[ccp4bb] Off-topic: Replacement CCD camera for Rigaku Dekstop Minstrel UV imager
Hi, I know the chance is low, but in a desperate try to fix our long-serving Rigaku crystal imager I'm wondering whether anyone is aware of any decommissioned (Desktop) Minstrel systems around which could provide spare sparts. Unfortunately Rigaku crystal automation systems are no longer supported . In particular, we are in need of the built-in replacement CCD camera (a QImaging Retiga 4000R, https://www.photometrics.com/wp-content/uploads/2020/03/Retiga-4000R-Datasheet.pdf), which is (not surprisingly) also not available any longer. As the Rigaku Minstrel system is rather closed (and the software no longer developed) I'm not sure if other cameras would work, too (it's connected via Firewire and has a standard C-mount, 2048x2048 pixels). Does anyone have experience or heard of other cameras working in a Minstrel system? Any help would be greatly appreciated (please contact off the list)! Thanks Christoph -- - - - - - - - - - - - - - - - - - - - - - - - - - - Dr. Christoph Parthier Arbeitsgruppe Röntgenkristallografie Institut für Biochemie/Biotechnologie Martin-Luther-Universität Halle-Wittenberg Kurt-Mothes-Str. 3a, Raum 3.47 06120 Halle (Saale), Germany Tel: ++49-345-5524898 Fax: ++49-345-5527014 E-Mail: christoph.parth...@biochemtech.uni-halle.de - - - - - - - - - - - - - - - - - - - - - - - - - - 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] used x-ray equipment
Due to system upgrade we would like to offer a Rigaku diffraction system consisting of the following components: - Rigaku MM007 rotating anode generator (2004, 0.8 kW, ~ 80.000 hours), good working condition (functional) - motorized R-Axis IV++ imaging plate detector (2004), good condition (functional) incl. spare parts for R-Axis IV++ imaging plate detector (spare erase lamps, spare belt) - single-phi axis goniometer + video microscope system - Osmic Varimax HR optics / collimator - XSTREAM 2000 cryostream system (air dryer, He-compressor, cryo-nozzle + nozzle-holder), functional but nozzle needs regular maintenance (evacuation) - Haskris R300 refrigerated water chiller (sufficient to cool X-ray generator and two cryostreams) The system will be available by end of august 2020. Interested parties should provide shipping and handling (organize pickup). Location is Halle (Saale), Germany. Please contact Christoph (christoph.parth...@biochemtech.uni-halle.de) for more details if you are interested in the system or individual components. Best wishes, Christoph 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] CCP4 update manager command line options?
Hi, In context of an unattended installation/update of CCP4 for Windows 7/10 in a computer pool environment, is it possible to install CCP4 (from scratch) via update manager (ccp4um) command line option to an earlier version than the latest (e.g. 7.0.072 instead of 7.0.078)? If yes, what would be the apropriate command line parameter(s)? Or would this rather be a job for the CCP4 package manager (ccp4pm)? What would be the respective command line paramters? Any other suggestion to do this task unattended (batch file)? Thanks, Christoph To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Coot 0.8.9.2 crashes upon CA Zone -> Mainchain conversion with >1 CA segment
Hi, Just noticed the new 'CA Zone -> Mainchain' feature (since version 0.8.9.2) crashes Coot when converting a CA baton molecule that contains more than one continous segment (e.g. contains two or more CA baton stretches in the same molecule). This occurs for instance if you create gaps in your baton, e.g. after skipping to a different region of the electron density. This problem did not exist in Coot versions <0.8.9.2 and is probably a side-effect of the new way 'CA Zone -> Mainchain' works. Same bug in WinCoot, too. I can provide data files if required. Thanks for a fix! :) Christoph To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Tenure Track Research Group Leader Position “Cryo-Electron Microscopy of Membrane Protein Complexes”
Dear ccp4 community, I just would like to call your attention about this opening at the Martin-Luther-University Halle-Wittenberg, Germany. Further information can be found in the attached PDF. Kind regards, Christoph HALOmem_8p138x255_09-01-17_s1.pdf Description: Adobe PDF document
[ccp4bb] Two tenure track research group leader positions - ZIK HALOmem - University of Halle-Wittenberg, Germany
Since its foundation in 2008, the *Centre for Innovation Competence (ZIK) HALOmem*at the Martin Luther University Halle-Wittenberg in Germany (www.halomem.de http://www.halomem.de) has devoted itself to the structural characterisation of membrane proteins together with analysis of the role played by the surrounding membrane. HALOmem is expanding its expertise platform with the establishment of *two new independent research groups*, working and collaborating within the stimulating multidisciplinary environment that has established Halle as an internationally recognised centre for pure and applied protein biochemistry, biotechnology and biophysics. HALOmem and the German Federal Ministry of Education and Research (BMBF) seek highly motivated and outstanding junior scientists for the positions of: *Research Group Leader “Cryo-Electron Microscopy of Membrane Protein Complexes”* The successful candidate will establish a team to study membrane protein complexes using cryo-electron microscopy (single particle reconstruction and/or tomography). The applicant will have trained in membrane protein biochemistry and/or cryo-EM, with documented experience in these fields at postgraduate and postdoctoral level. The candidate will have unrestricted access to the 300 kV JEOL JEM-3200FSC equipped with field emission gun, cryo-stage, in-line energy filter and GATAN K2 direct electron detector that are presently being installed. *Research Group Leader “Biophysical Characterisation of Medically Relevant Membrane Proteins”* The successful candidate will establish a team to develop technologies for the biophysical characterisation of membrane proteins and the analysis of their interactions with protein and synthetic ligands. The applicant will have received training in protein ligand interactions / membrane protein biochemistry covering a wide array of methods. Documented experience in these fields at postgraduate and postdoctoral level is expected; experience in an industrial environment is welcome. Furthermore, applicants should ideally have experience in: * Working in an international scientific environment * Project coordination and leadership * Obtaining third party funding * Interacting within an interdisciplinary milieu Each group will receive funding from the BMBF, including an additional four co-workers and consumables for five years, as well as laboratory equipment necessary for the project. Implementation of the extended ZIK HALOmem Strategy Concept is a requirement for both group leaders, and successful candidates are expected to contribute to establishment of the Research training programme “Halle School of Molecular Life Sciences (HaMol)”. Group leaders may be awarded the status of Junior Professor, in which case active participation in academic and administrative duties within the University is expected according to the /Hochschulgesetz Sachsen-Anhalt/(§ 34 HSG-LSA), with corresponding requirements for recruitment according to § 35 HSG-LSA. Junior Professorships are awarded initially for a period of three years, after which a further three years may be granted upon positive evaluation. In such a case, both positions offer the possibility of subsequent tenure at the Martin Luther University, which may or may not be submitted for tender depending on the success of the group leader. The Martin Luther University Halle-Wittenberg strives to promote equal opportunities in science. Female and disabled applicants, qualified according to the above criteria, will be given preference over other candidates with equivalent relevant qualifications. Salary scale is subject to legal and budgetary policies of the University and candidates are expected to start by the beginning of 2016. The University provides arrangements for coordinating occupation and family. Applications should be addressed to _both_ZIK HALOmem _and_the Project Management Organisation Jülich (representing the BMBF) with the subject headline “ZIK HALOmem II”: *ZIK HALOmem: Prof. Milton T. Stubbs, **stu...@biochemtech.uni-halle.de* *Organisation Jülich: **Dr. Christoph Wannek, **c.wan...@fz-juelich.de* *Application deadline: 12*^*th* *June 2015* *Interviews are planned from 6*^*th* *– 9*^*th* *July 2015* *For further information please contact:* i...@halomem.de; http://www.halomem.de *For further details on the application requirements please see: * http://www.unternehmen-region.de/de/374.php HALOmem_en 8p138x255 06-5.pdf Description:
Re: [ccp4bb] Stereo projectors
Hi Marie,
Do you have special reasons to go with an active system? What programs
do you intend to use for 3d projections?
Since about three years we use a passive system (most likely not
up-to-date anymore) consisting of 2 full-HD projectors (Epson
EB-G5450WU) wall-mounted on top of each other, each having circular
polarized filters in front of the lens (I guess this was
custon-fabricated, but I'm sure commercial solutions exist). We use a
special wall-mounted screen which retains polarization and lots of
passive glasses (light and cheap) with circular polarizing filters
(film). The setup is placed in a lecture hall for about 100 persons, 3d
perception is good from almost all distances and viewing angles, no
significant ghost images (I think the circular polarizing does the trick).
The projectors are connected via HDMI to a dual-port graphics card (low
end NVIDIA QUADRO). The two ports deliver a cloned image, the NVIDIA
graphics driver (Windows 7) converts (splits) hardware stereo signals
('quad-buffered stereo') to the two video ports. 3D vision is then
possible for all applications that use 'quad-buffered'/hardware stereo.
It's not directly available in PowerPoint, though! If you want to show
3D movies/images you need an external player (e.g. Stereoscopic Player)
which supports hardware stereo.
One of the drawbacks: the projectors need to be aligned quite accurately
to each other (screen size, focus, image position). Not so conveinient
for manual adjustment of wall-mounted projectors. I'm happy there are no
frequent earth quakes where we live... ;-)
Hope this helps... sorry, if this is a really 'old-fashioned'. I havn't
looked into recent solutions that might exist by now.
Christoph
Hello, Our Department is looking at purchasing a system to project in
stereo for perhaps 50 people in the audience. The current plan is to
go with an active system, although maintaining the glasses will
likely be a problem. If you have insight into currently available
systems that you are either happy with or disappointed in, could you
please send me your advice? Thank you, Marie (Department of
Biological Sciences, University of Calgary)
Re: [ccp4bb] stereo monitor for DELL T7600
Yes, it works with PyMOL and COOT using the 'quad buffered stereo' / 'hardware stereo' option, respectively. Best wishes, Christoph Hi Christoph, Thanks so much for your information. This is very helpful for us. One more question, will the *ASUS VG278H work with Pymol and coot?* Thanks so much! Jinyu On Fri, Mar 1, 2013 at 9:15 AM, Christoph Parthier cparth...@googlemail.com mailto:cparth...@googlemail.com wrote: We use the ASUS VG278 monitor with built-in IR emitter under linux.Stereo works perfectly without 3 pin connector. Monitor is connected via (dual-link) DVI cable (stereo option 10 in xorg.conf). This should work with any Quadro card. The monitor is big and esp. bright in 3D due to it's NVIDIA 3D LightBoost technology (3D Vision 2). Much better for use of 3D in not so dark rooms. Christoph Andrew Purkiss schrieb: And that is because the emitter is powered by the screen and its presence is detected via the HDMI monitor cable (and the signal to the emitter is sent the same way). Use of these screens is via different driver option (stereo option of 12) and there is a more limited range available. I have no experience of running with this option, as being early(ish) adopters, we have a mix of Alienware OptX AW2310 and Samsung SyncMaster 2233RZ screens. I would be interested in how stable the stereo is, when a low powered graphics card is under heavy load. Having a graphics card with more power is not a waste of money (the CUDA drivers used by the molecular simulation groups show what can be done). The extra cost is quite small compared to the costs of getting crystals in the first place!! On Fri, 2013-03-01 at 13:21 +0100, Joachim Reichelt wrote: On Linux here the ASUS Monitor with build in Emitter runs fine even on a FX 380 Quadro without 3pin connection! Am 01.03.13 13:17, schrieb Andrew Purkiss: On Fri, 2013-03-01 at 12:52 +0100, mesters wrote: Why a quadro 4000? For coot, pymol, etc., a quadro 2000 is more than sufficient. Even the quadro 600 will do fine.
Re: [ccp4bb] stereo monitor for DELL T7600
We use the ASUS VG278 monitor with built-in IR emitter under linux.Stereo works perfectly without 3 pin connector. Monitor is connected via (dual-link) DVI cable (stereo option 10 in xorg.conf). This should work with any Quadro card. The monitor is big and esp. bright in 3D due to it's NVIDIA 3D LightBoost technology (3D Vision 2). Much better for use of 3D in not so dark rooms. Christoph Andrew Purkiss schrieb: And that is because the emitter is powered by the screen and its presence is detected via the HDMI monitor cable (and the signal to the emitter is sent the same way). Use of these screens is via different driver option (stereo option of 12) and there is a more limited range available. I have no experience of running with this option, as being early(ish) adopters, we have a mix of Alienware OptX AW2310 and Samsung SyncMaster 2233RZ screens. I would be interested in how stable the stereo is, when a low powered graphics card is under heavy load. Having a graphics card with more power is not a waste of money (the CUDA drivers used by the molecular simulation groups show what can be done). The extra cost is quite small compared to the costs of getting crystals in the first place!! On Fri, 2013-03-01 at 13:21 +0100, Joachim Reichelt wrote: On Linux here the ASUS Monitor with build in Emitter runs fine even on a FX 380 Quadro without 3pin connection! Am 01.03.13 13:17, schrieb Andrew Purkiss: On Fri, 2013-03-01 at 12:52 +0100, mesters wrote: Why a quadro 4000? For coot, pymol, etc., a quadro 2000 is more than sufficient. Even the quadro 600 will do fine. Except for a linux installation, as the 3 pin bracket is only available on the Quadro 4000 (and higher) I noticed that the Nvidia linux driver has options for USB port etc. which suggests that in the near future USB ports can be used under linux for an external USB IR emitter. Can somebody comment on this please? The driver only seems to use the USB connection for power and for identifying that the emitter is connected. I don't think that there are any plans to use USB to drive the stereo synchronisation (the mention of USB has been in the release notes for many years now). -- Joachim Reichelt Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
Re: [ccp4bb] while on the subject of stereo
Hi Dave, We recently equipped a pool of 25 computers with Nvidia 3D shutter glasses, they're used in structural biology courses for undergraduate students of biochemistry . We teach mainly PyMOL, but (in an advanced course) also model building in COOT. Of course, we let the students decide whether they want to use hardware stereo or not. They all try. After several courses now I realized no more than 30% of the students keep using them in visualization and model building, while the majority of students put the glasses aside... Some of the 30% said, it helps, but could also do without. Haven't assessed this properly yet... ;-) Christoph David Roberts wrote: Thanks for the comments, I do appreciate them. I guess we went off in a direction I wasn't thinking of - related to your personal like or dislike of stereo. What I am really looking for is an answer to a simple question in that is stereo a nice thing from a pedagogy standpoint for showing students complex biomolecules. I am in a chemistry department - undergraduate only. We focus on 3-dimensional shape and the importance of shape of chemical function/reactivity/etc... With small molecules (PF5, etc...), it's easy to see how shape works by simply rotating the molecule. The molecules are small enough, the concept of 3D can be visualized easily in these systems. Furthermore, they can make a simple model using your standard organic or inorganic model kit, no worries. Now, bring in a huge protein, or a protein-protein complex. The issue of 3Dness becomes fuzzier. It's not so easy to see which hydrogen will get plucked off during a chemical reaction, even with careful zooming and mouse manipulation. So my question still is, how many of you feel stereo is important from a pedagogy standpoint (not looking at maps, just structures that are huge and complex). Is it something that we need to try to bring to the classroom, or is it just a cool toy like the 3D TV that hopefully is going nowhere and will soon fade out like the viewmaster of old. I know a large percentage of people cannot see stereo (at least the way we present it), and so it isn't for everybody. But, does it help, and if so, does it help when done in a huge classroom or when put on an individual screen. Has anybody tried to assess this (there's a horrible word for you). That's what I was wondering about. Presenting the stereo is a different issue (how is that done), but I think there are lots of avenues for that depending on your particular situation. Thanks again Dave
Re: [ccp4bb] while on the subject of stereo
Those must be older ones... The current Nvidia shutter glasses we use are about 50g. http://www.nvidia.co.uk/object/product_GeForce_3D_VisionKit_uk.html Christoph Jürgen Bosch wrote: I think the weight of the shutter glasses puts them off. Compared to the 30g or less of the Zalmans the shutter glasses feel like bricks. I would estimate them to at least 270g. After one hour wearing them you feel them on your nose. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Mar 23, 2011, at 9:40, Christoph Parthiercparth...@googlemail.com wrote: Hi Dave, We recently equipped a pool of 25 computers with Nvidia 3D shutter glasses, they're used in structural biology courses for undergraduate students of biochemistry . We teach mainly PyMOL, but (in an advanced course) also model building in COOT. Of course, we let the students decide whether they want to use hardware stereo or not. They all try. After several courses now I realized no more than 30% of the students keep using them in visualization and model building, while the majority of students put the glasses aside... Some of the 30% said, it helps, but could also do without. Haven't assessed this properly yet... ;-) Christoph David Roberts wrote: Thanks for the comments, I do appreciate them. I guess we went off in a direction I wasn't thinking of - related to your personal like or dislike of stereo. What I am really looking for is an answer to a simple question in that is stereo a nice thing from a pedagogy standpoint for showing students complex biomolecules. I am in a chemistry department - undergraduate only. We focus on 3-dimensional shape and the importance of shape of chemical function/reactivity/etc... With small molecules (PF5, etc...), it's easy to see how shape works by simply rotating the molecule. The molecules are small enough, the concept of 3D can be visualized easily in these systems. Furthermore, they can make a simple model using your standard organic or inorganic model kit, no worries. Now, bring in a huge protein, or a protein-protein complex. The issue of 3Dness becomes fuzzier. It's not so easy to see which hydrogen will get plucked off during a chemical reaction, even with careful zooming and mouse manipulation. So my question still is, how many of you feel stereo is important from a pedagogy standpoint (not looking at maps, just structures that are huge and complex). Is it something that we need to try to bring to the classroom, or is it just a cool toy like the 3D TV that hopefully is going nowhere and will soon fade out like the viewmaster of old. I know a large percentage of people cannot see stereo (at least the way we present it), and so it isn't for everybody. But, does it help, and if so, does it help when done in a huge classroom or when put on an individual screen. Has anybody tried to assess this (there's a horrible word for you). That's what I was wondering about. Presenting the stereo is a different issue (how is that done), but I think there are lots of avenues for that depending on your particular situation. Thanks again Dave
[ccp4bb] UV-transmissible plate seals 96-well format
Hi, Can anyone recommend any UV-transmissible (280 nm), adhesive seals (pre-cut) for 96-well crystallization plates (Greiner, MRC)? We would like to use them on an crystal imaging system with UV option (RIGAKU). I've checked seals from Zymark/Calliper Lifescience with a regular photometer and they're not UV-transmissible. The Crystal Clear tape from Hampton Research is actually UV-transmissible but it's less convenient to apply from the roll onto the plates and it has to be cut afterwards to make sure the plates fit in the plate hotel. Anyone experience with this? Thanks very much in advance, Christoph
