Re: [ccp4bb] Crystallography on BBC Radio 4 next week

[Gohlke, Ulrich]

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.de

http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/

[ccp4bb] about coot

[Qixu Cai]

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

[Tim Gruene]

-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

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7FQzwGMbz1G9LXBNsiCpVjo=
=R8Xt
-END PGP SIGNATURE-

Re: [ccp4bb] about coot

[Paul Emsley]

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

[Armando Albert]

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  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

[Laura Spagnolo]

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=41839&LID=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

[Petr Leiman]

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

[Antony Oliver]

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] : kCGErrorIllegalArgument: 
CGSGetSurfaceBounds
Nov 23 12:17:02 coot-real[80005] : kCGErrorFailure: Set a breakpoint @ 
CGErrorBreakpoint() to catch errors as they are logged.
Nov 23 12:17:02 coot-real[80005] : kCGErrorIllegalArgument: 
CGSBindSurface: Invalid window 0x8da
Nov 23 12:17:02 coot-real[80005] : kCGErrorIllegalArgument: 
CGSBindSurface: Invalid window 0x8da
Nov 23 12:17:02 coot-real[80005] : 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

[Martin Montgomery]

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  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

[Tim Gruene]

-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  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

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=WwM5
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[ccp4bb] Post-doc position in human ion channel structure/function studies at the SGC in Oxford

[Liz Carpenter]

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.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]

 
 
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 
 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

[Patrick Shaw Stewart]

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  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  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