[ccp4bb] regarding coot and loading an MTZ file
Hello, When I run coot in order to read the experimental MTZ corresponding to the PDB I am viewing, I got the following messages (attached is long lines original log): --- command: (refmac-for-phases-and-make-map /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz /DERIV_AU/DERIV_AU/FP /DERIV_AU/DERIV_AU/SIGFP) (refmac-for-phases-and-make-map /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz /DERIV_AU/DERIV_AU/FP /DERIV_AU/DERIV_AU/SIGFP) (molecule-name0) (calc-phases-generic /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz) INFO:: Creating directory coot-refmac (write-pdb-file0 coot-refmac/refmac-for-phases.pdb) got args: pdb-in-filename: coot-refmac/refmac-for-phases.pdb, pdb-out-filename: coot-refmac/refmac-for-phases-tmp.pdb, mtz-in-filename: /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz, mtz-out-filename: coot-refmac/refmac-for-phases.mtz, imol-refmac-count: 0, show-diff-map-flag: 1, phase-combine-flag: 0, phib-fom-pair: (), force-n-cycles: 0, f-col: /DERIV_AU/DERIV_AU/FP, sig-f-col: /DERIV_AU/DERIV_AU/SIGFP, r-free-col: () Not Passing LIBIN to refmac LIBIN DEBUG:: refmac-extra-params returns () INFO:: Running refmac with these command line args: (XYZIN coot-refmac/refmac-for-phases.pdb XYZOUT coot-refmac/refmac-for-phases-tmp.pdb HKLIN /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz HKLOUT coot-refmac/refmac-for-phases.mtz) INFO:: Running refmac with these data lines: (MAKE HYDROGENS NO NCYCLES 0WEIGHT AUTO LABIN FP=FP SIGFP=SIGFP) environment variable: SYMOP: #f environment variable: ATOMSF: #f environment variable: CLIBD: #f environment variable: CLIB: #f --- I am afraid coot is refining my molecule instead of just displaying the map. Am I right? Thanks a lot, Francois. command: (refmac-for-phases-and-make-map /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz /DERIV_AU/DERIV_AU/FP /DERIV_AU/DERIV_AU/SIGFP) (refmac-for-phases-and-make-map /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz /DERIV_AU/DERIV_AU/FP /DERIV_AU/DERIV_AU/SIGFP) (molecule-name0) (calc-phases-generic /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz) INFO:: Creating directory coot-refmac (write-pdb-file0 coot-refmac/refmac-for-phases.pdb) got args: pdb-in-filename: coot-refmac/refmac-for-phases.pdb, pdb-out-filename: coot-refmac/refmac-for-phases-tmp.pdb, mtz-in-filename: /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz, mtz-out-filename: coot-refmac/refmac-for-phases.mtz, imol-refmac-count: 0, show-diff-map-flag: 1, phase-combine-flag: 0, phib-fom-pair: (), force-n-cycles: 0, f-col: /DERIV_AU/DERIV_AU/FP, sig-f-col: /DERIV_AU/DERIV_AU/SIGFP, r-free-col: () Not Passing LIBIN to refmac LIBIN DEBUG:: refmac-extra-params returns () INFO:: Running refmac with these command line args: (XYZIN coot-refmac/refmac-for-phases.pdb XYZOUT coot-refmac/refmac-for-phases-tmp.pdb HKLIN /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz HKLOUT coot-refmac/refmac-for-phases.mtz) INFO:: Running refmac with these data lines: (MAKE HYDROGENS NO NCYCLES 0WEIGHT AUTO LABIN FP=FP SIGFP=SIGFP) environment variable: SYMOP: #f environment variable: ATOMSF: #f environment variable: CLIBD: #f environment variable: CLIB: #f
Re: [ccp4bb] regarding coot and loading an MTZ file
Hi Francois, your mtz file doesnt appear to have any phases, so Coot (or whoever) cannot make a map. What Coot cleverly tries to do in such a case is to use calculated phases from the given pdb (and mtz) file. So it runs refmac with the pdb and mtz to retrieve this phase information. There is no refinement within refmac going on as such (see below: NCYCLES 0). B Hello, When I run coot in order to read the experimental MTZ corresponding to the PDB I am viewing, I got the following messages (attached is long lines original log): --- command: (refmac-for-phases-and-make-map /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz /DERIV_AU/DERIV_AU/FP /DERIV_AU/DERIV_AU/SIGFP) (refmac-for-phases-and-make-map /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz /DERIV_AU/DERIV_AU/FP /DERIV_AU/DERIV_AU/SIGFP) (molecule-name0) (calc-phases-generic /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz) INFO:: Creating directory coot-refmac (write-pdb-file0 coot-refmac/refmac-for-phases.pdb) got args: pdb-in-filename: coot-refmac/refmac-for-phases.pdb, pdb-out-filename: coot-refmac/refmac-for-phases-tmp.pdb, mtz-in-filename: /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz, mtz-out-filename: coot-refmac/refmac-for-phases.mtz, imol-refmac-count: 0, show-diff-map-flag: 1, phase-combine-flag: 0, phib-fom-pair: (), force-n-cycles: 0, f-col: /DERIV_AU/DERIV_AU/FP, sig-f-col: /DERIV_AU/DERIV_AU/SIGFP, r-free-col: () Not Passing LIBIN to refmac LIBIN DEBUG:: refmac-extra-params returns () INFO:: Running refmac with these command line args: (XYZIN coot-refmac/refmac-for-phases.pdb XYZOUT coot-refmac/refmac-for-phases-tmp.pdb HKLIN /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz HKLOUT coot-refmac/refmac-for-phases.mtz) INFO:: Running refmac with these data lines: (MAKE HYDROGENS NO NCYCLES 0WEIGHT AUTO LABIN FP=FP SIGFP=SIGFP) environment variable: SYMOP: #f environment variable: ATOMSF: #f environment variable: CLIBD: #f environment variable: CLIB: #f --- I am afraid coot is refining my molecule instead of just displaying the map. Am I right? Thanks a lot, Francois.
Re: [ccp4bb] regarding coot and loading an MTZ file
Francois Berenger wrote: When I run coot in order to read the experimental MTZ corresponding to the PDB I am viewing, [snip] I am afraid coot is refining my molecule instead of just displaying the map. Well, Refmac is - at Coot's request. This usually happens because Coot doesn't detect phases in your MTZ file (i.e. you are using a phasing input file, rather than an output file). Or it could be a bug. Paul.
Re: [ccp4bb] regarding coot and loading an MTZ file
Paul Emsley wrote: Francois Berenger wrote: When I run coot in order to read the experimental MTZ corresponding to the PDB I am viewing, [snip] I am afraid coot is refining my molecule instead of just displaying the map. Well, Refmac is - at Coot's request. This usually happens because Coot doesn't detect phases in your MTZ file (i.e. you are using a phasing input file, rather than an output file). Or it could be a bug. Hello Paul, Yes, my MTZ doesn't have phase, it is not supposed to. But, as Bernhard C. Lohkamp just pointed out 3 minutes before on this same mailing list: does the fact that NCYCLES 0 is present means that refmac would just compute a map and not do any refinement of my PDB? From the refmac documentation, and not being a crystallographer (sorry for this fact), it is completely not clear for me. Thanks a lot, Francois.
[ccp4bb] wwPDB statement on Retraction of UAB PDB entries
wwPDB statement on Retraction of UAB PDB entries - In its December 4, 2009 issue, the Journal of Biological Chemistry (JBC) retracted an article by H.M. Krishna Murthy et al. describing the structure of dengue virus NS3 serine protease published 10 years earlier (http://www.jbc.org/content/284/49/34468.full). The JBC editors requested that the Protein Data Bank (PDB) entry described in that paper (PDB code 1BEF) be made obsolete and this request has been granted. It is the current wwPDB (Worldwide PDB) policy that entries can be made obsolete following a request from the people responsible for publishing it (be it the principal author or journal editors). Typically, authors themselves request an entry to be made obsolete because they have collected better experimental data or produced an improved interpretation of the existing data. In addition, the employer of an author may request this, but in that case the request must be fully documented and a retraction published in the journal that published the original paper describing the entry. This policy mirrors the manner in which Bell Labs/Lucent handled the case of its employee J.H. Schon (see http://en.wikipedia.org/wiki/Jan_Hendrik_Schon) and it ensures both due process and the scientific integrity of the worldwide structural archive. Earlier this month, the University of Alabama at Birmingham (UAB) announced on its website (http://main.uab.edu/Sites/reporter/articles/71570/) its plans to retract 12 PDB entries and 10 papers (including the one in JBC), although the case against the scientist involved is still being investigated by the Office for Research Integrity (ORI; http://ori.dhhs.gov/). In line with its current policy, wwPDB will make the remaining 11 entries obsolete if and when the corresponding papers are retracted. The PDB is a historical archive that stores, annotates and disseminates structure models and their related experimental data (deposition of which has been mandatory since February 2008). wwPDB has convened expert, community-driven Validation Task Forces for X-ray (in 2008) and NMR (in 2009) to advise on the most suitable criteria to use for validating structure entries (model, data and fit of model to data) when they are deposited. The recommendations of these task forces will be implemented as part of the deposition and annotation procedures of the wwPDB partners. Moreover, it is envisioned that the results of these validation procedures will be captured in a report that will be sent to the depositors and can be transmitted by them to the journal to which the corresponding manuscript is submitted. Availability of such a report would greatly facilitate assessment of the reliability of structural data and its interpretation by journal editors and referees alike. wwPDB hopes that eventually all journals that publish structural data on biological macromolecules will make submission of the PDB validation report mandatory. The continuing mission of the wwPDB partners is to safeguard the integrity and improve the quality of the structural archive, with the enthusiastic support of the international structural biology community. The Worldwide Protein Data Bank (wwPDB; http://www.wwpdb.org/) consists of organisations that act as deposition, data-processing and distribution centres for PDB data. The members are the RCSB PDB (USA), PDBe (Europe), PDBj (Japan), and the BMRB (USA). The mission of the wwPDB is to maintain a single Protein Data Bank archive of macromolecular structural data that is freely and publicly available to the global community. --- Posted on behalf of wwPDB, --Gerard Kleywegt --- Gerard Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk http://www.ebi.ac.uk/pdbe/ Secretary: Celia Copp pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] regarding coot and loading an MTZ file
Francois Berenger wrote: Paul Emsley wrote: Francois Berenger wrote: When I run coot in order to read the experimental MTZ corresponding to the PDB I am viewing, [snip] I am afraid coot is refining my molecule instead of just displaying the map. Well, Refmac is - at Coot's request. This usually happens because Coot doesn't detect phases in your MTZ file (i.e. you are using a phasing input file, rather than an output file). Or it could be a bug. Yes, my MTZ doesn't have phase, it is not supposed to.] I see. I was mislead by you writing to read the experimental MTZ, which I took to mean that you wanted to read an MTZ with experimental phases. But, as Bernhard C. Lohkamp just pointed out 3 minutes before on this same mailing list: does the fact that NCYCLES 0 is present means that refmac would just compute a map and not do any refinement of my PDB? Yes. Exactly so. Paul.
[ccp4bb] Postdoctoral Position - University of Puerto Rico
A postdoctoral research position is immediately available in the laboratory of Dr. Eric R. Schreiter, at the University of Puerto Rico - Rio Piedras Campus, to study the effects of S-nitrosylation on protein structure and function at the molecular level. Applicants should possess a PhD in a relevant field (chemistry, biochemistry, molecular biology, structural biology, etc.) and ideally have experience in structural characterization of macromolecules using x-ray crystallography. Experience in protein biochemistry and other biophysical techniques for characterizing proteins is also highly desirable. Excellent communication skills, motivation and the ability to work as part of a team are required. The PI's laboratory is equipped with state of the art instrumentation for macromolecular x-ray crystallography, including a Rigaku RU-H3R X-ray generator with a CCD detector and X-stream 2000 low temperature system as well as high-throughput crystallization robotics. The Rio Piedras Campus of the University of Puerto Rico is its flagship campus for basic science research and is only two miles away from the Medical Sciences Campus, accessible by train. It is located in San Juan, Puerto Rico, which offers a warm climate year-round and an abundance of outdoor activities in close proximity. Puerto Rico uses both Spanish and English as official languages, but laboratory business is conducted primarily in English. Interested individuals should submit a CV, a summary of research achievements, and names of three references to: Dr. Eric Schreiter (eschrei...@vmail.uprrp.edu) -- Eric R. Schreiter, PhD Assistant Professor of Chemistry University of Puerto Rico, Rio Piedras Campus PO Box 23346 San Juan, PR 00931-3346 Phone: 787-764- ext. 4796 http://chemistry.uprrp.edu/people/faculty/eric-schreiter
[ccp4bb] Postdoctoral position in RNA structural biochemistry at the Karolinska Institutet
A postdoctoral position in RNA structural biochemistry is open in my lab at the Department of Cell and Molecular Biology at the Karolinska Institutet in Stockholm. Successful candidates will participate in all steps involved in structure determination of RNA-protein complexes relevant to tRNA biogenesis. Suitable candidates have a PhD in a relevant area, preferably in RNA biochemistry, structural biology or closely related subjects. A general requirement to be eligible for this position is a recent doctoral degree from a University outside Sweden. The application should contain a cover letter and a CV with publication list. Contact details of two references should be also provided. Send the application as an email with attachments to martin.hallb...@ki.se Review of applications will begin immediately and continue until the position is filled. . B. Martin Hallberg, PhD Department of Cell and Molecular Biology Karolinska Institutet 171 77 Stockholm Sweden http://tinyurl.com/yzn9y5j
Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo
My current understanding is that 1) The new 120Hz LCD monitors are not compatible with the old goggles. Something about the type of polarization used for the shuttering effect. So if you were going to try out one of the new 120Hz monitors (~ $400) you might also want to spend on the nVidia glasses and emitter kit (~ $200) 2) The 120 Hz LCDs are not supported under Linux drivers by nVidia at present. Whether it might actually work or not, I can't say. I am encouraged by the mention that the nVidia emitter can accept a signal from the mini-DIN stereo port on some Quadro cards. http://www.nvidia.com/object/quadro_pro_graphics_boards.html 3) As someone mentioned already, the Zalman LCD monitors, which are not 120Hz and do not require goggles, but have diminished resolution, are currently supported. Cheers, -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Thu, 2009-12-17 at 11:09 -0500, Michael J Miley wrote: I have a linux workstation with a nvidia quadro graphics card and matching emitter/lcd glasses setup from realD. It is very hard to find CRTs that are able to support the high refresh rates needed for headache free 3D viewing. The old SGI one I have is terrible, as it flickers bad in 3d mode. My question is can i use one of these new 120hz LCD monitors with the above setup for coot. Basically just switch out the crt for the LCD. Has anyone tried this? I am aware that these monitors with a non-quadro nvidia card plus the nvidia emitter/glasses setup will not work with coot. But i think the reason is that the drivers for these non-quadro cards do not support true quad buffered stereo.
[ccp4bb] DNA prep for protein-DNA complex crystallization
Dear CCP4BBers, Sorry for the non-CCP4 question. I intend to set up some trials for protein-DNA complexes. In this regard, I have a few queries: 1. After annealing the oligos, how do I ensure that what goes into trials are only the annealed dsDNA and not other forms such as ones carrying hairpin loops. 2. Should I visualize it on the agarose gel and then try to get the dsDNA band? Sorry for these queries as I have little idea about this. Many thanks in advance. Cheers -- Amit Sharma, Ph.D. Postdoctoral Fellow, Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo
I got the information from a supplier that there is a beta driver from nvidia that supports the 120Hz LCD with nvidia stereo glasses. I have not seen it myself but we have a demo scheduled in January. Alexander -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David J. Schuller Sent: Thursday, December 17, 2009 6:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo My current understanding is that 1) The new 120Hz LCD monitors are not compatible with the old goggles. Something about the type of polarization used for the shuttering effect. So if you were going to try out one of the new 120Hz monitors (~ $400) you might also want to spend on the nVidia glasses and emitter kit (~ $200) 2) The 120 Hz LCDs are not supported under Linux drivers by nVidia at present. Whether it might actually work or not, I can't say. I am encouraged by the mention that the nVidia emitter can accept a signal from the mini-DIN stereo port on some Quadro cards. http://www.nvidia.com/object/quadro_pro_graphics_boards.html 3) As someone mentioned already, the Zalman LCD monitors, which are not 120Hz and do not require goggles, but have diminished resolution, are currently supported. Cheers, -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Thu, 2009-12-17 at 11:09 -0500, Michael J Miley wrote: I have a linux workstation with a nvidia quadro graphics card and matching emitter/lcd glasses setup from realD. It is very hard to find CRTs that are able to support the high refresh rates needed for headache free 3D viewing. The old SGI one I have is terrible, as it flickers bad in 3d mode. My question is can i use one of these new 120hz LCD monitors with the above setup for coot. Basically just switch out the crt for the LCD. Has anyone tried this? I am aware that these monitors with a non-quadro nvidia card plus the nvidia emitter/glasses setup will not work with coot. But i think the reason is that the drivers for these non-quadro cards do not support true quad buffered stereo.
Re: [ccp4bb] FW: [ccp4]: TDS upon flashcooling
good point! recently we managed to collect very good room temperature data with PILATUS detector at SLS. if your crystals are large enough, say 100 microns or so, you have chance. regards, meitian On Dec 15, 2009, at 1:42 PM, mjvanraaij wrote: why not stay with room temp? many structures have been solved at RT... Mark J. van Raaij Dpto de Bioquimica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ researcherID: B-3678-2009 On 15 Dec 2009, at 13:20, Natalie Zhao wrote: -Original Message- From: owner-c...@dl.ac.uk [mailto:owner-c...@dl.ac.uk] On Behalf Of Rafael Couñago Sent: 14 December 2009 20:22 To: c...@ccp4.ac.uk Subject: [ccp4]: TDS upon flashcooling Dear all, I got these beautiful looking crystals that grow in high salt (1.8M) and diffract under 2.0A at room temp. My attempts so far to cryo protect them have resulted in a loss of resolution (2.5A tops) and increased anisotropy. I have tried some of the usual suspects; no cryo, ethylene glycol, glycerol (even 5% makes my crystal crack), sucrose, glucose, paratone-n (no diffraction at all). I have tried both dipping the crystal straight into liquid nitrogen and flash cooling it in the cryostream. An interesting observation is that the diffraction pattern following freezing has a substantial amount of thermal diffuse scattering (but no ice rings). If I remove the crystal from the cryostream and re- anneal it at room temp (in air or in mother liquor or mother liquor + cryo) most of the TDS goes away, but the max resolution is still around 2.5A and the higher anisotropy is still there. Extending re-annealing times lead to cracking of the crystal. My two questions would be: - any thoughts on cryo solutions? - does the result from the re-annealing experiment ring any bells? Would this be an indication that I need the cooling to be faster or slower? Cheers, Rafael. -- Rafael Couñago Research Fellow Department of Biochemistry University of Otago 710 Cumberland St Dunedin, New Zealand ph: (03) 479 5148 -- Scanned by iCritical. __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone: +41 56 310 4175 Fax: +41 56 310 5292
Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo
On this note, I recently bought a viewsonic 120hz LCD (VX2265wm) in the naïve believe it should work as it has the right refresh rate. I tried to run it with the normal setup, quadro with emitter via DIN, nuVision glasses, Linux. Here's the problem: I have stereo in the top and the bottom but not in the middle of the screen. The image is stable (no flickering or moving of the part that shows stereo). It seems that I got the right refresh rate (any way to check that?), but I don't understand at all what's going on. Any clues? Jens -Original Message- From: David J. Schuller dj...@cornell.edu Subj: Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo Date: Thu Dec 17, 2009 9:19 Size: 2K To: CCP4BB@JISCMAIL.AC.UK My current understanding is that 1) The new 120Hz LCD monitors are not compatible with the old goggles. Something about the type of polarization used for the shuttering effect. So if you were going to try out one of the new 120Hz monitors (~ $400) you might also want to spend on the nVidia glasses and emitter kit (~ $200) 2) The 120 Hz LCDs are not supported under Linux drivers by nVidia at present. Whether it might actually work or not, I can't say. I am encouraged by the mention that the nVidia emitter can accept a signal from the mini-DIN stereo port on some Quadro cards. http://www.nvidia.com/object/quadro_pro_graphics_boards.html 3) As someone mentioned already, the Zalman LCD monitors, which are not 120Hz and do not require goggles, but have diminished resolution, are currently supported. Cheers, -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Thu, 2009-12-17 at 11:09 -0500, Michael J Miley wrote: I have a linux workstation with a nvidia quadro graphics card and matching emitter/lcd glasses setup from realD. It is very hard to find CRTs that are able to support the high refresh rates needed for headache free 3D viewing. The old SGI one I have is terrible, as it flickers bad in 3d mode. My question is can i use one of these new 120hz LCD monitors with the above setup for coot. Basically just switch out the crt for the LCD. Has anyone tried this? I am aware that these monitors with a non-quadro nvidia card plus the nvidia emitter/glasses setup will not work with coot. But i think the reason is that the drivers for these non-quadro cards do not support true quad buffered stereo.
Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo
On Thu, 2009-12-17 at 13:51 -0800, kai...@caltech.edu wrote: On this note, I recently bought a viewsonic 120hz LCD (VX2265wm) in the naïve believe it should work as it has the right refresh rate. I tried to run it with the normal setup, quadro with emitter via DIN, nuVision glasses, Linux. Here's the problem: I have stereo in the top and the bottom but not in the middle of the screen. The image is stable (no flickering or moving of the part that shows stereo). It seems that I got the right refresh rate (any way to check that?), but I don't understand at all what's going on. Any clues? Jens That monitor appears on the supported displays list: http://www.nvidia.com/object/3D_Vision_Requirements.html So the problem could be one (or more) of two things: 1) The glasses may be incompatible. You could try it out with the nVidia glasses. 2) The Linux driver may not be working properly yet. BTW, I see that some 1920x1080 monitors are listed on the above page, and should be available in January or so. -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo
The glasses are not compatible. I tested swapping glasses while keeping the emitter unchanged and it did not work. Yong David J. Schuller dj...@cornell.edu Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 12/17/2009 05:25 PM Please respond to schul...@cornell.edu To CCP4BB@JISCMAIL.AC.UK cc Subject Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo On Thu, 2009-12-17 at 13:51 -0800, kai...@caltech.edu wrote: On this note, I recently bought a viewsonic 120hz LCD (VX2265wm) in the naïve believe it should work as it has the right refresh rate. I tried to run it with the normal setup, quadro with emitter via DIN, nuVision glasses, Linux. Here's the problem: I have stereo in the top and the bottom but not in the middle of the screen. The image is stable (no flickering or moving of the part that shows stereo). It seems that I got the right refresh rate (any way to check that?), but I don't understand at all what's going on. Any clues? Jens That monitor appears on the supported displays list: http://www.nvidia.com/object/3D_Vision_Requirements.html So the problem could be one (or more) of two things: 1) The glasses may be incompatible. You could try it out with the nVidia glasses. 2) The Linux driver may not be working properly yet. BTW, I see that some 1920x1080 monitors are listed on the above page, and should be available in January or so. -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo
I just talked to the NVIDIA pre-sales people and they told me that this driver (195.22 beta) should work with 120Hz lcd monitors together with Nvidia 3D vision kit on a quadro graphics card. Ajit B. - Original Message - From: Yong Y Wang wang_yon...@lilly.com Date: Thursday, December 17, 2009 4:53 pm Subject: Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo To: CCP4BB@JISCMAIL.AC.UK Does anyone know if this beta driver ( works? Yong alexander.schif...@sanofi-aventis.com Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 12/17/2009 03:39 PM Please respond to alexander.schif...@sanofi-aventis.com To CCP4BB@JISCMAIL.AC.UK cc Subject Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo I got the information from a supplier that there is a beta driver from nvidia that supports the 120Hz LCD with nvidia stereo glasses. I have not seen it myself but we have a demo scheduled in January. Alexander -Original Message- From: CCP4 bulletin board [ On Behalf Of David J. Schuller Sent: Thursday, December 17, 2009 6:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo My current understanding is that 1) The new 120Hz LCD monitors are not compatible with the old goggles. Something about the type of polarization used for the shuttering effect. So if you were going to try out one of the new 120Hz monitors (~ $400) you might also want to spend on the nVidia glasses and emitter kit (~ $200) 2) The 120 Hz LCDs are not supported under Linux drivers by nVidia at present. Whether it might actually work or not, I can't say. I am encouraged by the mention that the nVidia emitter can accept a signal from the mini-DIN stereo port on some Quadro cards. 3) As someone mentioned already, the Zalman LCD monitors, which are not 120Hz and do not require goggles, but have diminished resolution, are currently supported. Cheers, -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Thu, 2009-12-17 at 11:09 -0500, Michael J Miley wrote: I have a linux workstation with a nvidia quadro graphics card and matching emitter/lcd glasses setup from realD. It is very hard to find CRTs that are able to support the high refresh rates needed for headache free 3D viewing. The old SGI one I have is terrible, as it flickers bad in 3d mode. My question is can i use one of these new 120hz LCD monitors with the above setup for coot. Basically just switch out the crt for the LCD. Has anyone tried this? I am aware that these monitors with a non-quadro nvidia card plus the nvidia emitter/glasses setup will not work with coot. But i think the reason is that the drivers for these non-quadro cards do not support true quad buffered stereo.
[ccp4bb] Postdoctoral Position in Computational Structural Biology at RIKEN, Japan
Dear ccp4 users, Postdoctoral Fellow Position in Computational Structural Biology at the Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, Japan We are seeking a highly motivated and experienced computational structural biologist to join the Zhang Initiative Research Unit at RIKEN. The successful candidate will use computational tools to tackle problems in the area of protein folding, structure prediction, crystallographic phasing or drug design. Qualifications: This position requires a PhD in biophysics, biochemistry, chemistry, bioinformatics or structural biology with experience in employing computational tools to solve biological or chemical problems. Experience in protein folding, protein structure prediction, protein structure analysis, protein crystallography or structure-based drug design are highly desired. Proficiency in object-oriented programming and scripting languages are also required. Experience in high performance computing, network computing or grid computing would be a plus. The ideal candidate should possess a track record of accomplishments demonstrating technical proficiency, independent thinking, and scientific creativity. The research environment in the unit is international and English will be used for communication and knowledge of Japanese is not required. Salary and benefits: This is a full-time position with an annual renewable contract. Salary will be commensurate with qualification and experience. Commuting and housing allowance will be provided. Application and required documents: Complete CV (including list of publications) and names and contact information of three references. Contact information: Ms. Hiroko Kani Zhang Initiative Research Unit Advanced Science Institute RIKEN 2-1 Hirosawa, Wako, Saitama 351-0198, Japan E-mail: zhang-unit [at] riken.jp
Re: [ccp4bb] contaminants in PEG - references
Zhang and Tanner, 2004, Detection of L-lactate in polyethylene glycol solutions confirms the identity of the active-site ligand in a proline dehydrogenase structure, Acta Cryst D. 60:985
[ccp4bb] 22 tickets left for Warren DeLano Memorial Fund Raffle
Please...22 more and I can close out the raffle with the last drawing. Merry Christmas, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com bernhardr...@sbcglobal.net http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
Re: [ccp4bb] FW: [ccp4]: TDS upon flashcooling
Hi Rafael, If it has not been already suggested: try DMSO (20% to 40%). In my limited experience I found that often DMSO works well for crystallization conditions with high-salt or high buffer component (like 1M D,L,-Malic acid). HTH, -Partha On Thu, Dec 17, 2009 at 1:39 PM, Meitian Wang meitian.w...@psi.ch wrote: good point! recently we managed to collect very good room temperature data with PILATUS detector at SLS. if your crystals are large enough, say 100 microns or so, you have chance. regards, meitian On Dec 15, 2009, at 1:42 PM, mjvanraaij wrote: why not stay with room temp? many structures have been solved at RT... Mark J. van Raaij Dpto de Bioquimica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ researcherID: B-3678-2009 On 15 Dec 2009, at 13:20, Natalie Zhao wrote: -Original Message- From: owner-c...@dl.ac.uk [mailto:owner-c...@dl.ac.uk] On Behalf Of Rafael Couñago Sent: 14 December 2009 20:22 To: c...@ccp4.ac.uk Subject: [ccp4]: TDS upon flashcooling Dear all, I got these beautiful looking crystals that grow in high salt (1.8M) and diffract under 2.0A at room temp. My attempts so far to cryo protect them have resulted in a loss of resolution (2.5A tops) and increased anisotropy. I have tried some of the usual suspects; no cryo, ethylene glycol, glycerol (even 5% makes my crystal crack), sucrose, glucose, paratone-n (no diffraction at all). I have tried both dipping the crystal straight into liquid nitrogen and flash cooling it in the cryostream. An interesting observation is that the diffraction pattern following freezing has a substantial amount of thermal diffuse scattering (but no ice rings). If I remove the crystal from the cryostream and re-anneal it at room temp (in air or in mother liquor or mother liquor + cryo) most of the TDS goes away, but the max resolution is still around 2.5A and the higher anisotropy is still there. Extending re-annealing times lead to cracking of the crystal. My two questions would be: - any thoughts on cryo solutions? - does the result from the re-annealing experiment ring any bells? Would this be an indication that I need the cooling to be faster or slower? Cheers, Rafael. -- Rafael Couñago Research Fellow Department of Biochemistry University of Otago 710 Cumberland St Dunedin, New Zealand ph: (03) 479 5148 -- Scanned by iCritical. __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone: +41 56 310 4175 Fax: +41 56 310 5292
Re: [ccp4bb] DNA prep for protein-DNA complex crystallization
Hi Amit, Normally, we optimize annealing conditions with labeled DNA (cy5, FAM) - adding MgCl2 and KCl usually improves annealing efficiency. You can detect fractions of single and double stranded DNA on standard PAGE gels. We then use the same condition to anneal the crystallization reagents. At times we order double stranded DNA cut from PAGE gels by the supplier - but that's expensive. Also, you can purify protein-DNA complexes using gel filtration - your protein shouldn't co-elute with ssDNA. There are also dyes that specifically stain double stranded DNA but we haven't tried those. -ralf --- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, disclose its content to any other person. Thank you. --- -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of amit sharma Sent: Friday, December 18, 2009 2:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] DNA prep for protein-DNA complex crystallization Dear CCP4BBers, Sorry for the non-CCP4 question. I intend to set up some trials for protein-DNA complexes. In this regard, I have a few queries: 1. After annealing the oligos, how do I ensure that what goes into trials are only the annealed dsDNA and not other forms such as ones carrying hairpin loops. 2. Should I visualize it on the agarose gel and then try to get the dsDNA band? Sorry for these queries as I have little idea about this. Many thanks in advance. Cheers -- Amit Sharma, Ph.D. Postdoctoral Fellow, Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
