March 2016 - phenixbb - phenix-online.org

Refine pixel size of map (for EM data)?
by Oliver Clarke 26 Jul '16

26 Jul '16

Hello, I wonder whether it would be possible to add an option for phenix.real_space_refine to allow refinement of the pixel size of the map (or the unit cell dimensions - just an overall size scale factor), and write out the altered map at the end of refinement. Although we try to calibrate this as best as we are able at the time of data collection, it is never perfect - for example, in one case I have dealt with, our nominal pixel size out of the scope is 1.19 Å, but the pixel size calibrated based on a crystal structure of a fragment of the protein is 1.25 Å. This is not a huge difference, but it is sufficient I think to have a substantial impact on refinement, particularly as regards clash assessment and H-bond/sec struc restraints. In cases where one does not have a solved crystal structure to use for calibration, perhaps refining the pixel size in conjunction with the geometry might be of some use? Cheers, Oli

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phenix.polder - tool for calculating omit maps by excluding bulk solvent
by Dorothee Liebschner 22 Apr '16

22 Apr '16

Dear phenix users, Starting from the nightly build dev-2356, a new tool for calculating ligand omit-maps, called 'polder', is included in phenix. Usage: phenix.polder model.pdb data.mtz selection='chain A and resseq 123’ Phenix.polder calculates omit maps for atom selections by preventing the bulk solvent mask to flood into the atom selection area and its vicinity. The tool can be useful in cases where the density of the selected atoms is weak and possibly obscured by bulk solvent. Polder produces less biased maps compared to procedures where the atom selection occupancy is set to zero, and the atoms are included in the solvent mask calculation (in that case, the resulting difference density can have similar shape than the selected atoms). Phenix.polder excludes a larger volume from the bulk solvent and therefore prevents misinterpreting bulk solvent density as omit density. If you want to know more about how the tool is working and to see some examples, have a look at the presentation file: https://www.phenix-online.org/presentations/phenix_polder.pdf. The documentation page can be found here: www.phenix-online.org/version_docs/dev-2356/reference/polder.html Best wishes, Dorothee

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Berkeley Server Downtime (3/30/2016)
by Billy Poon 31 Mar '16

31 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

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autosol error
by Schnicker, Nicholas J 31 Mar '16

31 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

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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.

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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

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BSR2016: 12th International Conference on Biology and Synchrotron Radiation
by Thomas Eriksson 30 Mar '16

30 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 -------------------------------------------

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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

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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

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.Trash_UID error message
by Michael Weyand 24 Mar '16

24 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

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