Re: [ccp4bb] Fwd: HR3699, Research Works Act
Dear Colleagues, Further to Herbert's summary, which I support, the publishers allowing the deposition of their published version/PDF in Institutional Repositories can be found listed here:- http://www.sherpa.ac.uk/romeo/PDFandIR.php?la=en Best wishes, John On Thu, Feb 16, 2012 at 6:52 PM, Herbert J. Bernstein wrote: > Dear Colleagues, > > If you want an excellent, painless transfer from journal to PUBMED, just > stick > to the IUCr journals. They do an excellent job of cooperating in the NIH > open access policy with an automatic transfer of the clean refereeded and > edited > paper to PUBMED. Yes, the IUCr journal copy does look prettier -- more > power to them -- but nothing is missing from the PUBMED version, so > everybody benefits: the IUCr has its subscription money from libraries and > individuals who need results as quickly as possible or in the best form, and > students and researchers without an institutional subscription can still get > a completely valid and complete copy on line. > > If you pay IUCr for open access and are NIH funded, they deposit in PUBMED > immediately. If you don't pay IUCr for open access and are NIH funded, they > deposit in PUBMED a year after publication. Either way it works and works > well, > you get excellent editing, you are publishing in very respectable journals, > and > your work ends up available to everybody. > > So, if you want a balanced, nuanced approach, please sign the petition, but > also > publish in the IUCr journals if you work fits, but don't publish in any > journals > that don't do automatic deposition or that support the NIH Open Access > policy poorly. > > Regards, > Herbert > > > On 2/16/12 12:27 PM, Enrico Stura wrote: >> >> Charlie, >> >> A much more balanced view than others have posted. >>> >>> NIH Open Access requirement is a vast overreach. >> >> I agree. >>> >>> HR 3699 appears to be as deeply flawed. >> >> It could be made better with amendments? >> >> Enrico. >> >> On Thu, 16 Feb 2012 17:06:24 +0100, Charles W. Carter, Jr >> wrote: >> >>> For what it's worth, my own experience with the issue of scholarly >>> publication and open access is nuanced enough that perhaps my two-bits worth >>> can add to this discussion. In short, I agree both with Ian's previous >>> message and with Herbert, and feel that the incompatibility between them >>> goes to the root of a problem for which the answer is certainly not quite >>> there. >>> >>> I have been much influenced by the work done on this issue by Fred Dylla, >>> Executive Director of the American Institute of Physics. Here is a link to >>> recent information concerning his four-year effort to reach consensus on >>> this issue: >>> >>> http://www.aip.org/aip/aipmatters/archive/2011/1_24_11.html >>> >>> I personally think that the NIH Open Access requirement is a vast >>> overreach. PubMed Central is very difficult to use and ultimately has never >>> satisfied me: I always go to the UNC library holdings. There are several >>> reasons why. The most immediate is that PubMed Central almost never gives a >>> satisfactory copy of a paper I want to read, and the most serious reason is >>> that I am convinced that the overhead exacted on authors and PIs by the NIH >>> means that few, if any authors give much more than a glance in the direction >>> of updating deposited manuscripts from journals that do not automatically >>> deposit the version of record. For this reason, many PubMed Central entries >>> are likely to have more than minor errors corrected in proof only in the >>> version of record. I don't personally see any way around the problem that >>> there is only one version of record and that version is the one for which >>> copyright is retained by the publisher. >>> >>> On the other hand, I am deeply sympathetic to the argument that >>> publicly-funded research must be freely accessible. After talking intensely >>> with the library administrators at UNC, I also believe deeply that >>> university library subscriptions satisfy the need for open access. Casting >>> aside for the moment the issue of Open Access journals, whose only real >>> difference lies in who pays the costs of publication, I have long believed >>> that careful validation through peer review constitutes serious added value >>> and that journals are entitled to being paid for that added value. What >>> makes this issue more difficult for me is that I share with many the deep >>> suspicions of corporate (as opposed to Member Society) publishing >>> organizations. Several years ago I withdrew my expertise from the Nature >>> group in protest over what I felt (after, again, long discussions with our >>> UNC librarians) was a power play designed only to weaken the library >>> systems. I have similar views about Elsevier. >>> >>> Finally, I am inclined to sign this petition for other reasons, including >>> the fact that HR 3699 appears to be as deeply flawed in the other direction >>> as the original enabling legislation
[ccp4bb] EMBL Advanced Course: Hybrid Structural Biology Approaches
REGISTRATION NOW OPEN!! EMBL Advanced Course: Hybrid Structural Biology Approaches EMBL Hamburg, Germany Monday 11 June - Saturday 16 June 2012 Organisers: V.Lamzin (EMBL Hamburg), R. Meijers (EMBL Hamburg), C.Sachse (EMBL Heidelberg), T.Schneider (EMBL Hamburg), D.Svergun (EMBL Hamburg), M.Wilmanns (EMBL Hamburg), R.Wilson (EMBL Hamburg) The course will cover theoretical and experimental approaches to Small Angle X-ray Scattering (SAXS), Macromolecular Crystallography (MX) and Electron Microscopy (EM) offered at EMBL Hamburg and EMBL Heidelberg. Combined use of these structural techniques will be demonstrated and discussed. The course is aimed at PhD students and postdocs who have at least a basic understanding of one (or more) of the techniques listed above, and are interested in learning more about hybrid structural biology approaches. For more information and to register please go to: http://www.embl-hamburg.de/training/events/2012/HYB12-01/index.html -- Dr. Rosemary Wilson Scientific Training and Outreach Officer EMBL c/o DESY, Building 25a Notkestrasse 85, 22603 Hamburg, Germany
Re: [ccp4bb] choice of wavelength
Bart >> Diffracted intensity goes up by the cube of the wavelength, but so >> does absorption and I don't know exactly about radiation damage. I think this statement should be "As an approximation, diffracted intensity (integrated) goes up by the square of the wavelength, but so does absorbed energy." See for example Arndt, U. W. (1984) Optimum X-ray wavelength for protein crystallography. J. Appl. Cryst. 17, 118-119. Fig. 1. Plot of Ie (not Ip). Note that this includes loss of signal due to absorption through the sample. Subsequent calculations have included Compton scattering and other factors. I believe Zachariasen first specifically pointed out the wavelength dependence of the integrated intensity (one has to include a Lorentz factor). For the second factor, the absorption of a photon approximately follows the cube of the wavelength but the absorbed energy itself follows the square of the wavelength. Regards Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bart Hazes Sent: 16 February 2012 15:01 To: ccp4bb Subject: Re: [ccp4bb] choice of wavelength Hi Andrew, I completely agree and it is what I meant by "(assuming the full photon energy is captured)". If the fraction of photons counted goes up at longer wavelengths than the relative benefit of using longer wavelength is even more pronounced on Pilatus. So for native data sets the wavelength sweet spot with a pilatus detector may be a bit longer then what used to be optimal for a given beamline on a previous generation detector. Bart On 12-02-16 02:09 AM, A Leslie wrote: > > On 15 Feb 2012, at 23:55, Bart Hazes wrote: > >> Diffracted intensity goes up by the cube of the wavelength, but so >> does absorption and I don't know exactly about radiation damage. One >> interesting point is that on image plate and CCD detectors the signal >> is also proportional to photon energy, so doubling the wavelength >> gives 8 times diffraction intensity, but only 4 times the signal on >> integrating detectors (assuming the full photon energy is captured). >> So it would be interesting to see how the equation works out on the >> new counting detectors where the signal does not depend on photon >> energy. > > > You make a good point about the variation in efficiency of the > detectors, but I don't think your comment about the "new counting > detectors" (assuming this refers to hybrid pixel detectors) is > correct. The efficiency of the Pilatus detector, for example, falls > off significantly at higher energies simply because the photons are > not absorbed by the silicon (320 microns thick). The DQE for the > Pilatus is quoted as 80% at 12KeV but only 50% at 16KeV and I think > this variation is entirely (or at least mainly) due to the efficiency > of absorption by the silicon. > > Andrew > > > >> Another point to take into account is that beamlines can have >> different optimal wavelength ranges. Typically, your beamline guy/gal >> should be the one to ask. Maybe James Holton will chime in on this. >> >> Bart >> >> On 12-02-15 04:21 PM, Jacob Keller wrote: >>> Well, but there is more scattering with lower energy as well. The >>> salient parameter should probably be scattering per damage. I >>> remember reading some systematic studies a while back in which >>> wavelength choice ended up being insignificant, but perhaps there is >>> more info now, or perhaps I am remembering wrong? >>> >>> Jacob >>> >>> On Wed, Feb 15, 2012 at 5:14 PM, Bosch, Juergen >>> wrote: No impact ? Longer wavelength more absorption more damage. But between the choices given no problem. Spread of spots might be better with 1.0 versus 0.9 but that depends on your cell and also how big your detector is. Given your current resolution none of the mentioned issues are deal breakers. 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 Feb 15, 2012, at 18:08, "Jacob Keller" wrote: > I would say the better practice would be to collect higher > multiplicity/completeness, which should have a great impact on maps. > Just watch out for radiation damage though. I think the wavelength > will have no impact whatsoever. > > JPK > > On Wed, Feb 15, 2012 at 4:23 PM, Seungil Han > wrote: >> All, >> I am curious to hear what our CCP4 community thoughts are >> I have a marginally diffracting protein crystal (3-3.5 Angstrom >> resolution) >> and would like to squeeze in a few tenth of angstrom. >> Given that I am working on crystal quality improvement, wou
[ccp4bb] modelling C-terminal COOH in coot
Dear all, I have a structure solved by molecular replacement. The C-terminus at the end of the chain shows as CO, not COOH. How do I make it into COOH in COOT? I tried to place an O in the relevant position, but seems not working this way. Thanks, Hubing
Re: [ccp4bb] modelling C-terminal COOH in coot
There is a button for doing this - add OXT, which if I recall is hidden in the "other modelling tools" menu. Tony. Sent from my iPhone On 17 Feb 2012, at 10:26, "Hubing Lou" wrote: > Dear all, > > I have a structure solved by molecular replacement. The C-terminus at > the end of the chain shows as CO, not COOH. How do I make it into COOH > in COOT? I tried to place an O in the relevant position, but seems not > working this way. > > Thanks, > > Hubing
[ccp4bb] Opinion on automation
Dear crystallographers I would like to get some opinion. For someone beginning to learn basic crystallography including indexing, scaling ..., should I start with automated tool like Xia2? Or is manual method for each step better for learning? Thank you. Theresa
Re: [ccp4bb] Opinion on automation
Dear theresa xia2 does a great job so it can be used as your reference when processing your data manually, either for learning or improvement. When comparing different processing programs and protocols try to judge data quality by some objectice criteria like HA site identification, anomalous patterson or fourier peak strength, mr solution or model refinement. Poul On 17/02/2012, at 12.31, "Theresa H. Hsu" wrote: > Dear crystallographers > > I would like to get some opinion. For someone beginning to learn basic > crystallography including indexing, scaling ..., should I start with > automated tool like Xia2? Or is manual method for each step better for > learning? > > Thank you. > > Theresa
Re: [ccp4bb] Opinion on automation
Dear Theresa, My answer would be - it depends. If you are in the business of learning crystallography, then I would absolutely suggest you start from doing everything by hand. Indeed, if you really want to get "stuck in" I would suggest starting with the programs you need (mosflm, scala, truncate etc) and scripts so you can get a proper idea what the programs are doing. There is of course CCP4i, but this can "hide" some of the details which may be instructive to know about. If however you're in the business of getting on with biological research, well I would say that automated tools (be they for data reduction or phasing / model building) are exceedingly useful. If you can find the time, I would always encourage people to do things with automation and by hand, to allow comparison of the results. If nothing else this may give you confidence in the automation software. Best wishes, Graeme On 17 February 2012 11:31, Theresa H. Hsu wrote: > Dear crystallographers > > I would like to get some opinion. For someone beginning to learn basic > crystallography including indexing, scaling ..., should I start with > automated tool like Xia2? Or is manual method for each step better for > learning? > > Thank you. > > Theresa
Re: [ccp4bb] Opinion on automation
Hello Teresa, I need to disagree with Graeme over the idea that ccp4i 'hides' what is happening. If you care to you can see all the gorey details of command files, log files etc.. You can run the programs one step at a time and with various modes with ccp4i and iMosflm and learn something of what is going on at each stage but the gui layer at least gives you a much quicker user-friendly way to control them rather than going back to prehistoric scripts. On the other hand pipelines such as xia2 will usually do the job and save you much time. Liz On 17 Feb 2012, at 12:09, Graeme Winter wrote: > Dear Theresa, > > My answer would be - it depends. > > If you are in the business of learning crystallography, then I would > absolutely suggest you start from doing everything by hand. Indeed, if > you really want to get "stuck in" I would suggest starting with the > programs you need (mosflm, scala, truncate etc) and scripts so you can > get a proper idea what the programs are doing. There is of course > CCP4i, but this can "hide" some of the details which may be > instructive to know about. > > If however you're in the business of getting on with biological > research, well I would say that automated tools (be they for data > reduction or phasing / model building) are exceedingly useful. > > If you can find the time, I would always encourage people to do things > with automation and by hand, to allow comparison of the results. If > nothing else this may give you confidence in the automation software. > > Best wishes, > > Graeme > > On 17 February 2012 11:31, Theresa H. Hsu wrote: >> Dear crystallographers >> >> I would like to get some opinion. For someone beginning to learn basic >> crystallography including indexing, scaling ..., should I start with >> automated tool like Xia2? Or is manual method for each step better for >> learning? >> >> Thank you. >> >> Theresa
Re: [ccp4bb] Opinion on automation
Hi In addition to what Poul and Graeme have said, it may be worthwhile attending one of the fine protein crystallography schools that are run, where you will hear lectures on integration & scaling etc that attempt to explain the basics of what's being done, and probably have a couple of practical sessions where you get to use the programs under the watchful eye of an expert. Or you could ask someone who has taught on (or attended) one of these schools if you could see their lecture slides and notes... "to read is to forget, to write is to remember, to do is to understand" . On 17 Feb 2012, at 11:31, Theresa H. Hsu wrote: > Dear crystallographers > > I would like to get some opinion. For someone beginning to learn basic > crystallography including indexing, scaling ..., should I start with > automated tool like Xia2? Or is manual method for each step better for > learning? > > Thank you. > > Theresa Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Opinion on automation
This is actually very true, I simply want to support/enforce Liz's statement by adding that ccp4i indeed provides for both ends: from elementary scripts, useful for experts, to a rather large-scale automated processing where low-level details are not on the front page, which is more useful for a general user. By far, not every piece of software offer such range of granularity :) Eugene On 17 Feb 2012, at 12:38, Liz Potterton wrote: > Hello Teresa, > > I need to disagree with Graeme over the idea that ccp4i 'hides' what is > happening. If you care to you can see all the gorey details of command > files, log files etc.. You can run the programs one step at a time and with > various modes with ccp4i and iMosflm and learn something of what is going on > at each stage but the gui layer at least gives you a much quicker > user-friendly way to control them rather than going back to prehistoric > scripts. > On the other hand pipelines such as xia2 will usually do the job and save you > much time. > > Liz > > On 17 Feb 2012, at 12:09, Graeme Winter wrote: > >> Dear Theresa, >> >> My answer would be - it depends. >> >> If you are in the business of learning crystallography, then I would >> absolutely suggest you start from doing everything by hand. Indeed, if >> you really want to get "stuck in" I would suggest starting with the >> programs you need (mosflm, scala, truncate etc) and scripts so you can >> get a proper idea what the programs are doing. There is of course >> CCP4i, but this can "hide" some of the details which may be >> instructive to know about. >> >> If however you're in the business of getting on with biological >> research, well I would say that automated tools (be they for data >> reduction or phasing / model building) are exceedingly useful. >> >> If you can find the time, I would always encourage people to do things >> with automation and by hand, to allow comparison of the results. If >> nothing else this may give you confidence in the automation software. >> >> Best wishes, >> >> Graeme >> >> On 17 February 2012 11:31, Theresa H. Hsu wrote: >>> Dear crystallographers >>> >>> I would like to get some opinion. For someone beginning to learn basic >>> crystallography including indexing, scaling ..., should I start with >>> automated tool like Xia2? Or is manual method for each step better for >>> learning? >>> >>> Thank you. >>> >>> Theresa
[ccp4bb] xia2 error
Dear all, I have come across an error when trying to run xia2 (version 0.3.3.1) via the ccp4 gui see below, #CCP4I TERMINATION STATUS 0 Error from script /home/applications/CCP4-6.2.0/ccp4-6.2.0/ccp4i/scripts/xia2.script: no files matched glob pattern "*.log" #CCP4I TERMINATION TIME 17 Feb 2012 12:49:21 #CCP4I TERMINATION OUTPUT_FILES /home/tfr35668/Diamond_I02_17012011/Steve/process/xia2_21 #CCP4I MESSAGE Task failed The error occurs before the program tries to read any image files and it seems to be complaining about a lack of log files before it has had a chance to write them. Any thoughts as to how to fix this would be greatly appreciated. I am running version 6.2.0 and performed a standard installation. best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717
Re: [ccp4bb] Opinion on automation
After putting up your quote in the lab, a student quickly replied "To do and fail is to remember and to understand" :-) On 2/17/12 1:43 PM, Harry Powell wrote: Hi In addition to what Poul and Graeme have said, it may be worthwhile attending one of the fine protein crystallography schools that are run, where you will hear lectures on integration& scaling etc that attempt to explain the basics of what's being done, and probably have a couple of practical sessions where you get to use the programs under the watchful eye of an expert. Or you could ask someone who has taught on (or attended) one of these schools if you could see their lecture slides and notes... "to read is to forget, to write is to remember, to do is to understand" . On 17 Feb 2012, at 11:31, Theresa H. Hsu wrote: Dear crystallographers I would like to get some opinion. For someone beginning to learn basic crystallography including indexing, scaling ..., should I start with automated tool like Xia2? Or is manual method for each step better for learning? Thank you. Theresa Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH -- J. Preben Morth, Ph.D Group Leader Membrane Transport Group Nordic EMBL Partnership Centre for Molecular Medicine Norway (NCMM) University of Oslo P.O.Box 1137 Blindern 0318 Oslo, Norway Email: j.p.mo...@ncmm.uio.no Tel: +47 2284 0794 http://www.jpmorth.dk
[ccp4bb] HKL2000/3000 Error
Hello all, I'm trying set up the latest version of HKL-2000 to be able to work with .cbf files and I get the following error when trying to run it. ~~~ HKL-3000 version 701c3 Checking program versions ... Error: could not read denzo_3d program version. Program output: dyld: unknown required load command 0x8022 In order to manually test the program run command: /usr/local/bin/denzo_3d ~~~ I've tried to run denzo_3d manually as the error suggests but get the same error. Just wanted to check if anyone else had encountered this error and if there's a fix for it. I'm running the software on Mac OS X 10.5.8. Thanks in advance! Best regards, -Rajintha
Re: [ccp4bb] HKL2000/3000 Error
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Rajintha, the binary denzo_3d is most likely not compatible with your operating system / your computer architecture. Can you send the output of the command file /usr/local/bin/denzo_3d issued from the command line? My guess is that this will tell you the binary is not for MacOSX or it is a 64bit binary which you are attempting to run on a 32bit machine. Tim On 02/16/2012 11:33 PM, Rajintha Bandaranayake wrote: > Hello all, > > I'm trying set up the latest version of HKL-2000 to be able to work with .cbf > files and I get the following error when trying to run it. > > ~~~ > HKL-3000 version 701c3 > Checking program versions ... > Error: could not read denzo_3d program version. > > Program output: > dyld: unknown required load command 0x8022 > > In order to manually test the program run command: > /usr/local/bin/denzo_3d > ~~~ > > I've tried to run denzo_3d manually as the error suggests but get the same > error. Just wanted to check if anyone else had encountered this error and if > there's a fix for it. I'm running the software on Mac OS X 10.5.8. > > Thanks in advance! > > Best regards, > -Rajintha - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPPlmcUxlJ7aRr7hoRApy9AJ4qlqWexqgMVD478CWLY/GwebmelgCfdhur NcoyXlQo1PMNucNQOhyXVpg= =mzc5 -END PGP SIGNATURE-
Re: [ccp4bb] Opinion on automation
You would hope one learns something from failed experiments. I feel prehistoric now after Liz comment. 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 Feb 17, 2012, at 8:30, "jens Preben Morth" wrote: > After putting up your quote in the lab, a student quickly replied "To do > and fail is to remember and to understand" :-) > > On 2/17/12 1:43 PM, Harry Powell wrote: >> Hi >> >> In addition to what Poul and Graeme have said, it may be worthwhile >> attending one of the fine protein crystallography schools that are run, >> where you will hear lectures on integration& scaling etc that attempt to >> explain the basics of what's being done, and probably have a couple of >> practical sessions where you get to use the programs under the watchful eye >> of an expert. Or you could ask someone who has taught on (or attended) one >> of these schools if you could see their lecture slides and notes... >> >> "to read is to forget, to write is to remember, to do is to understand" . >> >> On 17 Feb 2012, at 11:31, Theresa H. Hsu wrote: >> >>> Dear crystallographers >>> >>> I would like to get some opinion. For someone beginning to learn basic >>> crystallography including indexing, scaling ..., should I start with >>> automated tool like Xia2? Or is manual method for each step better for >>> learning? >>> >>> Thank you. >>> >>> Theresa >> Harry >> -- >> Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills >> Road, Cambridge, CB2 0QH > > -- > J. Preben Morth, Ph.D > Group Leader > Membrane Transport Group > Nordic EMBL Partnership > Centre for Molecular Medicine Norway (NCMM) > University of Oslo > P.O.Box 1137 Blindern > 0318 Oslo, Norway > > Email: j.p.mo...@ncmm.uio.no > Tel: +47 2284 0794 > > http://www.jpmorth.dk
Re: [ccp4bb] Opinion on automation
Hi Harry, Are you advertising our CCP4 Summer School coming up in June at APS? If not, then I'll shamelessly plug in: http://www.ccp4.ac.uk/schools/APS-school/ And if one visits previous years' school links, there are plenty of lectures posted. Thanks, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry Powell Sent: Friday, February 17, 2012 6:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Opinion on automation Hi In addition to what Poul and Graeme have said, it may be worthwhile attending one of the fine protein crystallography schools that are run, where you will hear lectures on integration & scaling etc that attempt to explain the basics of what's being done, and probably have a couple of practical sessions where you get to use the programs under the watchful eye of an expert. Or you could ask someone who has taught on (or attended) one of these schools if you could see their lecture slides and notes... "to read is to forget, to write is to remember, to do is to understand" . On 17 Feb 2012, at 11:31, Theresa H. Hsu wrote: > Dear crystallographers > > I would like to get some opinion. For someone beginning to learn basic > crystallography including indexing, scaling ..., should I start with > automated tool like Xia2? Or is manual method for each step better for > learning? > > Thank you. > > Theresa Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] still... problems with COOT and Pymol stereo
Dear CCP4ers, I'd sent this e-mail out a week or so ago. I'm still struggling with the 3D kit and 2 monitors. I'd purchased a stereo monitor from Sharper Technology with a Planar SA2311W stereo 3D LCD and the Nvidia 3D vision kit. However, I'm having a problem with the dual monitor setup. Everything works fine with Pymol and Coot when using a single 3D capable monitor (Planar SA2311W) and NVIDIA 3D Vision system (Quadro 4000But, whenever I plug in the second monitor the 3D image (Coot and Pymol) becomes unstable (jittery - the molecule actually starts jiggling). Oddly, I don't have the same problem with the example stereo pictures and movies the company sends along. I'm using the MS Windows platform and I use the 2nd monitor for simultaneous word-processing etc. Any ideas for fixes? Best, Elias
Re: [ccp4bb] xia2 error
Dear Steve, Thanks for getting in touch. It seems that for some reason the ccp4i interface to xia2 is not currently working correctly. I will look into this and get back to you with a fix, it currently has me confused. Best wishes, Graeme On 17 February 2012 12:54, wrote: > Dear all, > > I have come across an error when trying to run xia2 (version 0.3.3.1) via the > ccp4 gui see below, > > #CCP4I TERMINATION STATUS 0 Error from script > /home/applications/CCP4-6.2.0/ccp4-6.2.0/ccp4i/scripts/xia2.script: no files > matched glob pattern "*.log" > #CCP4I TERMINATION TIME 17 Feb 2012 12:49:21 > #CCP4I TERMINATION OUTPUT_FILES > /home/tfr35668/Diamond_I02_17012011/Steve/process/xia2_21 > #CCP4I MESSAGE Task failed > > The error occurs before the program tries to read any image files and it > seems to be complaining about a lack of log files before it has had a chance > to write them. Any thoughts as to how to fix this would be greatly > appreciated. I am running version 6.2.0 and performed a standard > installation. > > best wishes, > > Steve > > Dr Stephen Carr > Research Complex at Harwell (RCaH) > Rutherford Appleton Laboratory > Harwell Oxford > Didcot > Oxon OX11 0FA > United Kingdom > Email stephen.c...@rc-harwell.ac.uk > tel 01235 567717
Re: [ccp4bb] xia2 error
Dear Steve, There seems to be an error in the xinfo file making logic - if you set the project and crystal ID at the top of the GUI it works fine. If not there is an error in the xinfo file which it seems causes xia2 to silently exit. That's two bugs then. Thanks again & best wishes, Graeme On 17 February 2012 15:44, Graeme Winter wrote: > Dear Steve, > > Thanks for getting in touch. It seems that for some reason the ccp4i > interface to xia2 is not currently working correctly. I will look into > this and get back to you with a fix, it currently has me confused. > > Best wishes, > > Graeme > > > On 17 February 2012 12:54, > wrote: >> Dear all, >> >> I have come across an error when trying to run xia2 (version 0.3.3.1) via >> the ccp4 gui see below, >> >> #CCP4I TERMINATION STATUS 0 Error from script >> /home/applications/CCP4-6.2.0/ccp4-6.2.0/ccp4i/scripts/xia2.script: no files >> matched glob pattern "*.log" >> #CCP4I TERMINATION TIME 17 Feb 2012 12:49:21 >> #CCP4I TERMINATION OUTPUT_FILES >> /home/tfr35668/Diamond_I02_17012011/Steve/process/xia2_21 >> #CCP4I MESSAGE Task failed >> >> The error occurs before the program tries to read any image files and it >> seems to be complaining about a lack of log files before it has had a chance >> to write them. Any thoughts as to how to fix this would be greatly >> appreciated. I am running version 6.2.0 and performed a standard >> installation. >> >> best wishes, >> >> Steve >> >> Dr Stephen Carr >> Research Complex at Harwell (RCaH) >> Rutherford Appleton Laboratory >> Harwell Oxford >> Didcot >> Oxon OX11 0FA >> United Kingdom >> Email stephen.c...@rc-harwell.ac.uk >> tel 01235 567717
[ccp4bb] Brown University Structural Biology Core Facility Manager Position
Dear CCP4 community, Although this position requires expertise in NMR spectroscopy, I wanted to send the announcement to this community as many crystallographers have colleagues who are NMR spectroscopists that may be interested in this position. Please feel free to forward to anyone you think may be interested and thanks in advance. Rebecca Page *Brown University Structural Biology Core Facility Manager* *Job Description * The Division of Biology and Medicine at Brown University seeks a Facility Manager for its Structural Biology facility, which includes an NMR facility, as well as a biological crystallography and small angle X-ray facility. This rapidly growing shared use Facility is located in a research building adjacent to the main Medical School Building. The NMR facility consists of 2 spectrometers (both Bruker) operating at 11.7 and 19.97 T. The X-ray and SAXS facility consists of a combined Rigaku instrument (dual-port FRE+ anode). The core structural biology community at Brown consists currently of 3 tenured faculty with an additional tenure track search in progress. Additional growth in the number of structural biology faculty is anticipated. Furthermore, the facility and its instruments will serve any research group at Brown University and beyond. NMR spectrometers are used for modern NMR experiments on biomacromolecules in solution. The successful candidate will be responsible for operating and maintaining the instrumentation, for implementing new NMR experiments and for training and supervising student and postdoc users. The candidate will be expected to maintain a broad knowledge of state-of-the-art NMR technology and equipment. *Required Experience * • A Ph.D. in chemistry/physics/biophysics or a related area with four years of experience in solution NMR spectroscopy and its applications to biological systems. • A demonstrated expertise in solution NMR spectroscopy, including development and implementation of new NMR experiments - in particular multidimensional experiments for structural analysis of biological systems. • Knowledge of NMR hardware and software for data collection and processing in modern solution NMR spectrometers, as well as extensive experience with computers. • Knowledge of modern structure and/or relaxation analysis software. • Excellent communication and organizational skills, the ability to positively interact with a diverse group of NMR users, and a strong motivation to learn new NMR techniques. • An interest in learning new areas of structural biology, specifically for the upkeep of the X-ray and SAXS instrumentation, as well as training of a diverse group of users. • Ability to manage a shared use facility by complying with federal research guidelines and University fiscal policies governing shared use facilities. Applications should be submitted online via Brown’s automated application system at https://careers.brown.edu/applicants/Central?quickFind=118396. Applications should include an up-to-date curriculum vitae, three reference letters, as well as a statement of expertise in regards of all points mentioned above. Review of applications will begin on Feb 15, 2012, and will continue until the position is filled. Candidates offered a staff position at Brown are subject to an employment reference check and additional background screening satisfactory to Brown University. This additional background screening may include a criminal background check, drug testing, health screening and/or motor vehicle records checks. Brown University is an Equal Opportunity/Affirmative Action employer and welcomes
Re: [ccp4bb] HKL2000/3000 Error
Hello Rajintha, > HKL-3000 version 701c3 > Checking program versions ... > Error: could not read denzo_3d program version. > > Program output: > dyld: unknown required load command 0x8022 > > In order to manually test the program run command: > /usr/local/bin/denzo_3d Apple introduced a compressed linkedit loader section in Mach-O binary headers in 10.6; that error is the OS X 10.5 loader not understanding the header fields. You can verify this is the case if you have the Xcode development package installed. On a 10.5.8 machine, you'll get output like this: $ otool -l denzo_3d | grep -A10 "Load command 4" Load command 4 cmd ?(0x0022) Unknown load command cmdsize 48 00234000 0088 00234088 06f8 00234780 4828 Load command 5 cmd LC_SYMTAB cmdsize 24 symoff 2330536 nsyms 6088 stroff 2429640 And on a 10.6 machine it will look like this: $ otool -l denzo_3d | grep -A10 "Load command 4" Load command 4 cmd LC_DYLD_INFO cmdsize 48 rebase_off 0 rebase_size 0 bind_off 2310144 bind_size 136 weak_bind_off 0 weak_bind_size 0 lazy_bind_off 2310280 lazy_bind_size 1784 I have filed this exact bug report with HKL Software in the past. If you wait long enough, they will usually compile a version that runs on 10.5 machines. The support email for HKL Software is supp...@hkl-xray.com. No one here can help you. Have you tried iMosflm? -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
