- phenixbb - phenix-online.org

Postdoctoral research position
by Demetres D. Leonidas 15 Nov '17

15 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 24 Oct '17

24 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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