Re: [ccp4bb] Problem with fonts in Coot

[Martin Montgomery]

Just to follow up, XQuartz 2.8.0_rc1 fixes the issue I found with coot in 
ccp4-7.1.

Regards

MGM

> On 23 Feb 2021, at 11:33, Mark Brooks  wrote:
> 
> Hi Marc,
>   I hope you're well. Have you updated Xquartz recently? This may help 
> after what appears to be a major update to Big Sur. 
> 
> CCP4 7.1 and freshly installed XQuartz 2.8.0_rc1 https://www.xquartz.org 
>  work on Big Sur 11.2.1 for me with no font errors.
> 
> Kind regards,
> 
> Mark
> 
> On Tue, 23 Feb 2021 at 04:28, Marc Graille  > wrote:
> Dear colleagues,
> 
> I have recently upgraded my Apple OS from Catalina to Big Sur.
> I am afraid, it was not the most brilliant idea I had those last days.
> 
> When trying to run coot, I have the following message : 
> (coot-bin:25140): Pango-CRITICAL **: No fonts found:
> This probably means that the fontconfig
> library is not correctly configured. You may need to
> edit the fonts.conf configuration file. More information
> about fontconfig can be found in the fontconfig(3) manual
> page and on http://fontconfig.org 
> 
> 
> and Coot display looks like that :
> 
> 
> 
> Does anyone else faced the same problem? 
> Is there any easy way to solve this issue?
> I can recognize the icons but I don’t remember exactly were all Coot options 
> are in the various Menus.
> 
> Thanks a lot for your help.
> 
> Yours,
> 
> Marc
> 
> —
> Marc GRAILLE, PhD
> DR1-CNRS
> Laboratoire de Biologie Structurale de la Cellule  (BIOC; Ex-Laboratoire de 
> Biochimie)
> UMR7654 du CNRS
> 
> Head of the team: “Translation and degradation of eukaryotic mRNAs”
> 
> ÉCOLE POLYTECHNIQUE 
> 91128 PALAISEAU CEDEX
> FRANCE 
> : +33 (0)1 69 33 48 90
> 
>  : marc.grai...@polytechnique.edu 
>  / : @GrailleLab 
> 
> https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes
>  
> 
> —
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Problem with fonts in Coot

[Martin Montgomery]

Hi,

FYI coot 0.9.4.2 is working fine from the ccpem “nightly" distribution on my 
test laptop running Big Sur.

However, I have just tried to open the coot bundled with a freshly installed 
ccp4-7.1 and get the following errors:

% /Applications/ccp4-7.1/bin/coot 
dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib
  Referenced from: /Applications/ccp4-7.1/libexec/coot-bin
  Reason: image not found
/Applications/ccp4-7.1/bin/coot: line 339: 17324 Abort trap: 6   
$coot_bin "$@"
. -- Coot crashed - trying to diagnose -
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 
2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well.  For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
ERROR: In procedure dynamic-link:
ERROR: file: "libguilegtk-2.0", message: "file not found"


Cheers

MGM




> On 23 Feb 2021, at 09:28, Marc Graille  wrote:
> 
> Dear colleagues,
> 
> I have recently upgraded my Apple OS from Catalina to Big Sur.
> I am afraid, it was not the most brilliant idea I had those last days.
> 
> When trying to run coot, I have the following message : 
> (coot-bin:25140): Pango-CRITICAL **: No fonts found:
> This probably means that the fontconfig
> library is not correctly configured. You may need to
> edit the fonts.conf configuration file. More information
> about fontconfig can be found in the fontconfig(3) manual
> page and on http://fontconfig.org 
> 
> 
> and Coot display looks like that :
> 
> 
> 
> Does anyone else faced the same problem? 
> Is there any easy way to solve this issue?
> I can recognize the icons but I don’t remember exactly were all Coot options 
> are in the various Menus.
> 
> Thanks a lot for your help.
> 
> Yours,
> 
> Marc
> 
> —
> Marc GRAILLE, PhD
> DR1-CNRS
> Laboratoire de Biologie Structurale de la Cellule  (BIOC; Ex-Laboratoire de 
> Biochimie)
> UMR7654 du CNRS
> 
> Head of the team: “Translation and degradation of eukaryotic mRNAs”
> 
> ÉCOLE POLYTECHNIQUE 
> 91128 PALAISEAU CEDEX
> FRANCE 
> : +33 (0)1 69 33 48 90
> 
>  : marc.grai...@polytechnique.edu 
>  / : @GrailleLab 
> 
> https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes
>  
> 
> —
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] XQuartz and High Sierra OSX

[Martin Montgomery]

Dear Roberto,

You can install Xquartz 2.7.8 which is still available from the xquartz web 
site.  This was the last version where Xquartz behaved properly and it runs 
fine on High Sierra.

Regards

MGM


Martin G Montgomery
Medical Research Council Mitochondrial Biology Unit
University of Cambridge
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road 
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk

> On 2 Dec 2017, at 00:04, Steiner, Roberto  wrote:
> 
> Hi all
> 
> Since my recent upgrade to High Sierra, XQuartz (most recent version 2.7.11 - 
> fresh installation) does not longer behave properly. Essentially, X11 does 
> not seem to understand touchpad actions (for example cannot close X11 
> windows, cannot drag them around, etc.). This problems also affects programs 
> that rely on X11. Has anyone experienced (and ideally solved) this problem? 
> 
> Thanks in advance 
> Roberto
> 
> Roberto A. Steiner, PhD
> Randall Centre of Cell and Molecular Biophysics
> Faculty of Life Sciences and Medicine 
> King's College London
> 
> roberto.stei...@kcl.ac.uk 
> Phone 0044 20 78488216
> Fax0044 20 78486435
> 
> Room 3.10A
> New Hunt's House
> Guy's Campus
> SE1 1UL
> London
> 

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Martin Montgomery]

Hello,

You need to tell pymol what to do with the map.

Load your pdb file
Load the map

create an object with residues you wish to display the map around.  You can use 
the create command to do this or you can click on all the residues that you 
want to use in the main window then go to the object called (sele) in the right 
hand sidebar, click A and then copy to object.  This will create an object 
called obj01 with the selected residues.  You can rename this if you wish.

Then you need to use the isomesh command to display the map.


isomesh mapname, mapfilename.ccp4, 2.5, obj01, carve=2.0

mapname is the name you want to appear in the right hand sidebar for the mesh 
(can be the same as the mapfilename if you wish)

mapfilename would be D83Vchimmap1 (from your screen shot).

2.5 is the sigma setting and carve=2.0 means the mesh is created within 2.0 Å 
of the selected atoms.  Adjust these values to suit.

You might want to go back to go back and check your FFT log and look at the 
grid settings.  It is a good idea to re run the FFT job but double the grid 
values from the original job.

It is all covered here:

https://pymolwiki.org/index.php/Display_CCP4_Maps 


Regards

MGM

Martin G Montgomery
ATP Synthase Group
Medical Research Council Mitochondrial Biology Unit
University of Cambridge
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road 
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk






> On 18 Mar 2017, at 10:43, Eleanor Dodson  wrote:
> 
> I think CCP4MG does this very selectively?
> 
> Eleanor Dodson
> 
> On 17 March 2017 at 17:03, Xiao Lei  > wrote:
> Dear All,
> 
> Thanks for the information.
> I tried the way suggested by pymol wiki, but pymol fail to display the map. 
> This is what I did: Run Fft to generate simple mapin ccp4i, input mtz map 
> from refmac, set F1=FWT and PHIC=PHWT, Sigma=SigF, Weight=FOM.  Add the file 
> extension .map.ccp4 to the generated output map. After open by pymol, only a 
> unit cell sign is shown (I attach here), no map is displayed.. I use Pymol 
> 1.8.X in Win7.
> 
> Any further input is appreciated.
> 
> 
> 
> .
> 
> 
> 
> 
> On Fri, Mar 17, 2017 at 7:41 AM, Xiao Lei  > wrote:
> Dear All,
> 
> In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius, but 
> I'd like to show the density on selective residues, not on the unselected 
> part of structure, is there a way to do it? I am using WinCoot 0.81.
> 
> In addition, could Pymol do it? 
> 
> Thanks ahead!
> 
> 

Re: [ccp4bb] Issues with Coot & XQuartz

[Martin Montgomery]

Hi,

We have had these problems with coot and xquartz versions greater than 2.7.8.  
This affects coot running locally on OSX and via ssh -XY from the mac to our 
linux workstations.  You should still be able to download the xquartz-2.7.8 
package (https://www.xquartz.org/releases/XQuartz-2.7.8.html 
).  Rebooting after the 
installation of a later xquartz has not made any difference on our macs.

Regards

MGM




> On 22 Nov 2016, at 12:32, Phil Evans  wrote:
> 
> Something we [re]discovered at a recent workshop is that after installing 
> Quartz you need to reboot (I believe to start the X11 launch daemon). Could 
> this be the problem?
> 
> Phil
> 
>> On 22 Nov 2016, at 11:28, Laura Croenen  wrote:
>> 
>> Hello all,
>> 
>> I recently downloaded the CCP4 package on Mac (OS X Yosemite 10.10.2). With 
>> this I am using the latest update of XQuartz. Some aspects of the package 
>> (ccp4i2, QtMG) are working fine, but others, inc. Coot, are not working at 
>> all. When I try to open Coot, it appears to start opening (the icon appears 
>> at the bottom of my screen) and then disappears, with the message:
>> 
>> "student-10-245-174-102:MacOS lauracroenen$ ./coot
>> 2016-11-21 17:07:40.946 coot[39004:3369025] script to run 
>> /Applications/ccp4-7.0/coot.app/../bin/coot
>> 
>> (coot-bin:39010): Gtk-WARNING **: cannot open display: 
>> 
>> (coot-crash-catcher.scm:39011): Gtk-WARNING **: cannot open display:"
>> 
>> Has anyone else had this problem? Am I missing something?
>> 
>> Thank you in advance.
>> 
>> Laura Croenen

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

[Martin Montgomery]

Hi Randy,

You could try the beta version of the forthcoming version of Word and see if 
the bug is fixed.  Obviously, it is a beta version and therefore a bit risky 
but it installs along side the current version and I’ve been trying it on my 
laptop without issue so far.  One improvement for me is that this version of 
Word now uses the Mac’s in built special character palette and we use a lot of 
Greek characters.  This works a lot better than symbol browser in the current 
version of Word where we still see some of the greek characters getting screwed 
up when saving as PDF or sharing with a Window’s PC.  One thing to watch is 
that the beta version .docx format has changed so you should be careful to save 
as compatible with Office 2011.


https://products.office.com/en-us/mac/mac-preview 
https://products.office.com/en-us/mac/mac-preview

Regards

MGM


Martin G Montgomery
ATP Synthase Group
MRC Mitochondrial Biology Unit
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road 
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk






 On 18 May 2015, at 09:10, Randy Read rj...@cam.ac.uk wrote:
 
 Rather off-topic, but maybe someone on the list has found a way to work 
 around this!
 
 There’s a problem with the Equation Editor in Office 2011 for Mac (i.e. the 
 one that is based on a stripped-down version of MathType, which you get with 
 Insert-Object-Microsoft Equation).  You can insert an equation, re-open it 
 and edit it several times, and then suddenly (and seemingly randomly) the 
 equation object will be replaced by a picture showing the equation, which can 
 no longer be edited.  I’m writing a rather equation-heavy paper at the 
 moment, and this is driving me crazy.
 
 This seems to be a known bug, which has existed from the release of Office 
 2011.  Apparently it happens, unpredictably, when an AutoSave copy of the 
 document is saved, so you can avoid it by turning off the AutoSave feature.  
 The last time this drove me crazy, several years ago, I did try turning off 
 AutoSave.  For a while, I was very good about manually saving frequently, but 
 I got into bad habits and eventually Word crashed after I had worked for 
 several hours on a grant proposal without manually saving.  So I turned 
 AutoSave back on.
 
 At the moment, the least-bad solution seems to be to turn off AutoSave while 
 I’m working on a document with lots of equations and then (hopefully) 
 remember to turn it back on after that document is finished.  But it would be 
 great if someone has come up with a better cure for this problem.
 
 No doubt someone will suggest switching from Word to LaTeX, but I need to be 
 able to collaborate on paper-writing, and even though I might be willing to 
 invest the effort in learning LaTeX, I can’t really expect that of my 
 collaborators.  Most people in our field do use Microsoft Word, regardless of 
 its failings.  I’ve also tried using the professional version of MathType, 
 but that requires your collaborators to install it as well — and I don’t 
 think that cured the equation to picture problem anyway.
 
 Thanks!
 
 -
 Randy J. Read
 Department of Haematology, University of Cambridge
 Cambridge Institute for Medical ResearchTel: +44 1223 336500
 Wellcome Trust/MRC Building Fax: +44 1223 336827
 Hills RoadE-mail: 
 rj...@cam.ac.uk
 Cambridge CB2 0XY, U.K.   
 www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box

[Martin Montgomery]

Dear Steve,

You should not require an incubator if you have good, stable air con.  We 
routinely grow crystals in plates stored at room temperature in wall mounted 
cabinets in our crystallisation lab.  Another of the groups here have 
experience of growing crystals in an anaerobic box.  Hopefully they will post 
more information.

Regards

MGM


Martin G Montgomery
ATP Synthase Group
MRC Mitochondrial Biology Unit
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road 
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk






 On 11 Mar 2015, at 10:17, Stephen Carr stephen.c...@rc-harwell.ac.uk 
 Stephen Carr wrote:
 
 Dear CCP4BBer's
 
 Apologies for the off-topic post, but the CCP4BB seems to be the best place 
 to ask about crystallisation.
 
 I am looking to set up crystallisation in an anaerobic glove box and wondered 
 how other people did this, specifically the crystallisation stage.  My 
 initial thoughts were to place a small crystallisation incubator inside the 
 box, however the smallest I have come across so far (~27L) is still rather 
 large.  Has anyone come across smaller incubators?  Alternatively are 
 incubators even neccessary if the glove box is placed in a room with good air 
 conditioning and stable temperature control?
 
 Any recommendations would be very helpful.
 
 Thanks in advance,
 
 Steve Carr
 
 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
 
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Re: [ccp4bb] Measuring protein concentration with 2mM ATP around

[Martin Montgomery]

Dear Cedric,

Try the BCA protein assay.  We get reliable results with this, consistent with 
amino acid analysis.  I should say that this is using the 2ml format.  We do 
not get reliable results with the microplate method.  We use 5 μl samples and 
our regular buffer is not too different from the one you are using.

Regards

MGM


Martin G Montgomery
ATP Synthase Group
MRC Mitochondrial Biology Unit
Wellcome Trust/MRC Building
Hills Road 
Cambridge
CB2 0XY

www.mrc-mbu.cam.ac.uk


On 17 Jan 2014, at 14:00, Cedric Govaerts cgova...@ulb.ac.be wrote:

 Dear all,
 
 We're doing some crystallization trials on a protein that requires 2mM ATP in 
 the buffer and we are having trouble measuring reliably/reproducibly protein 
 concentration.
 This is a real problem for optimization (last screen failed because of 
 excessive protein concentration compared to the previous run).
 
 What we observe:
 
 -2mM ATP seems to prevent reliable estimation at 280nm with the nanodrop 
 (albeit the Akta led detector seems to do OK at 280nm) due to the major 
 contribution in the 200-300nm range. I guess blanking is difficult due to the 
 relatively large contribution of ATP vs.protein at 280
 
 -For some reason I cannot explain, Bradford measurment (using Pierce/Thermo 
 dye) is also unreliable, comparable sample giving different values. I cannot 
 see why ATP would do tha (buffer is 20mM Hepes, pH7.5, 150mM NaCl,  10 
 %Glycerol, 10% Ethylene glycol, 3mM MgCl2 and 2mM ATP).
 
 As this is for estimation of the protein concentration while concentrating 
 before going into crystallization plates, the assay should be quick (minutes) 
 and use little amount of material (say max 5µl per measure). An we're really 
 interested in relative concentration (from one experiment to the next) rather 
 than absolute value.
 
 I'm guessing as many of you have worked with ATPase etc, there must be a 
 smart way to do this.
 
 Thanks for any input
 
 Cedric
 
 -- 
 Cedric Govaerts, Ph.D.
 Universite Libre de Bruxelles
 Campus Plaine. Phone :+32 2 650 53 77
 Building BC, Room 1C4 203
 Boulevard du Triomphe, Acces 2
 1050 Brussels
 Belgium

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 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)

[ccp4bb] Mystery density

[Martin Montgomery]

Posting on behalf of Katia Baranova (see below).  Any suggestions gratefully 
received!




Hello,

we have a puzzling density and hope someone has an idea of what it may be.

The pictures of it are here:

http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/top.png
http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/front.png
http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/side.png

The space group is I422, resolution 1.6A

The trial contained Tris, DTT, EDTA, sodium, potassium, phosphate, and chloride.

The centre of our unknown feature is about 3.8A from the Arg and it is also on 
the four fold symmetry axis.
It is + 28 sigma in the center and  about + 9.5 sigma in each of the 
tentacles.

Thank you very much!

Katia.



On 30 Nov 2011, at 17:30, Katia Baranova wrote:

 Hello,
 
 Well, it doesn't work.
 Can you forward it please?
 
 thanks a lot,
 
 K
 
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