Re: [ccp4bb] any issues getting through to the CCP4 servers?

[Julian Nomme]

Hi,

I'm still facing the same issue today.
I just can't get access to the download section, the rest of the website 
being accessible.

I'm getting the following message:

"Service Unavailable
The server is temporarily unable to service your request due to 
maintenance downtime or capacity problems. Please try again later."


Was the problem fixed during the week?
Tom, have you got access to it?

Thanks,
Julian



Le 1/23/22 à 12:53 AM, Peat, Tom (Manufacturing, Clayton) a écrit :

Hello All,

I've had some issues getting through to the CCP4 website/ servers to 
do some updates and I was wondering if anyone else was having issues?
That is to say, is it something specific to what I'm doing or a more 
general issue?

The BB seems to be working fine...
Thanks, tom

Tom Peat, PhD

Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au



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Re: [ccp4bb] ContaMiner server down?

[Julian Nomme]

Hi Stephan,
Just got my results and  I crystallized a contaminant...
Thanks for providing such tools. You saved me several hours of work.
Best,
Julian

Le 12/5/21 à 2:23 PM, Stefan Arold a écrit :

Dear Julian
thank you for pointing out that our server had problems! We have now 
fixed them and jobs should run as usual. Please let me know if any 
problems persist.

Thanks for using ContaMiner!
With best wishes
Stefan

On Sat, 4 Dec 2021 at 21:27, Julian Nomme  wrote:

Hi all,

I sent several jobs on the ContaMiner web server more than a week ago.
My jobs have been submitted but for some reason, as of today they are
still not running.
I tried to download the software and run it on my computer but I only
get an error message telling me that something went wrong.

Does anyone know if there is a current known problem or if it has
been
discontinued?

Thanks,

Julian



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[ccp4bb] ContaMiner server down?

[Julian Nomme]

Hi all,

I sent several jobs on the ContaMiner web server more than a week ago.
My jobs have been submitted but for some reason, as of today they are 
still not running.
I tried to download the software and run it on my computer but I only 
get an error message telling me that something went wrong.


Does anyone know if there is a current known problem or if it has been 
discontinued?


Thanks,

Julian



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Re: [ccp4bb] ccp4 release 7.0 update 023

[Julian Nomme]

Same here on masOS Sierra...
Julian

Le 11/23/16 4:55 PM, Isupov, Michail a écrit :

Hi,
I have already uninstalled the latest update (23), on Snow Leopard
the new COOT was crushing
on attempt to mutate residue in graphical interface.
Regards,
Misha



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel 
[wtem...@gmail.com]
Sent: Wednesday, November 23, 2016 3:50 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ccp4 release 7.0 update 023

Hello,
after installing updates 22 and 23 on an Ubuntu-14.04 (x86_64) box, I have yet 
to successfully “mutate” any amino acid residue in COOT.
(setup-mutate 1) is printed to the terminal, followed by a line confirming on 
which atom I have clicked, but the residue type selection dialog does not 
appear. Coot just hangs at this point. Has anyone else encountered this problem?
Regards.
Wolfram

​

On Wed, Nov 23, 2016 at 9:41 AM, Charles Ballard 
> wrote:
Dear All

ccp4 update 23 has just been released.  It contains

   * coot:
  - update to coot 0.8.7 on linux and os x

   * phaser:
 - Bug fixes: ccp4i and interaction with Arcimboldo
 - Update: Improved treatment of systematically weak data (e.g. severe 
anisotropy)

   * ccp4i
  - bug fix: phaser, updated defaults for phaser tasks
  - bug fix: mrbump, updated defaults for phaser

All the best

Charles  Ballard on behalf of CCP4 core team


--
Julian Nommé
Institut de Pharmacologie et de Biologie Structurale (IPBS)
Equipe de biophysique structurale
CNRS UMR 5089
205 route de Narbonne BP 64182
31077 Toulouse Cedex 4 France
Tel : +335 61 17 54 40
Web:  http://www.ipbs.fr

[ccp4bb] cns .map in coot

[Julian Nomme]

Hi all,

I can easily convert my composite omit map from cns to ccp4 format and 
open it into coot.

However, how can I make coot use this map to fit density to my structure ?
I can only use this map for visual support and for example, coot doesn't 
assign any density on the bar graph generated by using the Density fit 
analysis option to check the geometry.

Does anyone have any idea how to fix this problem?

Thanks,

Julian

Re: [ccp4bb] Digital microscope camera

[Julian Nomme]

 Thanks all for the numerous answers !
I will post a summary of responses in a few days.

--
Julian

[ccp4bb] Digital microscope camera

[Julian Nomme]

 Dear all,

We are investigating the possibility to upgrade from an old 35mm film 
camera to a digital camera for taking crystal pictures through a 
microscope (Olympus CH30 already equipped with a trinocular port.)
To avoid overpriced cameras from optics companies (at least $900 not 
including adapters) I'm wondering if you have experienced good deals 
with cheap cameras controlled by a computer.
I've found the same thread in the ccp4 archives but it's pretty old now 
and I'm sure you guys have new ideas.

Any good and cheap suggestions are more than welcomed !

Thank you,

Julian

Re: [ccp4bb] Strange spots

[Julian Nomme]

Google books: 
http://books.google.com/books?id=RqNb241Q484Cprintsec=frontcoverdq=Macromolecular+Crystallography+with+Synchrotron+Radiationhl=enei=JA3LTMe2NMSnnQfAjN3mDwsa=Xoi=book_resultct=resultresnum=1ved=0CC8Q6AEwAA#v=onepageqf=false 
http://books.google.com/books?id=RqNb241Q484Cprintsec=frontcoverdq=Macromolecular+Crystallography+with+Synchrotron+Radiationhl=enei=JA3LTMe2NMSnnQfAjN3mDwsa=Xoi=book_resultct=resultresnum=1ved=0CC8Q6AEwAA#v=onepageqf=false


Julian

On 10/29/10 1:01 PM, Jrh wrote:

Dear Gerard
I will do a scan of fig 8.1b asap, probably Monday.
Greetings,
John


Sent from my iPad

On 29 Oct 2010, at 18:44, Gerard Bricogneg...@globalphasing.com  wrote:

   

Dear John,

 Would it be possible to know more about what you are referring to
without having to buy (or steal) your book :-)) ?

 Thank you in advance!


 With best wishes,

  Gerard.

--
On Fri, Oct 29, 2010 at 06:41:51PM +0100, John R Helliwell wrote:
 

Dear Dave,
You have a collector's item there!
The closest I have seen is illustrated in my book 'Macromolecular
Crystallography with Synchrotron Radiation' page 321, which is a small
molecule example.
Best wishes,
John
Prof John R Helliwell DSc


On Fri, Oct 29, 2010 at 5:08 PM, David Goldstone
david.goldst...@nimr.mrc.ac.uk  wrote:
   

Dear All,

Does anyone have any insight into what the circles around the spots might
be?

cheers

Dave
--
David Goldstone, PhD
National Institute for Medical Research
Molecular Structure
The Ridgeway
Mill Hill
London NW7 1AA


 



--
Professor John R Helliwell DSc
   

--

 ===
 * *
 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===
 
   

Re: [ccp4bb] Strange spots

[Julian Nomme]

Kris,
the link works for me and obviously for other people. I don't know why 
you don't have access to it...

Anyway, thank you Konstantin for providing the pdf!

Julian

On 10/29/10 4:17 PM, Konstantin v. Korotkov wrote:

The link worked for me, pages 320-322 attached.

-Konstantin


On Fri, 29 Oct 2010, Gerard Bricogne wrote:


Dear Liz,

You will be disappointed. I went immediately to that link, but 
page 321
is not available as part of the Googlebook sample, which jumps 
directly from

page 320 to page 325.


With best wishes,

 Gerard.

--
On Fri, Oct 29, 2010 at 09:13:27PM +0100, 
elizabeth.d...@diamond.ac.uk wrote:

There is always hope!!!

Seriously though, I have never seen anything like this before! I am 
watching this thread with interest to see what others suggest.


THanks Also thanks should go specifically to Julian Nomme who took 
the trouble to send us all the Helliwell book  link.


Liz



From: CCP4 bulletin board on behalf of Sanishvili, Ruslan
Sent: Fri 29/10/2010 21:08
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange spots



C'mon now! Everybody knows that frogs in real space become handsome 
princes in the reciprocal one...


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



From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf 
Of Jacob Keller

Sent: Friday, October 29, 2010 3:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange spots





Yes, but the question is what in real space gives rise to 
reciprocal-space frog spawn? (Frogs, I guess?)




- Original Message -

From: Marcus Winter mailto:marcus.win...@agilent.com

To: CCP4BB@JISCMAIL.AC.UK

Sent: Friday, October 29, 2010 2:56 PM

Subject: Re: [ccp4bb] Strange spots









Dear David,





Further to the previous learned responses, surely, this

is just frog spawn ?



My apologies: it is a Friday evening, after all...





Marcus Winter.







-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On 
Behalf Of David Goldstone

Sent: 29 October 2010 17:08
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Strange spots



Dear All,



Does anyone have any insight into what the circles around the 
spots might be?




cheers



Dave

--

David Goldstone, PhD

National Institute for Medical Research

Molecular Structure

The Ridgeway

Mill Hill

London NW7 1AA







***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***




--
Konstantin Korotkov, Ph.D.

Research Scientist
University of Washington
Department of Biochemistry
Box 357742
Seattle, WA 98195-7742

(206)616-4512
k...@u.washington.edu
--