Re: [ccp4bb] Crystallography on BBC Radio 4 next week
Dear Peter, Thanks for the hint. Another possibility to listen to Radio 4 is for people that have an internet streamer (e.g. Squeezebox) to subscribe (free) to Orange Liveradio. This allows one to receive all BBC channels even outside the UK. Thanks to that, I wake up every morning with the Shipping Forecast (sadly they stopped playing sailing by...), followed by Farming Today, so I know everything about Schmallenberg virus in sheep and TB in badgers... Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.demailto:ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
[ccp4bb] about coot
Dear all, I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? 2, And is there any option to prevent coot auto-loading ~/.coot file? Thank you very much for your help! Q. Cai
Re: [ccp4bb] about coot
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Q. Cai, ad 1) maybe Paul knows better, but 'stepped refine' sounds to me like coot refines step by step and displays the steps inbetween, which means that the combination with no-graphic mode makes little sense, doesn't it? You can run refmac5 directly from a script instead. ad 2) the scripts are located in coot/wheezy/share/coot/[python|scheme] relative to your coot installation directory unless you tell coot otherwise with your personal setup ad 3) you can remove or rename that file Cheers, Tim On 11/23/2012 09:54 AM, Qixu Cai wrote: Dear all, I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? 2, And is there any option to prevent coot auto-loading ~/.coot file? Thank you very much for your help! Q. Cai - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQr081UxlJ7aRr7hoRAvdsAJ9WQzLd736L37mW6ebd7PmticL8CwCeI/DS 7FQzwGMbz1G9LXBNsiCpVjo= =R8Xt -END PGP SIGNATURE-
Re: [ccp4bb] about coot
On 23/11/12 08:54, Qixu Cai wrote: I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? (let ((imol (read-pdb coot-download/3rso.pdb)) (imol-map (make-and-draw-map coot-download/r3rso-refmac.mtz FWT PHWT 0 0))) (map (lambda (chain) (fit-chain imol chain)) (chain-ids imol))) 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? All and more, I think. They are in coot-top-dir/share/coot/python 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that?
Re: [ccp4bb] about coot
Dear Paul, 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that? You may want to open a different session in the same directory and not spoil the one you are using for refinement Armando I am out of the lab El 23/11/2012, a las 12:32, Paul Emsley pems...@mrc-lmb.cam.ac.uk escribió: On 23/11/12 08:54, Qixu Cai wrote: I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? (let ((imol (read-pdb coot-download/3rso.pdb)) (imol-map (make-and-draw-map coot-download/r3rso-refmac.mtz FWT PHWT 0 0))) (map (lambda (chain) (fit-chain imol chain)) (chain-ids imol))) 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? All and more, I think. They are in coot-top-dir/share/coot/python 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that?
[ccp4bb] PhD studentship
Dear Colleagues, I would like to draw the attention of interested students to this opportunity to perform a PhD in my laboratory: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=41839LID=456 The deadline for applications is 18.01.2013. Best regards, Laura Dr Laura Spagnolo Institute of Structural Molecular Biology University of Edinburgh Room 506, Darwin Building King's Buildings Campus Edinburgh EH9 3JR United Kingdom T: +44 (0)131 650 7066 F: +44 (0)131 650 8650 http://www.biology.ed.ac.uk/research/institutes/structure/homepage.php?id=lspagnolo laura.spagn...@ed.ac.uk -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Re: [ccp4bb] Hgen ccp4i gui is broken
I have to follow up on my own thread because Hgen GUI does not start on my Mac
(10.6.8) either. The same error message, which tells me that the tcl/tk code is
broken. CCP4 is up-to-date.
It would be great if at least one person tries pressing the Hgen button in
ccp4i and gives a feedback to me or CCP4BB.
Thank you,
Petr
On Nov 22, 2012, at 3:04 PM, Petr Leiman wrote:
Dear all,
Hgen GUI does not start (the error message is below). The CCP4 version is
6.3.0-009 (64 bit). The system is 2.6.35-32-generic #67-Ubuntu SMP x86_64
GNU/Linux. Is this unique to our system configuration?
Thank you.
Petr
The error message is:
can't use non-numeric string as operand of !
can't use non-numeric string as operand of !
while executing
if { ![$task_setup typedef $arrayname] } {
PleaseWait
return
}
(procedure RunTask line 96)
invoked from within
RunTask hgen
invoked from within
.module.menu.action.canvas.frame.t.f_47 invoke
(uplevel body line 1)
invoked from within
uplevel #0 [list $w invoke]
(procedure tk::ButtonUp line 22)
invoked from within
tk::ButtonUp .module.menu.action.canvas.frame.t.f_47
(command bound to event)
Re: [ccp4bb] CCP4 - Coot in Applications
Forgive what may be a very simple question… I have recently installed coot using the very nice CCP4 .dmg (0.7.0-i386) - which now puts coot into /Applications I now need to set a $PATH to coot, such that various home-made scripts now 'know' where it is Here I have hit a hurdle. Which binary file do I need to point a path variable to? From terminal I can use the command ' open -a coot ' - everything works fine and dandy. However, I cannot use ' /Applications/coot.app/Contents/MacOS/coot ' reliably - sometimes it works, but most of the time it crashes with the following errors... Nov 23 12:17:02 coot-real[80005] Error: kCGErrorIllegalArgument: CGSGetSurfaceBounds Nov 23 12:17:02 coot-real[80005] Error: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Nov 23 12:17:02 coot-real[80005] Error: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da Nov 23 12:17:02 coot-real[80005] Error: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da Nov 23 12:17:02 coot-real[80005] Error: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da coot-real also fails - as it's obviously looking in the wrong place for files… Acquiring application resources from /Users/charlesb/autobuild/Darwin-ras03-006.rl.ac.uk/coot-0.7.0-gtk2-python/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Users/charlesb/autobuild/Darwin-ras03-006.rl.ac.uk/coot-0.7.0-gtk2-python/share/coot/pixmaps Any ideas or suggestions would be very welcome. With thanks, Antony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Nov 23, 2012, at 1:19 PM, Paul Emsley wrote:
Re: [ccp4bb] Hgen ccp4i gui is broken
Hello,
I get the same error message that you are seeing on either my mac (10.8.2 with
a fink installed 64 bit ccp4 6.3.0) or our main linux server, again running the
latest ccp4 with all the latest patches.
Regards
MGM
Martin G Montgomery
ATP Synthase Group
MRC Mitochondrial Biology Unit
Wellcome Trust/MRC Building
Hills Road
Cambridge
CB2 0XY
On 23 Nov 2012, at 13:20, Petr Leiman petr.lei...@epfl.ch wrote:
I have to follow up on my own thread because Hgen GUI does not start on my
Mac (10.6.8) either. The same error message, which tells me that the tcl/tk
code is broken. CCP4 is up-to-date.
It would be great if at least one person tries pressing the Hgen button in
ccp4i and gives a feedback to me or CCP4BB.
Thank you,
Petr
On Nov 22, 2012, at 3:04 PM, Petr Leiman wrote:
Dear all,
Hgen GUI does not start (the error message is below). The CCP4 version is
6.3.0-009 (64 bit). The system is 2.6.35-32-generic #67-Ubuntu SMP x86_64
GNU/Linux. Is this unique to our system configuration?
Thank you.
Petr
The error message is:
can't use non-numeric string as operand of !
can't use non-numeric string as operand of !
while executing
if { ![$task_setup typedef $arrayname] } {
PleaseWait
return
}
(procedure RunTask line 96)
invoked from within
RunTask hgen
invoked from within
.module.menu.action.canvas.frame.t.f_47 invoke
(uplevel body line 1)
invoked from within
uplevel #0 [list $w invoke]
(procedure tk::ButtonUp line 22)
invoked from within
tk::ButtonUp .module.menu.action.canvas.frame.t.f_47
(command bound to event)
Re: [ccp4bb] Hgen ccp4i gui is broken
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi,
the error message (which I also can reproduce) says, that the expression
$task_setup typedef $arrayname
does not evaluate to a number - it's a coding error, something that
the HGen tcl-code passes incorrectly to the function RunTask.
Should be OS independent and fixed by the responsible, I dare say.
You can run hgen from the command line while you are waiting for that
to happen, though.
Cheers,
Tim
On 11/23/2012 02:41 PM, Martin Montgomery wrote:
Hello,
I get the same error message that you are seeing on either my mac
(10.8.2 with a fink installed 64 bit ccp4 6.3.0) or our main linux
server, again running the latest ccp4 with all the latest patches.
Regards
MGM
Martin G Montgomery ATP Synthase Group MRC Mitochondrial Biology
Unit Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY
On 23 Nov 2012, at 13:20, Petr Leiman petr.lei...@epfl.ch wrote:
I have to follow up on my own thread because Hgen GUI does not
start on my Mac (10.6.8) either. The same error message, which
tells me that the tcl/tk code is broken. CCP4 is up-to-date. It
would be great if at least one person tries pressing the Hgen
button in ccp4i and gives a feedback to me or CCP4BB.
Thank you,
Petr
On Nov 22, 2012, at 3:04 PM, Petr Leiman wrote:
Dear all,
Hgen GUI does not start (the error message is below). The CCP4
version is 6.3.0-009 (64 bit). The system is 2.6.35-32-generic
#67-Ubuntu SMP x86_64 GNU/Linux. Is this unique to our system
configuration?
Thank you.
Petr
The error message is:
can't use non-numeric string as operand of ! can't use
non-numeric string as operand of ! while executing if {
![$task_setup typedef $arrayname] } { PleaseWait return }
(procedure RunTask line 96) invoked from within RunTask
hgen invoked from within
.module.menu.action.canvas.frame.t.f_47 invoke (uplevel
body line 1) invoked from within uplevel #0 [list $w invoke]
(procedure tk::ButtonUp line 22) invoked from within
tk::ButtonUp .module.menu.action.canvas.frame.t.f_47 (command
bound to event)
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iD8DBQFQr4FiUxlJ7aRr7hoRAvjNAKDwGipSuTe9yJwqmOHEhsD7nhCD+QCcDgBa
djEAWs+83XOPsu/ZHqdEReo=
=WwM5
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[ccp4bb] Post-doc position in human ion channel structure/function studies at the SGC in Oxford
We are seeking an enthusiastic and experienced membrane protein structural biologist with a strong interest in ion channel structure and function, to join the integral membrane proteins group at the Structural Genomics Consortium in Oxford. This post-doc position will involve purification, crystallisation, structure determination and functional studies of human ion channels and other membrane proteins. For more information please see: http://www.thesgc.org/careers/oxford/postdoc-imp or contact Liz Carpenter (liz.carpen...@sgc.ox.ac.ukmailto:liz.carpen...@sgc.ox.ac.uk) for informal enquiries. To apply for this position please follow this link: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=105253 The closing time/date for this post is 12 noon on the 3rd of December, 2012. With best wishes, Liz Carpenter, Dr Liz Carpenter, Principal Investigator, Integral Membrane Proteins group, Structural Genomics Consortium, Old road Campus Research Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7DQ, UK Phone: +441865617581 Structural Genomics Consortium, Old road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford, OX3 7DQ, England.
Re: [ccp4bb] Equilibrium Relative Humidity matching
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 This leads to a counter-intuitive observation - it is only the number of molecules in solution that affect the RH and not the type of molecule/ion - therefore one molecule of glycerol has the same contribution as a chloride ion or anything else. This means that there is no effect for charge etc. What does matter is how many species the salt dissociates into - this means that a given concentration of sodium malonate (3 species) will have a lower RH than ammonium sulphate (2 species (NH4 and (NH4SO4)-) and not 3 as might be expected). This means that relatvie humidity is a colligative property: http://en.wikipedia.org/wiki/Colligative_properties Doesn't it? So it should not be too surprising. Boaz On 22/11/2012 18:32, Patrick Shaw Stewart wrote: Matt My old Rubber Book (Handbook of Physics and Chemistry, 1976) has a table (attached) showing the lowering of vapor pressure by salts in aqueous solution, taken from the Smithsonian Tables. I've never been able to make any sense of it in terms of cations, anions, valency, or charge density (position in Hofmeister series), whether concentrations are expressed as M or N solutions. For example, of the salts mentioned on your website, MgSO4 seems to be anomalous. My spreadsheet also has a little converter that my colleague wrote many years ago to convert vapor diffusion conditions to batch. This might be of interest to people who have to work in batch, e.g. people making crystals for X-FEL data collection. You can download it as a program fromhttp://www.douglas.co.uk/vdtomb/vdtomb.htm - it seems to work pretty well. Best wishes Patrick On 22 November 2012 12:11, Matthew Bowler mbow...@embl.fr wrote: Dear All, after a few requests, I have now added equations to the online calculator that uses Raoult's law to calculate the relative humidity equilibria for precipitant solutions (see http://go.esrf.eu/RH). The new equations (4 and 5) allow the calculation of salt concentrations that will be in equilibrium with a certain PEG or other molecule solution - this will allow slow and controlled dehydration experiments to be designed in vapour diffusion plates, by slowly increasing the salt concentration in the reservoir above the equilibrium and thereby reducing the amount of water in the crystallisation drop by a controlled amount. Hope it is useful, cheers, Matt. -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: 33 (0) 4.76.20.76.37 Fax: 33 (0) 4.76.88.29.04 http://www.embl.fr/ === -- patr...@douglas.co.uk Douglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090 US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: 33 (0) 4.76.20.76.37 Fax: 33 (0) 4.76.88.29.04 http://www.embl.fr/ ===
Re: [ccp4bb] Equilibrium Relative Humidity matching
Matt, how well does it work in practice? Did you check the colligative predictions against the measurements that you originally made? I agree that the PEG has virtually no effect on the drop equilibration. This can be seen in comparisons of batch and v.d. e.g. http://www.douglas.co.uk/convert.htm. Therefore I always thought that equilibration in high-PEG experiments was driven by any salts that may be present - including the salt in the protein, which is easy to overlook. I remember a paper by Luft and De Titta about chaperone salts. However, unless you know the relative effects of different salts, the result is hard to predict! On 23 November 2012 16:05, Boaz Shaanan bshaa...@exchange.bgu.ac.il wrote: *Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710* ** ** * * -- This leads to a counter-intuitive observation - it is only the number of molecules in solution that affect the RH and not the type of molecule/ion - therefore one molecule of glycerol has the same contribution as a chloride ion or anything else. This means that there is no effect for charge etc. What does matter is how many species the salt dissociates into - this means that a given concentration of sodium malonate (3 species) will have a lower RH than ammonium sulphate (2 species (NH4+ and (NH4SO4)-) and not 3 as might be expected). This means that relatvie humidity is a colligative property: http://en.wikipedia.org/wiki/Colligative_properties Doesn't it? So it should not be too surprising. Boaz On 22/11/2012 18:32, Patrick Shaw Stewart wrote: Matt My old Rubber Book (Handbook of Physics and Chemistry, 1976) has a table (attached) showing the lowering of vapor pressure by salts in aqueous solution, taken from the Smithsonian Tables. I've never been able to make any sense of it in terms of cations, anions, valency, or charge density (position in Hofmeister series), whether concentrations are expressed as M or N solutions. For example, of the salts mentioned on your website, MgSO4 seems to be anomalous. My spreadsheet also has a little converter that my colleague wrote many years ago to convert vapor diffusion conditions to batch. This might be of interest to people who have to work in batch, e.g. people making crystals for X-FEL data collection. You can download it as a program from http://www.douglas.co.uk/vdtomb/vdtomb.htm - it seems to work pretty well. Best wishes Patrick On 22 November 2012 12:11, Matthew Bowler mbow...@embl.fr wrote: Dear All, after a few requests, I have now added equations to the online calculator that uses Raoult's law to calculate the relative humidity equilibria for precipitant solutions (see http://go.esrf.eu/RH). The new equations (4 and 5) allow the calculation of salt concentrations that will be in equilibrium with a certain PEG or other molecule solution - this will allow slow and controlled dehydration experiments to be designed in vapour diffusion plates, by slowly increasing the salt concentration in the reservoir above the equilibrium and thereby reducing the amount of water in the crystallisation drop by a controlled amount. Hope it is useful, cheers, Matt. -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.29.04 http://www.embl.fr/ === -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.29.04 http://www.embl.fr/ === -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
