Re: [ccp4bb] iMosflm in 6.1 under OS X
I've just now added these as fink packages (cvs unstable). Sorry for the delay. I dropped the ball. Steffen Schmidt did the hard work, so many thanks to Seffen!!! Bill On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] iMosflm in 6.1 under OS X
More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] iMosflm in 6.1 under OS X
Hi I should say, while this subject has been brought up, that Luke and I are working hard to remove many of these dependencies, so iMosflm should work with a more plain vanilla version of TclTk (but you will still need iTcl and iTk. On 17 Dec 2008, at 16:34, William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] O/T: microscopes
I can only recommend the Motic microscopes. i'm very impressed for $1,70O incl camera, not as sturdy as Leica (my favorite) but very good image quality. Drawback: no cold light source. But you can get a gooseneck light and do top illumination. Do not buy their polarizer, though. Cheers, Jens n Wednesday 17 December 2008 07:34:31 Uwe Mueller wrote: Dear Clint, Jerome is right. Do not expect to get a stereo microscope (these are more or less two microscopes within a smart arrangement) for this price. We purchased recently a Leica M205A, which defines the quality and price for a high-end system. It has a magnification range using a 0.8 plan objective and 10x oculars of 6-160x at a working distance of 90mm. The price for the objective alone is around 3000 US$, the full system with a CCD camera and the Leica application suite software cost then 13x more then you are expecting. Best regards, Uwe mesters wrote: The combination of for example 10-120x stereo-zoom magnification, good optical quality, bright- and dark-field illumination, and only 3000 US$ is NOT possible unless: 1) you are willing to buy a second hand of quality brands like Leica, Zeiss, Olympus or Nikon (my preference) 2) you buy a low quality brand and you will later regret having done that . My two cents of advice, go for a SECOND HAND or, get more funding i.e. at least triple the amount - J. - Clint Spiegel wrote: Hi, I am looking to buy a modestly-priced zoom scope for x-ray crystallographic purposes ($2-3000). Does anyone have suggestions about what/where to possibly find this? I currently have a cheap one that goes from 7.5-50X, but I'd like something with a little more magnification, a better light source and better optics. Thanks, Clint Clint Spiegel Assistant Professor, Chemistry Western Washington University 516 High Street Bellingham, WA 98225-9150. -- +-+-+ | Dr. Jens T. Kaiser | Office: +1(626)395-2662 | | California Institute of Technology | Lab:+1(626)395-8392 | | m/c 114-96 | Cell: +1(626)379-1650 | | Pasadena, CA 91125, USA | Email: kai...@caltech.edu | +-+-+
[ccp4bb] Postdoctoral position in Edinburgh
I would like to draw your attention to the following opening: Vacancy Reference 3010245 Applications are invited for a Post-doctoral position funded by Cancer Research UK, to work on structure/function studies of the NMD machinery in Dr Laura Spagnolo's group. Applicants must hold a PhD in a biological science. Innovative thinking, strong motivation and experience in molecular biology, protein expression and purification are essential. Previous experience in crystallisation and X-ray crystallography and/or electron microscopy coupled to single particle analysis would be considered an advantage. Informal enquiries at the address lspag...@staffmail.ed.ac.uk are welcome. Applications at web address: http://www.jobs.ed.ac.uk/vacancies/index.cfm?fuseaction=vacancies.detailvacancy_ref=3010245 Best regards, Laura -- Dr Laura Spagnolo Institute of Structural Molecular Biology Room 702/705, Darwin Building King's Buildings Mayfield Road University of Edinburgh Edinburgh EH9 3JR United Kingdom Mobile: (0)7793 018 625 From 05/01/2009: T: +44 (0)131 650 7066 F: +44 (0)131 650 8650 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
[ccp4bb] O/T: use of heparin in crystallisation
Dear All, Does anybody has any comment on using heparin as an additive to co-crystallise an RNA-binding protein? I am not asking about using it to form a complex with proteins that are know to bind heparin specifically, but using it as a general RNA analogue, when we lack the knowledge of the RNA target sequence. Thanks a lot. Wai -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
Re: [ccp4bb] iMosflm in 6.1 under OS X
By the way, is anyone experiencing the following problem with fink-installed coot? dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0 [1]Trace/BPT trapcoot Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
[ccp4bb] XAS software
Hi, I have some XAS spectra but I'm new in the area. I'm looking for a free software. I just want to normalize the data and compare between them. Any suggestion? Thank you very much. Eugenio De la Mora Insituto de Biotecnologia, UNAM.
Re: [ccp4bb] iMosflm in 6.1 under OS X
Yep, this happened because of the latest Mac OS 10.5.6 update. With the update, my X11 version got downgraded from 2.3.1 to 2.1.5. Engin William G. Scott wrote: Hi Engin: What do you get in response to the command otool -L /usr/X11/lib/libXdamage.1.dylib | grep libXdamage.1.dylib You should see /usr/X11/lib/libXdamage.1.dylib (compatibility version 3.0.0, current version 3.0.0) If you don't, update X11 here (free) to at least 2.3.1: http://xquartz.macosforge.org/trac/wiki If you do see what I do, then I suspect you need to unset the evil $DYLD_LIBRARY_PATH variable Bill On Dec 17, 2008, at 1:53 PM, Engin Ozkan wrote: By the way, is anyone experiencing the following problem with fink-installed coot? dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0 [1]Trace/BPT trapcoot Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] iMosflm in 6.1 under OS X
Hi Engin: What do you get in response to the command otool -L /usr/X11/lib/libXdamage.1.dylib | grep libXdamage.1.dylib You should see /usr/X11/lib/libXdamage.1.dylib (compatibility version 3.0.0, current version 3.0.0) If you don't, update X11 here (free) to at least 2.3.1: http://xquartz.macosforge.org/trac/wiki If you do see what I do, then I suspect you need to unset the evil $DYLD_LIBRARY_PATH variable Bill On Dec 17, 2008, at 1:53 PM, Engin Ozkan wrote: By the way, is anyone experiencing the following problem with fink- installed coot? dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0 [1]Trace/BPT trapcoot Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
[ccp4bb] Depositing coordinates with riding hydrogens
Hi all- Just wondering what the consensus is - should a structure refined with riding hydrogens be deposited with the coordinates for the hydrogens included? One could argue that, since they were used in the refinement to obtain the model and statistics reported, they should be included in the deposited pdb file. On the other hand, the presence of hydrogens in the pdb file might lead some to think the hydrogens were refined against density when they really weren't. Thoughts? Thanks, Jon
Re: [ccp4bb] iMosflm in 6.1 under OS X
Yes, William I do agree with you, and in the same line of doubt, I have one more thing to ask you. Where is this .cvspass resides. I have problem in updating my fink , with fink selfupdate-cvs. thanks S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Wed, Dec 17, 2008 at 11:54 PM, William G. Scott wgsc...@chemistry.ucsc.edu wrote: Please, we all need to mention this to the Apple people. This is totally unacceptable. On Dec 17, 2008, at 2:54 PM, Engin Ozkan wrote: Yep, this happened because of the latest Mac OS 10.5.6 update. With the update, my X11 version got downgraded from 2.3.1 to 2.1.5. Engin William G. Scott wrote: Hi Engin: What do you get in response to the command otool -L /usr/X11/lib/libXdamage.1.dylib | grep libXdamage.1.dylib You should see /usr/X11/lib/libXdamage.1.dylib (compatibility version 3.0.0, current version 3.0.0) If you don't, update X11 here (free) to at least 2.3.1: http://xquartz.macosforge.org/trac/wiki If you do see what I do, then I suspect you need to unset the evil $DYLD_LIBRARY_PATH variable Bill On Dec 17, 2008, at 1:53 PM, Engin Ozkan wrote: By the way, is anyone experiencing the following problem with fink-installed coot? dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0 [1]Trace/BPT trapcoot Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] Depositing coordinates with riding hydrogens
On Wednesday 17 December 2008 15:53:42 Jonathan Winger wrote: Hi all- Just wondering what the consensus is - should a structure refined with riding hydrogens be deposited with the coordinates for the hydrogens included? One could argue that, since they were used in the refinement to obtain the model and statistics reported, they should be included in the deposited pdb file. On the other hand, the presence of hydrogens in the pdb file might lead some to think the hydrogens were refined against density when they really weren't. Thoughts? It doesn't hurt to include them, bu I don't see much point in it. The riding-model parameters are sufficient to regenerate the hydrogen positions. Of the things one might worry about not including in a PDB file, I'm more concerned about the omission of scattering factors used for refinement and the continuing ambiguity of the precise meaning of the B factor reported in the ATOM record. And I am still scratching my head over the meaning of B factors attached to atoms with 0 occupancy. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] Depositing coordinates with riding hydrogens
Hi Jon, - obviously, the model should not be manipulated once the final statistics is obtained, or if it is manipulated, then the final statistics must be re-calculated; - I can't imagine someone thinking that hydrogens were refined individually in a X-ray structure say at 2A resolution. - also, it's much easier to remove H atoms later on, rather than add them back the *exact same *way you did. I don't see any logic of making the depositing information artificially less complete by removing hydrogens. Cheers, Pavel. On 12/17/2008 3:53 PM, Jonathan Winger wrote: Hi all- Just wondering what the consensus is - should a structure refined with riding hydrogens be deposited with the coordinates for the hydrogens included? One could argue that, since they were used in the refinement to obtain the model and statistics reported, they should be included in the deposited pdb file. On the other hand, the presence of hydrogens in the pdb file might lead some to think the hydrogens were refined against density when they really weren't. Thoughts? Thanks, Jon
[ccp4bb] CCP4 6.1.0 release and CCP4MG
Hi After all v6.1.0 did arrive before Christmas :-) Thank you all. Still I guess Santa, after freezing in the car park, still had to endure beeing stuck in some chimney, as a consequence of all of us who wanted to grab a fresh copy, flooding poor CCP4 server. So, after 2 days I finally wgetted my 1 Gigabyte Lin-RH8 copy for installation in Ubuntu. Even before installing, I browsed all the tarball and couldn't find CCP4MG? Since the documentation states it should be a separate package (like COOT), am I missing something? Also, if you choose a custom tarball, there is no option to include CCP4MG. Thank you Victor Alves Dear All as we continue our journey up the A65 (towards the heart of Yorkshire) we are pleased to announce the release of Clapham (or 6.1.0). This is available form the usual locations http://www.ccp4.ac.uk/download/downloadman.php or ftp://ftp.ccp4.ac.uk/ccp4/6.1/ Obviously special thanks to the program authors, testers etc. Go enjoy Please note that the downloads are large (very large if you include the balbes database), so there may be an issue of browsers timing out (observed for firefox so far). Charles Ballard on behalf of the CCP4 team. This message was sent using IMP, the Internet Messaging Program.
[ccp4bb] LDAO SDS-PAGE
Hello everyone... I have a protein solubilised in 1% LDAO, 50 mM Phosphate pH 7.5, 150 mM NaCl. When I mix it with laemmli buffer and heat at 95C, 3 mins for SDS-PAGE, it aggregates (as in when you mix GuHCl with SDS) and can't be loaded onto the gel. Does anyone know why it happens? Thanks a lot!!! Kien
Re: [ccp4bb] LDAO SDS-PAGE
Is your phosphate a Na-K phosphate? If it is, then you're probably getting a K salt of SDS which is considerably less soluble than Na or Li salts. Artem -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Subscribe Ccp4Bb Kn L Sent: Wednesday, December 17, 2008 9:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] LDAO SDS-PAGE Hello everyone... I have a protein solubilised in 1% LDAO, 50 mM Phosphate pH 7.5, 150 mM NaCl. When I mix it with laemmli buffer and heat at 95C, 3 mins for SDS-PAGE, it aggregates (as in when you mix GuHCl with SDS) and can't be loaded onto the gel. Does anyone know why it happens? Thanks a lot!!! Kien
Re: [ccp4bb] LDAO SDS-PAGE
Besides the K-SDS precipitation it can also be the problem of membrane proteins generally having a tendency to aggregate when boiled with SDS. Try to just add the Laemmli buffer and load the gel without boiling. This is the general procedure for membrane proteins. Poul On 18/12/2008, at 06.20, Artem Evdokimov wrote: Is your phosphate a Na-K phosphate? If it is, then you're probably getting a K salt of SDS which is considerably less soluble than Na or Li salts. Artem -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Subscribe Ccp4Bb Kn L Sent: Wednesday, December 17, 2008 9:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] LDAO SDS-PAGE Hello everyone... I have a protein solubilised in 1% LDAO, 50 mM Phosphate pH 7.5, 150 mM NaCl. When I mix it with laemmli buffer and heat at 95C, 3 mins for SDS-PAGE, it aggregates (as in when you mix GuHCl with SDS) and can't be loaded onto the gel. Does anyone know why it happens? Thanks a lot!!! Kien
Re: [ccp4bb] iMosflm in 6.1 under OS X
Now that everything with coot and imosflm has been settled, how about sftools? I am getting errors when I try to open an sftools window with ccp4i, with 6.1.0. I get the same error with a fink-installed mac version, and a linux installation. Here is the error: bad window path name .main.canvas.contents.param_1.body bad window path name .main.canvas.contents.param_1.body while executing pack $wframe.body -side top -fill x (procedure update_folder_display line 23) invoked from within update_folder_display 1 sftools_PROJECT view invoked from within .w_sftools_PROJECT.main.canvas.contents.param_1.top.but invoke (command bound to event) Any ideas? Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] LDAO SDS-PAGE
Hi, you could try without heating. Just vortex your sample a few times after adding the sample buffer and then load the gel. good luck, Daniela Is your phosphate a Na-K phosphate? If it is, then you're probably getting a K salt of SDS which is considerably less soluble than Na or Li salts. Artem -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Subscribe Ccp4Bb Kn L Sent: Wednesday, December 17, 2008 9:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] LDAO SDS-PAGE Hello everyone... I have a protein solubilised in 1% LDAO, 50 mM Phosphate pH 7.5, 150 mM NaCl. When I mix it with laemmli buffer and heat at 95C, 3 mins for SDS-PAGE, it aggregates (as in when you mix GuHCl with SDS) and can't be loaded onto the gel. Does anyone know why it happens? Thanks a lot!!! Kien
