- phenixbb - phenix-online.org

Re: [phenixbb] Is it harmful to to use Imean SigImean in Phenix Refine by default?
by Jeffrey, Philip D. 04 Dec '17

04 Dec '17

To put this in context: I originally wrote that page when phenix.refine used a |F|>0 cutoff in refinement. Given that I<0 often results in |F|=0 after the conversion the program threw out data for which we knew something (i.e. it was weak) albeit imprecisely. That was a self-evidently bad idea. However the defaults in phenix.refine have changed and as Ed Berry observes it does emulate CCP4's TRUNCATE now (in "truncate yes" mode, probably). I convert my data with CCP4's TRUNCATE or CTRUNCATE programs. For strong data I don't apply the French and Wilson intensity data remapping. For weak data I do - but only for refinement purposes, not for SAD/MAD phasing. My standard ploy is to use CAD to strip out Imean and SigImean from the MTZ file so that phenix.refine cannot attempt to "outsmart" me again. And by outsmart I really mean "usurp my intentions". I would suggest that everyone do the same - or at least test the difference. My known bias is to trust CCP4 programs more. Cheers Phil Jeffrey Princeton ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Xiao Lei [xiaoleiusc(a)gmail.com] Sent: Saturday, December 02, 2017 9:05 PM To: PHENIX user mailing list Subject: [phenixbb] Is it harmful to to use Imean SigImean in Phenix Refine by default? Dear All, I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF. I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful" ( web link http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead." This may force rejecting weak data according to the post. The latest Phenix version may be updated from the version the post author used, I wonder if this risk is still in the newest version of Phenix ?

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Is it possible to restrain Cartesian NCS for ligands?
by Edward A. Berry 03 Dec '17

03 Dec '17

Is it possible to restrain cartesian NCS for ligands in phenix.refine? I included a ligand in an paired ncs-group and it seems to be omitted from the listing of those groups in the log file. When I made an ncs_group including only ligands, it halted complaining of empty selection. Ed

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Is it harmful to to use Imean SigImean in Phenix Refine by default?
by Xiao Lei 03 Dec '17

03 Dec '17

Dear All, I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF. I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful" ( web link http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead." This may force rejecting weak data according to the post. The latest Phenix version may be updated from the version the post author used, I wonder if this risk is still in the newest version of Phenix ?

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 20 Nov '17

20 Nov '17

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the January 2018 issue is 20 December 2017. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Bug in 2.10.3 with scrolling
by Mark Saper 20 Nov '17

20 Nov '17

If one scrolls an alignment (not WRAP mode), the names of the sequences scroll but not the sequences with it. Using the scroll bar works correctly. Running 2.10.3 on MacOS 10.12.6 with Java version: 1.8.0_151. Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

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Ligand library error in Phenix.Refine
by Gyanendra Kumar 16 Nov '17

16 Nov '17

Hi there, My Phenix.Refine run crashes because of non-availability of dictionary file for "ACP", a non-hydrolyzable ATP. Could this ligand be added to the next nightly build? Phenix.Refine suggested using "ReadySet", but that also failed. I sent the error reports to bugs(a)phenix-online.org, all emails bounced back. Refmac runs fine. Thanks! -Gyan -- Gyanendra Kumar, PhD Associate Scientist, St. Jude Children's Research Hospital, Department of Structural Biology, 262, Danny Thomas Place, MS-311 Memphis, TN 38105 Cell: 631-875-9189 https://www.linkedin.com/in/gyanendrakumar https://scholar.google.com/gyanendrakumar <https://scholar.google.com/citations?user=lnil0IQAAAAJ&hl=en> https://www.researchgate.net/profile/Gyanendra_Kumar3 http://stjude.academia.edu/GyanendraKumar -------------------------------------------------------

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(no subject)
by Rajendra Sharma 15 Nov '17

15 Nov '17

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Max_reasonble_bond_distance error in phene.resl.space.refine
by Rune Thomas Kidmose 15 Nov '17

15 Nov '17

I have been playing around with phenix.real.space.refine as part of a small pipeline I am making for EM structures. Testing various deposited EM structures and their corresponding maps, within my pipeline, I sometimes run in to the below error: RuntimeError: Bond distance > max_reasonable_bond_distance: 79.8663 > 50: Followed by a list of distances between, what I am assuming is, atom numbers and the actual distance. I can get past it simply by changing the max_reasonable_bond_distance for the run to, in this case, 80. But I tend to see, that the final results gets significantly worse when I use this bypass. This is based on very similar models going through the pipeline, where the ones which yields the error, scores much worse when using the above mentioned bypass, compared to the models that showed no max_reasonable_distance_error. So I was wondering: A: What does "max reasonable bond distance" actual mean? B: Any ide what I can do, to avoid running into this bond distance problem? I know the latter is asking a lot, as I have not disclosed any of the details surrounding how the error arose etc. but if such info is needed, I would prefer to do so off list and then return with the solution on list, if possible. Maybe I was hoping for a setting that ignores the outliers, without changing the max value. But that all depends on, what the setting actual is, which I dont know Cheers Ruki

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Twin refinement problem
by Leonid Sazanov 15 Nov '17

15 Nov '17

Dear all, there seems to be a problem with twin refinement of some of our datasets, and I wanted to see if that is something specific to our data or if anybody else has seen it. These crystals have been reproduced many times and are always twinned in P21 space group with twin operator: -h,-k,h+l and twin fraction in the range 0.45 - 0.49. Data always refines fine in Refmac and in many cases in Phenix as well, giving similar twin fraction in both programs. However, with some datasets (at 3.4-3.6 A resolution) in Phenix there is a problem: refinement of twin fraction is unstable and jumps each macro-cycle between about 0.40 (wrong?, giving high R-factors) and 0.47 or so (true?, giving much lower R-factors). This can be clearly seen from log file extract: cycle stage r-work r-free twin_fraction 0 : 0.3002 0.3084 1_adp: 0.2511 0.2701 0.49 2_adp: 0.2724 0.2837 0.42 3_adp: 0.2296 0.2465 0.47 4_adp: 0.2464 0.2587 0.40 5_adp: 0.2230 0.2420 0.47 6_adp: 0.2393 0.2554 0.40 7_adp: 0.2225 0.2423 0.47 8_adp: 0.2416 0.2590 0.40 9_adp: 0.2184 0.2376 0.47 10_adp: 0.2380 0.2556 0.40 end: 0.2393 0.2568 0.39 ------------------------------------------- The same dataset refines with stable twin fraction = 0.48 in refmac. When Phenix accepts higher twin_fraction with its lower R-factors, it does cycles 0 and 1 of twin fraction refinement once, while when it fails to update and falls back to low twin_fraction, it does this twice, as shown below. Updates OK: =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2383 0.2381 0.2565 n_refl.: 191608 twin_fraction=0.40 re-set all scales: r(all,work,free)=0.2926 0.2926 0.2950 n_refl.: 191608 twin_fraction=0.40 cycle 0: update twin fraction: r(all,work,free)=0.2910 0.2910 0.2933 n_refl.: 191608 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2910 0.2910 0.2933 n_refl.: 191608 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2910 0.2910 0.2933 n_refl.: 191608 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2249 0.2246 0.2473 n_refl.: 191608 twin_fraction=0.48 cycle 1: update twin fraction: r(all,work,free)=0.2249 0.2246 0.2472 n_refl.: 191608 twin_fraction=0.47 update scales twin start: r(all,work,free)=0.2249 0.2246 0.2472 n_refl.: 191608 twin_fraction=0.47 reset f_part, k_(total,mask): r(all,work,free)=0.2910 0.2911 0.2934 n_refl.: 191608 twin_fraction=0.47 bulk-solvent and scaling: r(all,work,free)=0.2249 0.2246 0.2472 n_refl.: 191608 twin_fraction=0.47 r_work=0.2246 r_free=0.2472 twin_fraction=0.47 twin_law=-H,-K,H+L ============================ Set refinement target ============================ Falls back: =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2216 0.2214 0.2408 n_refl.: 191608 twin_fraction=0.47 re-set all scales: r(all,work,free)=0.2855 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.47 cycle 0: update twin fraction: r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 cycle 1: update twin fraction: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 start: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 re-set all scales: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 cycle 0: update twin fraction: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2330 0.2329 0.2486 n_refl.: 191509 twin_fraction=0.48 cycle 1: update twin fraction: r(all,work,free)=0.2306 0.2305 0.2458 n_refl.: 191509 twin_fraction=0.40 update scales twin start: r(all,work,free)=0.2306 0.2305 0.2458 n_refl.: 191509 twin_fraction=0.40 reset f_part, k_(total,mask): r(all,work,free)=0.2781 0.2780 0.2846 n_refl.: 191509 twin_fraction=0.40 bulk-solvent and scaling: r(all,work,free)=0.2295 0.2293 0.2439 n_refl.: 191509 twin_fraction=0.40 r_work=0.2374 r_free=0.2522 twin_fraction=0.40 twin_law=-H,-K,H+L ============================ Set refinement target ============================ With some other datasets Phenix just gets stuck at apparently in-correctly low twin fraction - each cycle it tries to update to 0.47-0.48 (and R factors are better in this case) but then it always falls back to 0.36-0.40 again. So I wonder if anybody else has seen this with their data? Many thanks for any info! Leonid -- Prof. Leonid Sazanov IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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Postdoctoral research position
by Demetres D. Leonidas 14 Nov '17

14 Nov '17

Postdoctoral research position: molecular biologist/bioinformatician A 2-year Post-Doctoral position is available immediately in the Laboratory of Molecular Biology and Genomics in the Department of Biochemistry and Biotechnology of the University of Thessaly, located in the city of Larissa. The selected candidate will work in the framework of a national Research Infrastructure program on Synthetic Biology. Research in the Laboratory of Molecular Biology and Genomics focuses on various aspects of insect olfaction, reproduction and evolution, aiming at the development of new approaches for control of insects of agricultural or medical importance. We are seeking a highly motivated and creative scientist with a track record of successful research. A good bioinformatics background is strongly desired. The ideal candidate should be able to analyze raw sequencing data, perform genome assembly and annotation and have a good understanding of comparative and functional genomics. At the same time, he/she should be able to design and perform experiments in support of the bioinformatics analyses. Candidates should have a PhD and should have training in one or more of the following disciplines: bioinformatics, molecular biology, biochemistry, cell biology, and genome-wide technologies. Familiarity with insect rearing is desirable but not essential. Curriculum Vitae, a brief letter describing interests and prior experience and names of three references should be sent to: kmathiop(a)bio.uth.gr. Research position: MSc Bioinformatician A 2-year position for an MSc Bioinformatician is available immediately in the Laboratory of Molecular Biology and Genomics in the Department of Biochemistry and Biotechnology of the University of Thessaly, located in the city of Larissa. The selected candidate will work in the framework of a national Research Infrastructure program on Synthetic Biology. Research in the Laboratory of Molecular Biology and Genomics focuses on various aspects of insect olfaction, reproduction and evolution, aiming at the development of new approaches for control of insects of agricultural or medical importance. We are seeking a highly motivated individual with a BSc in Biology or related science and an MSc in Bioinformatics. The successful candidate will be involved in raw sequencing data analysis, genome assembly and annotation and comparative and functional genomics studies. His/her research could also lead to a PhD. Curriculum Vitae, a brief letter describing interests and prior experience and names of three references should be sent to: kmathiop(a)bio.uth.gr. -- ----------------------------------------------- Dr. Demetres D. Leonidas Professor of Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece --------------------------------------------- Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleonidas(a)bio.uth.gr http://www.bio.uth.gr ORCID ID orcid.org/0000-0002-3874-2523 ----------------------------------------------- --- Αυτό το e-mail ελέγχθηκε για ιούς από το πρόγραμμα Avast antivirus. https://www.avast.com/antivirus

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bgroup refinement of ZN ions
by Ursula Schulze-Gahmen 13 Nov '17

13 Nov '17

I have 2 Zn ions which are defined as HETATM, in my structure. I am using tls and bgroup refinement for the whole structure. It seems like the Zn ions are treated as one group. They always have the same B-value. I would like to refine the B-value of the ZN ions separately, but refine the rest of the structure with bgroup refinement. Is that possible? How would I do this? 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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mmtbx.prepare_pdb_deposition sequence file
by Ursula Schulze-Gahmen 09 Nov '17

09 Nov '17

I have problems running 'mmtbx.prepare_pdb_deposition' on the cif file created in phenix. I think the problem may be the sequence file. The coordinates are from a complex of 4 proteins plus an RNA. I created a text file with 5 chains, each chain sequence in one letter code. I am getting the following error code when I try to run the program: Traceback (most recent call last): File "/home/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 99, in <module> run(sys.argv[1:]) File "/home/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 69, in run alignment_params=params) File "/home/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 1052, in as_cif_block_with_sequence assert len(chain.residue_groups) + chain.n_missing_start + chain.n_missing_end == len(sequence) There seems to be something wrong with chain N, but I am not sure what. Is it ok to have a longer sequence in the sequence file than in the coordinates? 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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chain and residue ID in phenix.erraser
by Ursula Schulze-Gahmen 08 Nov '17

08 Nov '17

I am trying to run phenix.erraser, but I am not able to define the single residue for rebuilding correctly. I am getting error messaheg: Please make sure that you include both the chain ID and residue number, for example 'A15'. I want to rebuild nucleotide G32 in chain N, and defined the residue as N32. That is not correct. What would be the correct syntax for this case? 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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Question about writing cif files at the last round of refinement
by Boaz Shaanan 07 Nov '17

07 Nov '17

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kicked map calculations
by Ursula Schulze-Gahmen 07 Nov '17

07 Nov '17

I am trying to calculate kicked maps in the phenix GUI, but I don't get the option, nit in the mtz files, and not in the CCP4 map option. Could that have something to do with this error message I am getting when starting Phenix: Gtk-Message: Failed to load module "canberra-gtk-module" Gtk-Message: Failed to load module "pk-gtk-module" Or are there any settings I need to change? 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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data fill in in phenix refine?
by Ursula Schulze-Gahmen 26 Oct '17

26 Oct '17

I have data from a crystal with anisotropic diffraction. After scaling and merging using the webserver staraniso, I would like to refine using phenix refine. Could you tell me if phenixrefine will try to fill in the missing reflections that were removed in the staraniso procedure? If so, is there a a way to prevent this fill in? Following is the warning message for the Staraniso server: We are grateful to Andrew Leslie (MRC-LMB) for identifying a potentially undesirable 'feature' of CCP4/REFMAC (and possibly other refinement software), namely the 'fill-in' of unobserved data with *DF*calc which makes it effectively *incompatible* with the MTZ file output by STARANISO. Our advice is therefore to use *BUSTER <http://www.globalphasing.com/buster>* for refinement using the downloaded MTZ file, unless the user can find a way to disable that feature in the alternative software. In general, any treatment of STARANISO's output data that adds missing reflections out to the resolution limit may result in a very high proportion of unobserved data compared with data that have had a cut-off applied according to an isotropic criterion. Where missing reflections have been added in this way the user should take care to verify that any applications used to process the data subsequently can handle it correctly. 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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Announcing the release of CryoFIT
by Nigel Moriarty 23 Oct '17

23 Oct '17

Dear colleagues, We are excited to announce the release of CryoFIT, a program for fitting atomistic models to cryo-EM maps. The current version is designed for fitting lower resolution maps but this does not preclude use with higher resolution maps. The CryoFIT modules is built on Gromacs and accessible through Phenix (https://www.phenix-online.org/documentation/reference/ cryo_fit.html), currently via GitHub. It supports both the Phenix GUI and the command line. CryoFIT is based on the algorithm in Kirmiziatltin, et al., Methods of Enzymology 2015 (https://doi.org/10.1016/bs.mie.2015.02.011). This is an alpha version. Please send any feature requests and bug reports to Doo Nam Kim (doonam(a)lanl.gov). Happy Modeling! Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Email addresses for bug reports
by Billy Poon 23 Oct '17

23 Oct '17

Hi everyone, We've been receiving bug reports with incorrect or dummy email addresses (e.g. "go away.com"). While we read through all of these bug reports, we cannot respond to them without correct email address. Before submitting a bug report from the Phenix GUI, please make sure that the email address is correct. Alternatively, bug reports can be sent to bugs(a)phenix-online.org. Thanks! -- 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

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Re: [phenixbb] [cctbxbb] Update to allsvn script?
by Billy Poon 20 Oct '17

20 Oct '17

Hi all, Is anyone still using "allsvn" from the phenix_regression repository? If not, we'll just delete it next Friday (10/27) since it's hopelessly out of date. The functionality has been superseded by bootstrap.py. Thanks! -- 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 On Thu, Oct 19, 2017 at 11:22 PM, <Graeme.Winter(a)diamond.ac.uk> wrote: > Folks, > > phenix_regression/allsvn assumes if you are using git that you are using > git/svn > > These days probably not true ;o) > > Viz: > > > cd cctbx_project; git svn rebase > > Unable to determine upstream SVN information from working tree history > > > ccp4io: At revision 160. > > ccp4io_adaptbx: At revision 142. > > cd dials; git svn rebase > > Unable to determine upstream SVN information from working tree history > > someone on phenix-land want to have a look at this? Obviously not a > blocker but is untidy! > > Thanks Graeme > > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

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Job opening: Postdoctoral Fellow in Structural Biology and Drug Discovery
by Schonbrunn, Ernst 19 Oct '17

19 Oct '17

Dear Madam/Sir, Please post the following open postdoctoral position on your job-board. Thank you, Ernst Schonbrunn ----------------------------------------------------------------------------------------------- Postdoctoral Fellow in Structural Biology and Drug Discovery Location: Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612 Department: Drug Discovery Department Job Details: Moffitt Cancer Center is internationally recognized for our focus on personalized cancer care and translational research. The mission of Moffitt is clear, focused, and fully stated in nine words, "To contribute to the prevention and cure of cancer." With a tradition of excellence that began with the first patient admission in 1986, dedicated Moffitt physicians, scientists, and staff members have remained committed to excellence in an atmosphere characterized by kindness, caring, and hope. The Schönbrunn lab studies the structure-function relationship of medicinally relevant proteins along with the discovery and development of novel small molecule inhibitors as therapeutics. We are involved in multiple projects working in team with medicinal chemists, biologists and clinicians on the targeting of proteins involved in cell signaling and epigenetic events. For an overview of our research approach and current projects please visit our web site at labpages2.moffitt.org/schonbrunn/<http://labpages2.moffitt.org/schonbrunn/>. Position Highlights: · We seek highly motivated postdoctoral researchers to work on inter-disciplinary projects towards the characterization and inhibitor development of diverse kinases and bromodomain-containing proteins. * The position provides exciting opportunities for biochemical, structural and cell-based studies of various drug-target interactions and rational drug design. The Ideal Candidate: · The ideal candidate has a Ph.D. degree in Biochemistry, Biology, Chemistry, Physics or related field and expertise in protein crystallography and biochemistry as demonstrated by publications in internationally recognized scientific journals. * Additional experience in cell biology is preferred. Responsibilities: · Candidates must be enthusiastic and dedicated to science with excellent organizational skills and effective at working independently, while also collaborating and assisting the team in its collective research goals. * Attention to detail and ability to work on multiple projects is required. * Excellent verbal and written communication skills are required. Credentials and Qualifications: * Ph.D. degree in Biochemistry, Biology, Chemistry, Physics or related field. A competitive salary and benefits package will be offered to the successful candidate. Interested applicants should send a single PDF file that includes a current CV with recent publications, a personal statement of scientific interests and goals (2-page maximum) and contact information for three references to Dr. Ernst Schönbrunn at Ernst.Schonbrunn(a)moffitt.org<mailto:[email protected]> Equal Employment Opportunity Moffitt Cancer Center is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, or protected veteran or disabled status. We seek candidates whose skills, and personal and professional experience, have prepared them to contribute to our commitment to diversity and excellence. [MOFFITT_2c_RGB for signature] Ernst Schönbrunn, PhD Associate Professor Moffitt Cancer Center 12902 Magnolia Drive, Tampa, FL 33612 | tel: 813-745-4703 | email: ernst.schonbrunn(a)moffitt.org Please consider the environment before printing this email. This transmission may be confidential or protected from disclosure and is only for review and use by the intended recipient. Access by anyone else is unauthorized. Any unauthorized reader is hereby notified that any review, use, dissemination, disclosure or copying of this information, or any act or omission taken in reliance on it, is prohibited and may be unlawful. If you received this transmission in error, please notify the sender immediately. Thank you.

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Install Phenix 2926 on Linux Fail
by Xiao Lei 18 Oct '17

18 Oct '17

Dear All, I was trying to install Phenix 2926 on Ubuntu Mate, after type sudo ./install I got the following fail message: ========================================================= Phenix Installation version: dev-2926 machine type: intel-linux-2.6-x86_64 OS version: 4.4.0-97-generic destination: /usr/local/phenix-dev-2926 # of processors: 4 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 275, in <module> installer(sys.argv[1:]).install() File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 197, in install self.install_from_binary() File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 319, in install_from_binary self.reconfigure(log=log) File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 379, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-dev-2926/base/bin/python /usr/local/phenix-dev-2926/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-dev-2926/build --command_version_suffix dev-2926 phenix phaser solve_resolve labelit dials xia2 iota prime' failed with exit code 1 What I need to do to fix this?

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SHELX sites to use in Phenix.
by Mahmudul Hasan 18 Oct '17

18 Oct '17

Dear All, I am trying to solve a structure using Phenix with very low anomalous signal. After several trials it seems like the signal from Manganese is not enough to solve this protein structure. Reading information that SHELX is good in finding sites from low molecular weight molecules (e.g. S, etc.), I tried the online version of SHELX in CCP4 to find the sites. Now I would like use these sites found by SHELX to see if that help to solve the structure. My question is, what is the best way to include extra sites besides the program Autosol find itself? Your valuable suggestions will help me a lot to get going with my structure solution effort. Best wishes, Mahmudul Lund Sweden

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Model_vs_data speed
by Eric Williams 16 Oct '17

16 Oct '17

I'm having a devil of a time getting model_vs_data to run in a timely fashion. Running the latest stable Linux build on Ubuntu 14.04 takes on the order of 3 minutes per structure. That wouldn't be so bad if I weren't trying to run it on every entry in the PDB. Is it just a limitation of Python? SFCheck, which I think is written mostly in FORTRAN, runs in a few seconds. Any help anyone could offer would be appreciated. Thanks. :) Eric

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Re: [phenixbb] Small change in molprobity report on output pdb between dev-2873 and dev-2919?
by Christopher Williams 09 Oct '17

09 Oct '17

I'll take a look. Thanks for noticing! -Christopher Williams ---Richardson Lab On Mon, Oct 9, 2017 at 12:44 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Boaz, > > I had to disable it because it required re-calculation of all other > Molprobity metrics twice, which it time waste. > > @developers: Can someone from Richardson Lab fix this? > > Pavel > > > > On 10/9/17 09:35, Boaz Shaanan wrote: > > Hi, > > I noticed a small change in output pdb between these two versions in the > molprobity report (these are two different runs, so ignore the numerical > values)t: > > *dev-2919:* > > REMARK 3 REMARK 3 > REMARK 3 MOLPROBITY STATISTICS. > REMARK 3 ALL-ATOM CLASHSCORE : 3.13 > RAMACHANDRAN PLOT: > REMARK 3 OUTLIERS : 0.46 % > REMARK 3 ALLOWED : 3.24 % > REMARK 3 FAVORED : 96.30 % > > *dev-2873:* > > REMARK 3 MOLPROBITY STATISTICS. > REMARK 3 ALL-ATOM CLASHSCORE : 2.56 > REMARK 3 MOLPROBITY SCORE : 1.24 This line is missing from the > newer version > REMARK 3 RAMACHANDRAN PLOT: > REMARK 3 OUTLIERS : 0.46 % > REMARK 3 ALLOWED : 2.78 % > REMARK 3 FAVORED : 96.76 % > > I am just wondering whether this change is intentional. > > 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 <bshaanan(a)bgu.ac.il> Phone: 972-8-647-2220 Skype: > boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > > > _______________________________________________ > phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > >

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Rosetta installation
by Daniele de Sanctis 08 Oct '17

08 Oct '17

Hi all I have some trouble installing rosetta. I followed the instruction as in https://www.phenix-online.org/documentation/reference/rosetta_install.html and everything went ok up to % rosetta.build_phenix_interface nproc=n but then % rosetta.run_tests fails with Rosetta command-line arguments: -parser:protocol /buffer/desancti/xtal/rosetta_src_2016.32.58837_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s 1yjp_rosetta_in.pdb -mtzfile 1yjp_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1yjp_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -score:weights talaris2013_cart -nstruct 1 Generating 2 models on 1 processors... DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) Traceback (most recent call last): File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in <module> run(sys.argv[1:], create_dir=True) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs check_result(result) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Any idea? thanks Daniele

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