAGE ON DISK. ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 0.3 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.4 SECONDS, CPU UTILIZATION IS 86.84% -------------------------- RHF SCF CALCULATION -------------------------- NUCLEAR ENERGY = 2520.5794603055 MAXIT = 199 NPUNCH= 2 EXTRAP=T DAMP=T SHIFT=F RSTRCT=F DIIS=F DEM=F SOSCF=T DENSITY MATRIX CONV= 2.00E-05 SOSCF WILL OPTIMIZE 16544 ORBITAL ROTATIONS, SOGTOL= 0.250 MEMORY REQUIRED FOR RHF ITERS= 640658 WORDS. DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 SCHWARZ INEQUALITY OVERHEAD: 30854 INTEGRALS, T= 0.00 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD VIR. SHIFT DAMPING INTEGRALS SKIPPED 1 0 0 -2059.2212832191 -2059.2212832191 0.988797951 0.000000000 0.000000000 1.000000000 191835514 22895770 2 1 0 -2042.8253644320 16.3959187871 1.142306775 0.674963723 0.000000000 1.000000000 192284889 22920383 3 2 0 -2053.1297307637 -10.3043663316 0.401569267 0.408533345 0.000000000 54.508125229 192386468 22914751 4 3 0 -2054.8896748699 -1.7599441062 0.681705613 0.974133914 0.000000000 3.406757827 185808214 23658736 ---------------START SECOND ORDER SCF--------------- 5 4 0 -2060.2884381280 -5.3987632581 1.089757171 0.228307597 0.000000000 0.000000000 191024572 23175415 6 5 0 -2062.5678087125 -2.2793705845 0.335341404 0.164617327 0.000000000 0.000000000 191517675 23118064 7 6 0 -2063.0509541215 -0.4831454090 0.503307418 0.129756838 0.000000000 0.000000000 189580417 23389152 I think the coords are the final config. Thanks for your help, Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

2 1

phenix.elbow with GAMESS
by Nigel Moriarty 01 Mar '16

01 Mar '16

Fred Does the .gam have a final geometry? You'll need to check because performing a QM geometry minimisation is not straight forward. BTW. A PDB file is the lowest quality input format. It's recommended that you try for a most information rich input such as SMILES or mol2. 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

1 0

5th International Symposium on Diffraction Structural Biology (ISDSB2016)
by Leighton Coates 01 Mar '16

01 Mar '16

Hi All On behalf of the organizing committee, I am pleased to announce the “5th International Symposium on Diffraction Structural Biology” (ISDSB2016). The Symposium will take place on Sunday, August 7, 2016 through Wednesday, August 10, 2016 in Knoxville, Tennessee, USA. This symposium will report on the latest discoveries in structural biology using X-ray, neutron, and electron diffraction, and complementary techniques such as small-angle scattering, nuclear magnetic resonance spectroscopy, electron microscopy, and advanced computational approaches. Scientific insights at the molecular level allow structure guided drug discovery and protein engineering for improved biocatalysis. This basic research is important for supporting applications in the pharmaceutical industry and for new, sustainable, and environmentally friendly approaches to the production of chemical reagents and biofuels. Session topics include: Bioenergy Drug Design Enzyme Mechanism and Allostery Macromolecular Complexes Membranes and Membrane Proteins New Instruments and Methods Sources and Facilities A list of confirmed, invited speakers can be found on the conference web pages. The Symposium will be accompanied by two optional 1-day workshops on August 6, focused on Neutron Protein Crystallography and on Small-Angle Scattering, respectively. Please visit the conference website for further information: https://conference.sns.gov/event/2/ Thanks Leighton

1 0

Command line version of Reflection_file _editor
by Rahel Woldeyes 29 Feb '16

29 Feb '16

Hi all, I was wondering if anyone has implemented command line compatible version of phenix.reflection_file_editor . Thanks! Rahel

2 1

Command line version of Reflection_file _editor
by Rahel Woldeyes 29 Feb '16

29 Feb '16

Hi all, I was wondering if anyone has implemented command line compatible version of phenix.reflection_file_editor . Thanks!

1 0

Simulated annealing composite omit map
by Appu kumar 29 Feb '16

29 Feb '16

Hello All, I am trying to make the simulated annealing composite omit map for a protein ligand complex at 4.37A resolution. I think, Simulated annealing is harsh and rendering the protein distorting a lot as is evident from the helix turning into the some random structure. In order to avoid this protein distortion in protein backbone, do I need to fix some weight or specific parameter or provide reference structure and put harsh weight ? Any advice or suggestions would be much appreciated. Appu

2 1