[ccp4bb] Scientific software programmer at UCLA
Dear all; The Gonen lab at UCLA's Department of Biological Chemistry is looking for a research specialist in scientific software programming to develop software for computational biological image analysis. The Gonen lab works toward understanding how membrane proteins help cells maintain homeostasis. To that end, the lab studies channels, transporters, and receptors, structurally and functionally. More information about the lab can be found by visiting https://cryoem.ucla.edu/. Details about the position and application instructions here: https://hhmi.wd1.myworkdayjobs.com/External/job/University-of-California-Los-Angeles/Research-Specialist---Scientific-Software-Programming_R-412 // Best wishes; Johan To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] MicroED workshop 2020
On 2020-12-08 15:23, Johan Hattne wrote: Dear all; We are pleased to announce the 6th MicroED workshop to be held on December 21, 2020. This will be a free virtual event. Please register at the following website to receive your link https://cryoem.ucla.edu/course Topics covered will include all aspects of microcrystal electron diffraction (MicroED) of diverse samples such as soluble proteins, membrane proteins, small molecules, natural products, and other materials. We will cover 1. Sample preparation methodologies 2. EPU-D for data collection 3. Camera systems and performance 4. FIB-milling procedures for soluble and membrane protein samples 5. Data analysis software, refinement, and structure solution The schedule is available on the registration page. We have now increased the capacity of the Zoom webinar and reopened registration. Unless we exceed the Zoom limitation again, registration will remain open until Saturday, December 19. // Sincerely; on behalf of the organizing committee (Tamir Gonen, Brandon Mercado, Brent Nannenga) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] MicroED workshop 2020
Dear all; We are pleased to announce the 6th MicroED workshop to be held on December 21, 2020. This will be a free virtual event. Please register at the following website to receive your link https://cryoem.ucla.edu/course Topics covered will include all aspects of microcrystal electron diffraction (MicroED) of diverse samples such as soluble proteins, membrane proteins, small molecules, natural products, and other materials. We will cover 1. Sample preparation methodologies 2. EPU-D for data collection 3. Camera systems and performance 4. FIB-milling procedures for soluble and membrane protein samples 5. Data analysis software, refinement, and structure solution The schedule is available on the registration page. // Sincerely; on behalf of the organizing committee (Tamir Gonen, Brandon Mercado, Brent Nannenga) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [xds] how to specify measuring angle
On 2020-10-09 01:59, Dirk Kostrewa wrote: Dear Doo Nam Kim, On 09.10.20 08:43, Doo Nam Kim wrote: Since I don't know correct value of OSCILLATION_RANGE, I just changed to the example value (0.1) from (0.89976, I know it is not a positive multiple of 0.0001, but worked for ketone data). without knowing the correct value for the OSCILLATION_RANGE, data processing might run through but produces non-sense results, independent of the data processing program you use. So, it is absolutely important to know the correct value for the oscillation range per frame. For these data, the oscillation range should be 0.37 degrees, because the rotation rate is 0.09 degrees per second (as per SBGrid reprocessing instructions) and the time between successive frames is ~4.1 s (as determined by tvips2smv). I just checked, and this is indeed what's in OSC_RANGE header item, assuming you actually used tvips2smv to make the SMV files. // Cheers; Johan To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] MicroED Imaging Center
Dear Structural biology community; We are delighted to announce that the National Institutes of Health is helping us establish a Biotechnology Development Research Center focused on MicroED at UCLA School of Medicine, named MicroED Imaging Center (MEDIC). The main thrust of MEDIC is for method development and research focused on MicroED. As part of community engagement, the center will host the annual MicroED course as well as an annual MicroED Summit, both of which will be staged at the UCLA School of Medicine, and open to the community on a first come first serve basis until spaces are filled. Approximately 90% of available spots will be allocated to academic attendees and 10% to industry attendees. This will be a continuation of almost 10 years of tradition of providing workshops and training to the community. Also, there is some opportunity for the community to collect data on MEDIC microscopes. There is also limited availability for one-on-one user training at the center at UCLA for microscope set up and data collection. Users and trainees will be invited based on replies to a call for proposals, which will be advertised shortly. The proposals will be reviewed by an advisory committee. Because of the COVID19 pandemic and the limitations on travel and hosting imposed by UCLA we cannot begin these activities at this stage. On a related note, UCLA School of Medicine is also running a MicroED Imaging Core which is open as a pay per use service for academia and industry. This activity is independent of the Gonen Lab and from the NIH funded research program on MicroED. Details can be found online. Kind regards Tamir Gonen and Pawel Penczek To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Open postdoc positions in the Gonen lab
Dear all; We would like to draw your attention to two HHMI-funded postdoc positions in the laboratory of Tamir Gonen at the University of California, Los Angeles. The first position concerns the biochemistry of membrane proteins, the second is focused on computational methods development. For further information, as well as application instructions, see the links below. Biochemistry https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobinfo=23=1194_id=16908=2=ONLINE=992841=levelid1=36316=2 Programming https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobinfo=23=1195_id=16908=2=ONLINE=992841=levelid1=36316=2 // Best wishes; Johan To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Final reminder: MicroED Workshop 2019
Final reminder: the application deadline for the 2019 MicroED workshop is October 1, 2019. From the initial announcement: The Gonen Laboratory will hold the 5th MicroED Workshop in 2019. The workshop will be held at the MicroED Imaging Center at the UCLA David Geffen School of Medicine during December 9-12, 2019 and is open to both academia and industry. Space is limited and historically, the workshop is typically oversubscribed. Topics covered: * MicroED conception, practice, and future opportunities * Electron optics for MicroED * Microscope alignment and calibration for MicroED * Sample preparation: protein and organic/inorganic materials, small molecules * Data collection for both protein and small molecules * Data analysis software, structure solution, and refinement * Choice of electron microscope hardware and cameras * MicroED publication standards: what statistics to include and when is your structure publication-ready? Further application information is available from https://cryoem.ucla.edu/pages/Workshop // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Reminder: MicroED Workshop 2019
Just a reminder: the application deadline for the 2019 MicroED workshop is October 1, 2019. From the initial announcement: The Gonen Laboratory will hold the 5th MicroED Workshop in 2019. The workshop will be held at the MicroED Imaging Center at the UCLA David Geffen School of Medicine during December 9-12, 2019 and is open to both academia and industry. Space is limited and historically, the workshop is typically oversubscribed. Topics covered: * MicroED conception, practice, and future opportunities * Electron optics for MicroED * Microscope alignment and calibration for MicroED * Sample preparation: protein and organic/inorganic materials, small molecules * Data collection for both protein and small molecules * Data analysis software, structure solution, and refinement * Choice of electron microscope hardware and cameras * MicroED publication standards: what statistics to include and when is your structure publication-ready? Further application information is available from https://cryoem.ucla.edu/pages/Workshop // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] MicroED Workshop 2019
The Gonen Laboratory will hold the 5th MicroED Workshop in 2019. The workshop will be held at the MicroED Imaging Center at the UCLA David Geffen School of Medicine during December 9-12, 2019 and is open to both academia and industry. Space is limited and historically, the workshop is typically oversubscribed. Topics covered: * MicroED conception, practice and future opportunities * Electron optics for MicroED * Microscope alignment and calibration for MicroED * Sample preparation: protein and organic/inorganic materials, small molecules * Data collection for both protein and small molecules * Data analysis software, structure solution, and refinement * Choice of electron microscope hardware and cameras * MicroED publication standards: what statistics to include and when is your structure publication-ready? Further application information is available from https://cryoem.ucla.edu/pages/Workshop The application deadline is October 1, 2019. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Opportunity in the Gonen lab
Dear all; There is an exciting opportunity for a research technician to join the Gonen lab at UCLA, supporting ongoing projects in membrane biophysics and biochemistry. This role will perform research using biochemical and molecular biology techniques. The Gonen Lab at the University of California works toward understanding how membrane proteins help cells maintain homeostasis. To that end we study channels, transporters, and receptors structurally and functionally. Complete job posting and application instructions can be found at: https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobinfo=23=1064_id=16908=2=ONLINE=992450=levelid1=36316=2 // Best wishes; Johan Research Specialist @ Gonen Lab UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] VERY old mtz file..
Related by not exactly on topic: would anybody on the list be able to share old map files (not MTZ:s) with Convex, Cray, Fujitsu, or VAX reals/strings? I’d be interested to see what those files actually look(ed) like. // Best wishes; Johan > On Nov 9, 2018, at 18:38, Zhijie Li wrote: > > Hi all, > > On linux there are a few good GUI HEX editors. Here I’d like to recommend > BLESS, which conveniently displays all possible numerical interpretations of > the four bytes under cursor. It also allows the user to switch between big > endian or little endian through a checkbox. Unfortunately all floats are > assumed to be IEEE754, therefore VAX floats won’t be interpreted correctly. > ( The simplest way to convert vax to ieee float would be to write a little > program to do some bit operations. I’d be happy to take that as my weekend > project) > > > BTW, along the line of space efficiency, I can’t help noticing that the > miller indices are saved as float32 in mtz, as all other numbers in mtz. This > certainly have made mtz format a beautiful homogeneous data format ;). In > this particular case, if we have doubts about the reliability of the machine > stamp, trying to restore the miller indices would be a good way to test > hypotheses. > > Zhijie > > On Nov 9, 2018, at 9:04 PM, James Holton > <270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote: > >> As a beamline scientist I must say I am glad that diffraction image data is >> not usually stored as ASCII text. In fact, I am slowly warming to the idea >> of storing it as not just binary, but compressed formats. Problem, I'm sure >> will be that it won't be long before we forget how to decompress them, as >> most of the algorithms we are using aren't all that widespread. Probably >> around the same time future generations will curse us for using ASCII >> instead of unicode, which is a 16-bit standard. I'm sure we will be reviled >> for limiting ourselves so, just to save a factor of two in disk space. >> In situations like this I always use the unix "od" command. It makes >> everything "human readable" by converting the bytes into strings you can >> read. Then it is just a matter of figuring out what the bytes are. >> Unfortunately, "od" only decodes floats on the native platform, so if the >> mtz is from another platform (Windows vs Linux, for example), then you might >> need to do some swapping. Thus far, I have encountered files that require >> one of a few swapping strategies in order to make them work: >> >> 1 2 3 4 - no swapping >> >> 4 3 2 1 - reverse all bytes >> >> 3 4 1 2 - swap words and swap bytes within the words >> 2 1 4 3 - reverse of previous >> >> 2-1 1 4 3 - same as last, but if not all zero, decrement byte #2 before >> swapping >> 3 4 1 2+1 - same as 3412, but if not all zero increment byte #2 before >> swapping >> I'm sure there are other combinations, but the oldest MTZ I have is only >> from 1996. >> >> -James Holton >> MAD Scientist >> >> >> On 11/9/2018 4:47 AM, Eleanor Dodson wrote: >>> Anyone any idea what to do about this?? Created in 1992!! >>> Seems unreadable.. >>> >>> No CTYP lines input for file: 1 >>> Indices output even if all data items flagged "missing" >>> Warning, NOT all LABOUT data lines given >>> Warning: Machine stamp corrupted? Assuming native format. >>> >> CCP4 library signal library_file:End of File (Error) >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >>> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > Research Specialist @ Gonen Lab UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] D37
> On Sep 12, 2018, at 15:51, Murpholino Peligro wrote: > > I just found a paper* where this metric, D37, is used. > > Third page, line #8: > D37 (the radiation dose which reduces the activity to 37% of the control > value" > > * http://www.jbc.org/content/257/22/13297.full.pdf > > The question is why 37? why not 50 or something else? Because it’s 1/e? // Cheers; Johan Research Specialist @ Gonen Lab UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] In need of SGI computer genius
On Oct 25, 2013, at 11:14 , David Roberts drobe...@depauw.edu wrote: Hello all, OK - small school - old NMR (really old). We set this up around 14 years ago with an O2 system as the user interface, with an indigo system as the interface between the O2 and the NMR. This is a JEOL system, has really been a workhorse with little issues over the last 14 years. We are obviously at the end here. We are working on getting a new one - but that's a work in progress. Anyway - today the hard drive failed on the indigo system. The simple issue is this - we access the indigo strictly via telnet. I do have a backup (I believe) on tape of the indigo. What is the best way to proceed here? There is no monitor on the indigo (nor is there a keyboard). I don't even have a monitor for it (no graphics card - and I don't have an old terminal). I'd suggest first restoring the tape backup onto another machine on the network. Then, you could access the console on the Indigo via a serial cable [from Sabuj's post--many more recent machines appear to lack a serial port, but you can get RS232 = USB adaptors for cheap that work well enough], and configure the Indigo to netboot off the restored tape backup. // Johan Postdoctoral Fellow @ Physical Biosciences Division ___ Lawrence Berkeley National Laboratory * 1 Cyclotron Rd. Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055
Re: [ccp4bb] Average B-factor
On Aug 30, 2013, at 14:45 , Dhanasekaran Varudharasu dhana...@gmail.com wrote: I need to complete my crystal-data table. So, I want to calculate Average B-factor for protein atoms and water. Can anyone please tell me which CCP4 program that I have to use to calculate average B-factor. I'd suggest baverage, http://www.ccp4.ac.uk/html/baverage.html. // Johan Postdoctoral Fellow @ Physical Biosciences Division ___ Lawrence Berkeley National Laboratory * 1 Cyclotron Rd. Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055
Re: [ccp4bb] CCP4 Update victim of own success
On 11 Apr 2013, at 13:53, David Schuller dj...@cornell.edu wrote: My method is to run the updater graphically on one machine, then spread it around with rsync. Although being able to run it on the command line would allow me to accomplish that from my own desk, without crossing campus to another building. Even with gigabit, running X remotely is rather slow and bothersome. In some cases I've found that compressing the ssh-traffic (i.e. ssh -C user@host) is enough to transform an unusably slow session to a workable one. // Johan
Re: [ccp4bb] off topic - legacy hardware help needed
On 23 Jan 2013, at 16:07, Dave Roberts drobe...@depauw.edu wrote: Anyway, we have an old Indigo SGI that runs our NMR. It's a console only system, and we access it via the network from another old SGI (toaster model - blue). The console does not have a video card (nor space for one), so I can't plug in to it and see what's happening. Anyway, our network was recently updated, and in doing so it has made access to our console system unavailable. We can't get there because the IP's that used to be needed are no more. I'm not familiar with the Indigo, but I presume it has a serial port over which you could log in to the machine. Connect the Indigo to an accessible machine with a serial cable (you can even get serial/USB adapters that sort-of work, too) and run something like minicom or screen. // Cheers; Johan Postdoctoral Fellow @ Physical Biosciences Division ___ Lawrence Berkeley National Laboratory * 1 Cyclotron Rd. Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055
Re: [ccp4bb] Script for removing/gathering select rows of data
On 7 Nov 2012, at 19:49, Jacob Keller j-kell...@fsm.northwestern.edu wrote:
Dear Crystallographers,
does anyone have a script on hand which can:
-read in a tab-delimited dataset
-determine whether each row in column X is above or below some input cutoff
value Y,
-outputs all such rows to a new file?
if someone already has this on hand, I would appreciate it--seems like it
should be a very generally useful script to have around, and I need such
right now…
This may work (at least with GNU and OS X awk):
awk -F'\t' '{if ($X Y) print $0;}' infile outfile
where X is the column number starting from 1, and Y is your cutoff.
// Johan
Postdoctoral Fellow @ Physical Biosciences Division
___
Lawrence Berkeley National Laboratory * 1 Cyclotron Rd.
Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055
