Hi, everyone, I think I found the cause and solution. It was due to the project folder of CCP4i,which was set by me to E:/***/** p reviously, based on which imosflm automatically set its processing folder also as E:/***/. Because disk E: used to be the flash disk on my computer, when I unplug the flash disk, the software cannot find the disk then it will report the error. When I change the project folder in CCP4i to D:/***/**, which was present on my computer, the problem was solved. Best! Jiang
On Thu, Jan 19, 2017 at 4:00 PM, CCP4BB automatic digest system < lists...@jiscmail.ac.uk> wrote: > There are 23 messages totaling 6640 lines in this issue. > > Topics of the day: > > 1. on space group (2) > 2. error in startup script > 3. AW: [ccp4bb] on space group > 4. *** WARNING SUSPECTED VIRUS, SPAM or SCAM *U* [ccp4bb] error in > startup > script > 5. Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, > 2017 > 6. Off-topic, protein in dye-front (ion front?) on native-PAGE (5) > 7. 6th Edition of the ISBC2017 > 8. Cryosystems series 600 > 9. Unique postdoctoral research opportunity in Tromsø, Norway > 10. PhD fellowships in Spain > 11. Anisotropy and temperature (4) > 12. CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) (3) > 13. Joint Postdoctoral Position in the Grishin and Chook Labs at UT > Southwestern > > ---------------------------------------------------------------------- > > Date: Thu, 19 Jan 2017 02:33:14 +0000 > From: Smith Lee <smith_lee...@yahoo.com> > Subject: on space group > > > Dear All, > In the literature, somebody call space group P65 crystal as "six fold > screw axis crystal packing", then I would not make any mistake if I call > P64 space group crystal also as "six fold screw axis crystal packing",am I > right? > I am looking forward to getting a reply from you. > > ------------------------------ > > Date: Wed, 18 Jan 2017 19:40:30 -0800 > From: Jiang Xu <foxj...@gmail.com> > Subject: error in startup script > > Hi, Mr/Ms, > I am a user of CCP4i. I recently discovered that imosflm cannot be used > on my win7. the error message is shown below. > [image: Inline image 1] > However, when I go to 'bin' folder and double click the imosflm.bat, the > program can be start up successfully. I don't know what's the problem. > Thank you! > Best! > Jiang Xu > Department of Molecular and Computational Biology > University of Southern California > > ------------------------------ > > Date: Thu, 19 Jan 2017 05:22:24 +0000 > From: Smith Lee <smith_lee...@yahoo.com> > Subject: Re: on space group > > Dear All, > Here may I make my question much clear? For the space group P 65 crystal, > it seems we can call it "6-fold packing of subunits around a screw axis in > the crystal". Then for the space group P 64 crystal, can it also be called > "6-fold packing of subunits around a screw axis in the crystal"? > Smith > > On Thursday, January 19, 2017 11:50 AM, Ethan Merritt < > merr...@u.washington.edu> wrote: > > > On Thursday, 19 January 2017 02:33:14 AM you wrote: > > > > Dear All, > > In the literature, somebody call space group P65 crystal as "six fold > screw axis crystal packing", then I would not make any mistake if I call > P64 space group crystal also as "six fold screw axis crystal packing",am I > right? > > I am looking forward to getting a reply from you. > > Smith > > "six-fold screw axis" refers to the symmetry. > > "crystal packing" refers to the molecule-to-molecule contacts regardless > of symmetry. > > So no, I don't think "six fold screw axis crystal packing" makes any sense. > > -- > Ethan A Merritt, Dept of Biochemistry > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > > ------------------------------ > > Date: Thu, 19 Jan 2017 08:47:52 +0000 > From: herman.schreu...@sanofi.com > Subject: AW: [ccp4bb] on space group > > Dear Smith, > > I think your question was clear, and the answer you got was clear as well. > > However, I think the question you asked was not the right question. You > want to use a particular phrase to describe your crystal packing and you > want the CCP4BB to endorse this. When the answer was negative, you asked > again the same question. > > The real question, in my eyes, is “What is the best way to describe my P65 > crystal packing” since I guess you want to use this in your paper. Here I > would use something like “in the crystal, the subunits are related by a > 6-fold screw axis”. To be more precise, you could even mention a 65-screw > axis. Other board members may even have better descriptions. > > By the way, 61, 62, 63, 64 and 65 axes are all 6-fold screw axes, but of > different types. > > Best, > Herman > > > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von > Smith Lee > Gesendet: Donnerstag, 19. Januar 2017 06:22 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: Re: [ccp4bb] on space group > > Dear All, > > Here may I make my question much clear? For the space group P 65 crystal, > it seems we can call it "6-fold packing of subunits around a screw axis in > the crystal". Then for the space group P 64 crystal, can it also be called > "6-fold packing of subunits around a screw axis in the crystal"? > > Smith > > On Thursday, January 19, 2017 11:50 AM, Ethan Merritt < > merr...@u.washington.edu<mailto:merr...@u.washington.edu>> wrote: > > On Thursday, 19 January 2017 02:33:14 AM you wrote: > > > > > Dear All, > > In the literature, somebody call space group P65 crystal as "six fold > screw axis crystal packing", then I would not make any mistake if I call > P64 space group crystal also as "six fold screw axis crystal packing",am I > right? > > I am looking forward to getting a reply from you. > > Smith > > > "six-fold screw axis" refers to the symmetry. > > "crystal packing" refers to the molecule-to-molecule contacts regardless > of symmetry. > > So no, I don't think "six fold screw axis crystal packing" makes any sense. > > -- > Ethan A Merritt, Dept of Biochemistry > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > > ------------------------------ > > Date: Thu, 19 Jan 2017 10:09:39 +0000 > From: Harry Powell <ha...@mrc-lmb.cam.ac.uk> > Subject: Re: *** WARNING SUSPECTED VIRUS, SPAM or SCAM *U* [ccp4bb] error > in startup script > > Hi > > It looks like you've got the Windows environment variable "MOSDIR" set to > "E:\" when running CCP4i - I have no idea how that would happen; it's > normally set to something like C:\MOSDIR. If you haven't got an E:\ drive > that would be the root of your problem... > > Have a look in the list of Windows environment variables - I haven't done > this since my XP days, but you should be able to find it by looking at the > advanced system settings, were there should be a button to give you a list > of environment variables. > > Since I'm not familiar with ccp4i on W7 I can't say much more. > > On 19 Jan 2017, at 03:40, Jiang Xu wrote: > > > Hi, Mr/Ms, > > I am a user of CCP4i. I recently discovered that imosflm cannot be > used on my win7. the error message is shown below. > > <image.png> > > However, when I go to 'bin' folder and double click the imosflm.bat, > the program can be start up successfully. I don't know what's the problem. > > Thank you! > > Best! > > Jiang Xu > > Department of Molecular and Computational Biology > > University of Southern California > > Harry > -- > Dr Harry Powell > Chairman of International Union of Crystallography Commission on > Crystallographic Computing > Chairman of European Crystallographic Association SIG9 (Crystallographic > Computing) > > > > > > > > > > > > ------------------------------ > > Date: Thu, 19 Jan 2017 12:18:43 +0100 > From: "Manfred S. Weiss" <manfred.we...@helmholtz-berlin.de> > Subject: Call for MX beamtime proposals at HZB, BESSY II, deadline March > 01, 2017 > > Next MX-proposal application deadline: March 01, 2017 is approaching > http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html > > Hereby we would like to invite the submission of new proposals for > MX-beamtime at the HZB-MX beamlines for the next beam time period > (08/2017-01/2018). > > In order to apply for beamtime, please register at the HZB on-line > access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate) > and submit a new beam time application proposal. > > What's new: In situ-screening in crystallization plates on BL14.1 > will be reinstalled from March 2017 onwards! > > HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2 > and BL14.3. The three beamlines are equipped with state-of-the-art > instrumentation and are currently the most productive MX-stations > in Germany with over 300 PDB depositions annually. Beamtime is > granted based on the reviewed proposals and on reports from > previous research activities. Please make sure to include them > if available. > > Experimental setup: > > BL14.1: > - Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position > (0.1-1 sec exposure time per frame) > - User defined beam shaping from 50µm-100µm diameter possible > - Pilatus 6M detector, 141mm-680mm max. distance from the sample > - Microdiffractometer (MD2) with Mini-kappa goniometer MK3 > - Automatic sample changer (CATS), 90 sample storage capacity > (SPINE-Pin & EMBL sample magazine compatibility) > - 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M > - Data collection control via MXCuBE > - EDNA > - Common MX-software installed including XDS, iMOSFLM, CCP4, > Phenix, SHELXC-E, etc. > - Automated data processing with XDSAPP > - Remotely controlled cryo-shutter for crystal annealing > - Pressure chamber for noble gas derivatization (Xe, Kr > available upon request) > - AMPTEK-XRF detector and XFEPLOT software available > > We are also offering the hard- and software environment for > carrying out: > - UV-RIP experiments at BL14.1. For further information, please visit: > > http://www.helmholtz-berlin.de/forschung/funkma/soft- > matter/forschung/bessy-mx/ancillary-facilities/uvrip_en.html > > BL14.2: > - Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position > (0.1-1 sec exposure time per frame) > - Pilatus 3S-2M detector with 1000 micron Si sensor thickness, > 55mm-600mm distance from the sample > - Nanodiffractometer (DESY P11 design) and on-axis sample microscope > - User defined beam shaping from 30µm-150µm diameter possible > - GROB sample changer for SPINE and UNIPUCK support > - 60-core XEON-CPU server, with fibre channel SAN up-link data > processing environment > - Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix, > SHELXC-E, etc. > - Automated data processing with XDSAPP > - Amptek XRF detector > - Pressure chamber for noble gas derivatization (Xe, Kr available > upon request) > - Ultra high performance stereo microscope Leica M205A, 20-255x zoom, > 8 Mpixel CCD-camera > - UV-Microsprectrophotometer offline setup available > - AMPTEK-XRF detector and XFEPLOT software available > > BL14.3: > - Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position > (3-20 sec exposure time per frame) > - Rayonix MX-225 X-ray detector, 45mm-380mm distance from the > sample, 30 deg 2-Theta possible > - MARdtb goniometer > - 60-core XEON-CPU server, with fibre channel SAN up-link data > processing environment > - EDNA installed and available > - Common MX software installed including XDS, iMOSFLM, CCP4, Phenix, > SHELXC-E, etc. > - Automated data processing using XDSAPP > - Remotely controlled cryo-shutter for crystal annealing > - HC1c dehydration device installed (please specify HC1-beamtime > in your proposal if needed) > - Pressure chamber for noble gas derivatization (Xe, Kr available > upon request) > - Ultra high performance stereo microscope Leica M205A, 20-255x zoom, > 8 Mpixel CCD-camera > > S1-biolab facilities (separate registration required): > - Protein production and purification > - Nanoliter 96 well crystallization plate formulation and storage at > 5 °C and 20 °C > - Biophysical characterization with real time PCR (thermofluor assay) > > The HZB-MX group is also providing expert assistance as well as > access to a library of fragments for carrying out crystallographic > fragment-screening experiments. For more information please contact > us at mswe...@helmholtz-berlin.de. > > Please visit our web page www.helmholtz-berlin.de/bessy-mx to obtain > updated information about our experimental setup and other > requirements. > > Manfred Weiss and the HZB-MX group > > -- > Dr. Manfred. S. Weiss > Helmholtz-Zentrum Berlin für Materialien und Energie > Macromolecular Crystallography (HZB-MX) > Albert-Einstein-Str. 15 > D-12489 Berlin > GERMANY > Fon: +49-30-806213149 > Fax: +49-30-806214975 > Web: http://www.helmholtz-berlin.de/bessy-mx > Email: mswe...@helmholtz-berlin.de > > ________________________________ > > Helmholtz-Zentrum Berlin für Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher > Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. > Jutta Koch-Unterseher > Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > ------------------------------ > > Date: Thu, 19 Jan 2017 20:33:50 +0900 > From: Walt <ofe...@gmail.com> > Subject: Off-topic, protein in dye-front (ion front?) on native-PAGE > > Hi, > > I have a small protein (~9 kDa) with acidic pI (~4). > When I run 18% native-PAGE, it appears my protein is in the dye front. > How can I fix this problem? Changing the pH of separating gel > might help? How about gradient native-PAGE? Thank you! > > Walt > > ------------------------------ > > Date: Thu, 19 Jan 2017 20:33:50 +0900 > From: Walt <ofe...@gmail.com> > Subject: Off-topic, protein in dye-front (ion front?) on native-PAGE > > Hi, > > I have a small protein (~9 kDa) with acidic pI (~4). > When I run 18% native-PAGE, it appears my protein is in the dye front. > How can I fix this problem? Changing the pH of separating gel > might help? How about gradient native-PAGE? Thank you! > > Walt > > ------------------------------ > > Date: Thu, 19 Jan 2017 06:57:04 -0500 > From: Artem Evdokimov <artem.evdoki...@gmail.com> > Subject: Re: Off-topic, protein in dye-front (ion front?) on native-PAGE > > A) change dye or use pure glycerol to load gel > > B) change gel pH or add various substances to it (easy to do with the > buffer) > > Artem > > On Jan 19, 2017 6:34 AM, "Walt" <ofe...@gmail.com> wrote: > > > Hi, > > > > I have a small protein (~9 kDa) with acidic pI (~4). > > When I run 18% native-PAGE, it appears my protein is in the dye front. > > How can I fix this problem? Changing the pH of separating gel > > might help? How about gradient native-PAGE? Thank you! > > > > Walt > > > > ------------------------------ > > Date: Thu, 19 Jan 2017 13:09:28 +0000 > From: "Jose A. Gavira" <jgav...@ugr.es> > Subject: 6th Edition of the ISBC2017 > > Dear Colleague, > The Laboratory of Crystallographic Studies is pleased to announce the > 6th International School on Biological Crystallization (ISBC2017), to be > held in Granada (Spain) during May 29th to Jun 02nd, 2017. ISBC2017 is > intended for postgraduate/postdoctoral students and research scientists > from industrial and academic backgrounds. > The International School will provide five days of lectures, posters and > practical demonstrations focused on the fundamentals of crystallization. > The aim of the School is to introduce all participants into the fundamental > knowledge about the behaviour of crystallizing solutions and their > applications to the field of biological crystallization, including large > crystals for neutron diffraction and tiny crystals for XFEL. This year we > will focus on the crystallization of membrane proteins, protein complexes > characterization, including EM, and biomineralization. > For more information, please visit http://www.isbcgranada.org/. > Best regards, > ISBC 2017 Organizing Committee > > LIST OF CONFIRMED SPEAKERS > • Bernhard Rupp, k. k. Hofkristallamt, US. > • Terese Bergfors, Uppsala University, Sweden. > • Janet Newman, CSIRO, Australia. > • Allan D´Arcy, Actelion Pharmaceuticals, Switzerland. > • Martin Caffrey, Trinity College Dublin, Ireland. > • Petra Fromme, Arizona State University, US. > • Juan Manuel Garcia-Ruiz, IACT, CSIC-UGR, Spain. > • Jeroen Mesters, University of Lüebeck, Germany. > • Marc Pusey, iXpressGenes, Huntsville, US. > • Howard Einspahr, IUCr Journal Comission, US. > • José A. Gavira, IACT, CSIC-UGR, Spain. > • Hudel Luecke, University of California, US. > • Naoko Mizuno, Max Planck Institute, Germany. > • Sergio Martínez, UGR, Spain. > • Ivana Kuta Smatanova, University of South Bohemia, Czech Republic. > • Stephane Veesler, CINam-Marseille, France. (tbc) > • Claude Sauter, IBMC, CNRS, France. > • Christian Betzel, University of Hamburg, Germany. > • Fermin Otálora, IACT, CSIC-UGR, Spain. > • Guillermo Calero, University of Pittsburg, US. > • Christian Biertümpfel, Max Planck Institute, Germany. > • Edward H. Snell, Hauptman-Woodward Institute, Buffalo, US. > • May Marsh, Swiss Light Source at Paul Scherrer Institut, Swiss. > • Jose Manuel Martin-Garcia, Arizona State University, US. > • Giuseppe Falini, University of Bolonia, Italia. > • Karim Benzerara, Université Pierre et Marie Curie, France. > • Helmut Cölfen, University of Konstanz, Germany. > • Monica Budayova-Spano, Université Grenoble Alpes, France. > • Yves Nys, URA, INRA, France > • Pavlina Rezachova, University of Prague, Czech Republic. > TOPICS > ♣ Nucleation: Classical and non-classical approaches. > ♣ Crystal growth kinetics and mechanisms. > ♣ Properties of macromolecular solutions (DLS/SAXS). > ♣ Screening: The search for crystallization conditions. > ♣ Crystallization techniques: Batch, Vapour and Counter Diffusion, > How do they work? > ♣ Crystallization and diffusion transport: gels, microfluidics and > microgravity. > ♣ Crystallization of large crystals for Neutron diffraction. > ♣ In vivo crystallization of tiny crystals. > ♣ Novel crystallization strategies for XFEL studies. > ♣ Serial Crystallography. > ♣ Polymorphism in protein crystals. > ♣ Case studies in Membrane Protein Crystallization. > ♣ Lipid cubic phase, bicelles and detergents. > ♣ Crystallization of Macromolecular Complexes. > ♣ Characterization by electron microscopy (EM). > ♣ In vitro and in vivo studies of Biomineralization processes. > > ------------------------------ > > Date: Thu, 19 Jan 2017 11:47:02 -0200 > From: zeyaul islam <zeya1...@gmail.com> > Subject: Re: Off-topic, protein in dye-front (ion front?) on native-PAGE > > Try Tricine gel. It is particularly suited for low molecular wt proteins > and it will give you very good resolution. Even you can run it overnight at > 30 V (16-18 hours). > > On Thu, Jan 19, 2017 at 9:33 AM, Walt <ofe...@gmail.com> wrote: > > > Hi, > > > > I have a small protein (~9 kDa) with acidic pI (~4). > > When I run 18% native-PAGE, it appears my protein is in the dye front. > > How can I fix this problem? Changing the pH of separating gel > > might help? How about gradient native-PAGE? Thank you! > > > > Walt > > > > ------------------------------ > > Date: Thu, 19 Jan 2017 13:56:11 +0000 > From: Johan Turkenburg <johan.turkenb...@york.ac.uk> > Subject: Cryosystems series 600 > > We are having a clear out and have several Oxford cryosystems 600 going > spare. They are not in working order, and they are really only for spare > parts. Free to a good home, pick up only. > > Contact me off list if you are interested. > > If we don't hear within 10 days, they will go in the bin. > > Johan > > -- > Dr. Johan P. Turkenburg X-ray facilities manager > York Structural Biology Laboratory > University of York Phone (+) 44 1904 328251 > York YO10 5DD UK Fax (+) 44 1904 328266 > http://orcid.org/0000-0001-6992-6838 > > ------------------------------ > > Date: Thu, 19 Jan 2017 16:14:16 +0100 > From: Richard Engh <richard.e...@uit.no> > Subject: Unique postdoctoral research opportunity in Tromsø, Norway > > Dear all, > > I would like to call your attention to a unique postdoctoral fellowship > opportunity in structural chemistry at the UiT The Arctic University of > Norway in Tromsø. The project area is "Crystallography, biophysical and > cheminformatics studies for next-generation kinase inhibitor design". > > The program is described in more detail here: > > https://euraxess.ec.europa.eu/jobs/163137 > > The deadline for a preliminary application (2 pages and a CV) is soon, > February 3. > > Promising candidates will then be invited to prepare a more detailed > application for submission in autumn. If the application is successful, > the position will be funded starting in 2018. > > Besides hosting the Norwegian Center for Structural Biology, Tromsø is a > fascinating location, with its 2-month long "Polar Night", illuminated > by some midday twilight and Northern Lights, and its compensating > 2-month long Midnight Sun period. (We don't lack total sunshine hours, > but have only about 245 sunrises and sunsets per year, depending on the > view of the horizon from where you live.) As the link above describes > it, Tromsø is "uniquely located at the top of the world surrounded by > some of Europe’s last pristine wild nature." > > Please feel free to ask me for more details if you are interested. > > Sincerely, > Rick Engh > > -- > Professor Richard Engh > The Norwegian Center for Structural Biology > Forskningsparken 3, Sykehusvegen 23 > Fakultet for naturvitenskap og teknologi > Universitetet i Tromsø > 9037 Tromsø > > ------------------------------ > > Date: Thu, 19 Jan 2017 16:59:40 +0100 > From: Didier Spittler <spittlerdid...@gmail.com> > Subject: Re: Off-topic, protein in dye-front (ion front?) on native-PAGE > > Yes Tris-Tricine gel ! > > Try to obtain this article from nature protocol. > > Best, > > Didier > > > 2017-01-19 14:47 GMT+01:00 zeyaul islam <zeya1...@gmail.com>: > > > Try Tricine gel. It is particularly suited for low molecular wt proteins > > and it will give you very good resolution. Even you can run it overnight > at > > 30 V (16-18 hours). > > > > On Thu, Jan 19, 2017 at 9:33 AM, Walt <ofe...@gmail.com> wrote: > > > >> Hi, > >> > >> I have a small protein (~9 kDa) with acidic pI (~4). > >> When I run 18% native-PAGE, it appears my protein is in the dye front. > >> How can I fix this problem? Changing the pH of separating gel > >> might help? How about gradient native-PAGE? Thank you! > >> > >> Walt > >> > > > > > > > -- > Didier Spittler, PhD > Phone number : +33658576481 > > ------------------------------ > > Date: Thu, 19 Jan 2017 20:03:08 +0100 > From: Mark J van Raaij <mjvanra...@cnb.csic.es> > Subject: PhD fellowships in Spain > > Dear future PhD student, > > For prospective PhD students there is the current fellowship call open: > https://obrasociallacaixa.org/el/educacion-becas/becas-de- > posgrado/inphinit/programme-description > This is a competitive call with good conditions (salary, mobility, > complementary training), especially for Spanish standards. > If you go to “Search for a Position” and then look for our centre “Centro > Nacional de Biotecnologia- CNB”, my vacancy on “Structural Biology on > Bacteriophage Fibres and Tailspikes" turns up. > If you are interested, please apply. There is no need to contact me, > because the application process selection committee is independent from the > proposed supervisors. There are also other structural biology projects, and > I think selected candidates can choose their favourite project based on the > final shortlist order. > The deadline for application is 2 February, academic records, reference > letters and a B2 level certificate in english need to be supplied > (nationals of english-speaking countries are exempted). > > Greetings, > > Mark J van Raaij > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > calle Darwin 3 > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 > http://wwwuser.cnb.csic.es/~mjvanraaij > > ------------------------------ > > Date: Thu, 19 Jan 2017 20:35:14 +0000 > From: D Bonsor <dbon...@ihv.umaryland.edu> > Subject: Anisotropy and temperature > > A PhD student asked me what causes diffraction anisotropy. Quoting from > the Diffraction Anisotropy Server webpage that it is caused by whole-body > anisotropic vibration of unit cells. He asked whether a colder cyrostream > could improve anisotropy. My answer would be yes, as colder temperatures > would lower the vibrations. > > My two questions are; (1) am I right? and (2) if so, has it ever been done > before in practice? > > Thanks, > > Dan > > ------------------------------ > > Date: Thu, 19 Jan 2017 21:54:03 +0100 > From: "Panneerselvam, Saravanan" <saravanan.panneersel...@desy.de> > Subject: Re: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) > > Dear All, > Sorry for the little bit off topic. Is there a possibility for covalent > bond formation between beta phosphate of ADP and acetate molecule both > are coordinated by divalent metal ions? I am working on a Kinase > structure which was crystallized with ADP and in presence of 1M sodium > acetate. We observed additional density around ADP that fits perfectly > like a gamma phosphate , mimicking like ATP bound state, surrounded and > coordinated by two metal ions(resolution is 1.4A). There is a change in > space group (from I212121 to P212121 ) and further important > conformation changes are observed around ATP binding pocket and distant > region. This is the only xtal we obtained in this space group, and all > other xtals(measured 10 xtals) from the same plate belong to I212121. > > > > Thanks your help and time! > > Saravanan > ----- Original Message ----- > From: "CCP4BB automatic digest system" <lists...@jiscmail.ac.uk> > To: CCP4BB@JISCMAIL.AC.UK > Sent: Sunday, 15 January, 2017 01:01:37 > Subject: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) > > There are 2 messages totaling 45 lines in this issue. > > Topics of the day: > > 1. Phenix (2) > > ---------------------------------------------------------------------- > > Date: Sat, 14 Jan 2017 20:58:09 +0000 > From: D Bonsor <dbon...@ihv.umaryland.edu> > Subject: Phenix > > Is the phenix website down? Anyone know when it will be back up? > > ----------------------------- > > Date: Sat, 14 Jan 2017 14:45:06 -0800 > From: Pavel Afonine <pafon...@gmail.com> > Subject: Re: Phenix > > See notice on Phenix mailing list that answers your question. > > On Sat, Jan 14, 2017 at 12:58 PM, D Bonsor <dbon...@ihv.umaryland.edu> > wrote: > > > Is the phenix website down? Anyone know when it will be back up? > > > > ----------------------------- > > End of CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) > ************************************************************ > > ------------------------------ > > Date: Thu, 19 Jan 2017 21:16:51 +0000 > From: "Keller, Jacob" <kell...@janelia.hhmi.org> > Subject: Re: Anisotropy and temperature > > The actual vibrations don't exist at 100 K (similar to the case of > B-factors/ADPs, sometimes called mildly misleadingly "temperature > factors"), but are rather "frozen" where they were when they get cold. So a > colder cryo stream would not help. > > JPK > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of D > Bonsor > Sent: Thursday, January 19, 2017 3:35 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Anisotropy and temperature > > A PhD student asked me what causes diffraction anisotropy. Quoting from > the Diffraction Anisotropy Server webpage that it is caused by whole-body > anisotropic vibration of unit cells. He asked whether a colder cyrostream > could improve anisotropy. My answer would be yes, as colder temperatures > would lower the vibrations. > > My two questions are; (1) am I right? and (2) if so, has it ever been done > before in practice? > > Thanks, > > Dan > > ------------------------------ > > Date: Thu, 19 Jan 2017 16:17:18 -0500 > From: Phil Jeffrey <pjeff...@princeton.edu> > Subject: Re: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) > > On 1/19/17 3:54 PM, Panneerselvam, Saravanan wrote: > > We observed additional density around ADP that fits perfectly > > like a gamma phosphate > > Hello Saravanan > > At 1.4 Angstrom resolution wouldn't that suggest that you've somehow got > ATP in there ? I don't think I understand the other option - were you > proposing a ADP-O-C(O)2 arrangement to explain the density ? Surely > that has a rather different shape, considerably different scattering > power at the center of the terminal group (C vs P) and probably > different X-O bond lengths. All of these should show in the density > maps at 1.4 Å, although the bond length issue could be quite subtle. > > Phil Jeffrey > Princeton > > > > > mimicking like ATP bound state, surrounded and > > coordinated by two metal ions(resolution is 1.4A). There is a change in > > space group (from I212121 to P212121 ) and further important > > conformation changes are observed around ATP binding pocket and distant > > region. This is the only xtal we obtained in this space group, and all > > other xtals(measured 10 xtals) from the same plate belong to I212121. > > > > > > > > Thanks your help and time! > > > > Saravanan > > ------------------------------ > > Date: Thu, 19 Jan 2017 13:16:43 -0800 > From: Ethan A Merritt <merr...@u.washington.edu> > Subject: Re: Anisotropy and temperature > > On Thursday, 19 January, 2017 20:35:14 you wrote: > > A PhD student asked me what causes diffraction anisotropy. Quoting from > the Diffraction Anisotropy Server webpage that it is caused by whole-body > anisotropic vibration of unit cells. He asked whether a colder cyrostream > could improve anisotropy. My answer would be yes, as colder temperatures > would lower the vibrations. > > > > My two questions are; (1) am I right? and (2) if so, has it ever been > done before in practice? > > I do not know if there is past work and literature that answers your > question with specific regard to whole-body anisotropic vibration of > unit cells. > > However with regard to anisotropy in general you must consider two > components. > > (1) Vibration that is still present in the crystal, so that > atoms or larger groups are moving while the diffraction is measured. > The vibrational amplitude will be temperature dependent, but > the anisotropy may remain the same since it depends on the ratio of > vibration amplitude in different directions rather than the > magnitude in any one direction. > > (2) Vibrational displacement of a group in one unit cell relative > to copies of the same group in other unit cells that was "locked in" > when the crystal was frozen. The frozen crystal captures a > sampling of states that were present at room temperature. > The diffraction experiment sees a positional average over space > that is equivalent to a single-copy average over time. > This component is not temperature dependent so long as the > crystal stays frozen. > > Diffraction measurements at a single temperature do not distinguish > between these two components. In principle a series of diffraction > measurements from the same crystal at different temperatures would > allow partitioning the observed vibrational into the two components. > [Burgi (2000) Rev. Phys. Chem. 51:275] So far as I know this has > been confirmed for small molecule crystals but is too difficult > experimentally to be worth the trouble for protein crystals > (and I've tried :-) > > This equivalence of states sampled from a single copy over time > to multiple copies in a frozen crystal is the basis for TLSMD > analysis. In the special case of a single molecule per unit cell > I suppose a one-group TLS treatment reduces to what you originally > asked about - vibration of whole unit cells - but in general > it does not. > > cheers, > > Ethan > > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > ------------------------------ > > Date: Thu, 19 Jan 2017 15:33:48 -0600 > From: Yuh Min Chook <yuhmin.ch...@utsouthwestern.edu> > Subject: Joint Postdoctoral Position in the Grishin and Chook Labs at UT > Southwestern > > The Grishin (http://prodata.swmed.edu/ <http://prodata.swmed.edu/>) and > Chook (http://www4.utsouthwestern.edu/chooklab/ < > http://www4.utsouthwestern.edu/chooklab/>) Labs at UT Southwestern seek a > recent PhD graduate for a postdoctoral fellow position to study structural > determinants of nuclear export signals and predict them in protein > sequences. The project will involve both experimental and computational > approaches. The experimental aspect requires experience in protein > crystallography, biochemical and biophysical techniques. The computational > aspect will involve sequence bioinformatics and structure modeling > techniques. Synergy between computation and experiment is key to this > project. > Applicants should hold a recent PhD degree and have strong laboratory > skills in all aspects of protein crystallography. Computational biology > experience is helpful. Good communication and organizational skills are > critical. > > Please email application to yuhmin.ch...@utsouthwestern.edu <mailto: > yuhmin.ch...@utsouthwestern.edu> > Application should include curriculum vitae, a summary of current and > future research interests, a description of past research experience and > accomplishments, expected availability date and three references. > > > > > Yuh Min Chook, Ph.D. > Professor > and Eugene McDermott Scholar in Biomedical Research > Department of Pharmacology & > Department of Biophysics > University of Texas Southwestern Medical Center > 6001 Forest Park, ND8.136E > Dallas, TX 75390-9041 > > (214) 645-6167 (Office) > (214) 645-6168 (Laboratory) > (214) 645-6166 (Fax) > e-mail: yuhmin.ch...@utsouthwestern.edu > http://www4.utsouthwestern.edu/chooklab/ > > ------------------------------ > > Date: Thu, 19 Jan 2017 13:48:26 -0800 > From: Stephen Rader <ra...@unbc.ca> > Subject: Re: Anisotropy and temperature > > > Diffraction measurements at a single temperature do not distinguish > > between these two components. In principle a series of diffraction > > measurements from the same crystal at different temperatures would > > allow partitioning the observed vibrational into the two components. > > [Burgi (2000) Rev. Phys. Chem. 51:275] So far as I know this has > > been confirmed for small molecule crystals but is too difficult > > experimentally to be worth the trouble for protein crystals > > (and I've tried :-) > > In an early effort to investigate the role of protein dynamics in enzyme > funciton, I studied this question as part of my PhD thesis. We found that, > for a well-behaved protein that already crystallized well, we were able to > nicely distinguish thermal disorder (only present at the higher temp, 300 > K) from static disorder (ie differences protein packing in the crystal or > more local vibrations that get frozen in). We published it in Rader and > Agard, Protein Science, 1997 (https://www.ncbi.nlm.nih.gov/pubmed/9232638 > ). > > Note that the key for us was to do multiple conformation refinement, so we > could actually observe the clustering of states in the disordered regions > at low temp. This required high resolution data to have sufficient > refinement constraints. > > Stephen Rader > Dept of Chemistry > U. of Northern BC > > On 2017-01-19, at 1:16 PM, Ethan A Merritt <merr...@u.washington.edu> > wrote: > > > On Thursday, 19 January, 2017 20:35:14 you wrote: > >> A PhD student asked me what causes diffraction anisotropy. Quoting > from the Diffraction Anisotropy Server webpage that it is caused by > whole-body anisotropic vibration of unit cells. He asked whether a colder > cyrostream could improve anisotropy. My answer would be yes, as colder > temperatures would lower the vibrations. > >> > >> My two questions are; (1) am I right? and (2) if so, has it ever been > done before in practice? > > > > I do not know if there is past work and literature that answers your > > question with specific regard to whole-body anisotropic vibration of > > unit cells. > > > > However with regard to anisotropy in general you must consider two > > components. > > > > (1) Vibration that is still present in the crystal, so that > > atoms or larger groups are moving while the diffraction is measured. > > The vibrational amplitude will be temperature dependent, but > > the anisotropy may remain the same since it depends on the ratio of > > vibration amplitude in different directions rather than the > > magnitude in any one direction. > > > > (2) Vibrational displacement of a group in one unit cell relative > > to copies of the same group in other unit cells that was "locked in" > > when the crystal was frozen. The frozen crystal captures a > > sampling of states that were present at room temperature. > > The diffraction experiment sees a positional average over space > > that is equivalent to a single-copy average over time. > > This component is not temperature dependent so long as the > > crystal stays frozen. > > > > Diffraction measurements at a single temperature do not distinguish > > between these two components. In principle a series of diffraction > > measurements from the same crystal at different temperatures would > > allow partitioning the observed vibrational into the two components. > > [Burgi (2000) Rev. Phys. Chem. 51:275] So far as I know this has > > been confirmed for small molecule crystals but is too difficult > > experimentally to be worth the trouble for protein crystals > > (and I've tried :-) > > > > This equivalence of states sampled from a single copy over time > > to multiple copies in a frozen crystal is the basis for TLSMD > > analysis. In the special case of a single molecule per unit cell > > I suppose a one-group TLS treatment reduces to what you originally > > asked about - vibration of whole unit cells - but in general > > it does not. > > > > cheers, > > > > Ethan > > > > > > -- > > Ethan A Merritt > > Biomolecular Structure Center, K-428 Health Sciences Bldg > > MS 357742, University of Washington, Seattle 98195-7742 > > ------------------------------ > > Date: Thu, 19 Jan 2017 22:37:00 +0000 > From: Phil Evans <p...@mrc-lmb.cam.ac.uk> > Subject: Re: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) > > Remember that 2xADP can disproportionate into ATP + AMP > > > On 19 Jan 2017, at 20:54, Panneerselvam, Saravanan < > saravanan.panneersel...@desy.de> wrote: > > > > Dear All, > > Sorry for the little bit off topic. Is there a possibility for covalent > > bond formation between beta phosphate of ADP and acetate molecule both > > are coordinated by divalent metal ions? I am working on a Kinase > > structure which was crystallized with ADP and in presence of 1M sodium > > acetate. We observed additional density around ADP that fits perfectly > > like a gamma phosphate , mimicking like ATP bound state, surrounded and > > coordinated by two metal ions(resolution is 1.4A). There is a change in > > space group (from I212121 to P212121 ) and further important > > conformation changes are observed around ATP binding pocket and distant > > region. This is the only xtal we obtained in this space group, and all > > other xtals(measured 10 xtals) from the same plate belong to I212121. > > > > > > > > Thanks your help and time! > > > > Saravanan > > ----- Original Message ----- > > From: "CCP4BB automatic digest system" <lists...@jiscmail.ac.uk> > > To: CCP4BB@JISCMAIL.AC.UK > > Sent: Sunday, 15 January, 2017 01:01:37 > > Subject: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) > > > > There are 2 messages totaling 45 lines in this issue. > > > > Topics of the day: > > > > 1. Phenix (2) > > > > ---------------------------------------------------------------------- > > > > Date: Sat, 14 Jan 2017 20:58:09 +0000 > > From: D Bonsor <dbon...@ihv.umaryland.edu> > > Subject: Phenix > > > > Is the phenix website down? Anyone know when it will be back up? > > > > ------------------------------ > > > > Date: Sat, 14 Jan 2017 14:45:06 -0800 > > From: Pavel Afonine <pafon...@gmail.com> > > Subject: Re: Phenix > > > > See notice on Phenix mailing list that answers your question. > > > > On Sat, Jan 14, 2017 at 12:58 PM, D Bonsor <dbon...@ihv.umaryland.edu> > > wrote: > > > >> Is the phenix website down? Anyone know when it will be back up? > >> > > > > ------------------------------ > > > > End of CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) > > ************************************************************ > > ------------------------------ > > End of CCP4BB Digest - 18 Jan 2017 to 19 Jan 2017 (#2017-20) > ************************************************************ >
