Hi Douglas,
Have you applied all of the automatic updates to your installed version
of CCP4? There was a bug relating to this that I fixed at one point and
it was pushed out using our update system. However, if you've installed
from source code you won't have this option.
Best wishes,
Dear Jie,
Thanks for spotting this problem. I've made a fix for MrBUMP that should
address the problem. It will be included in the next CCP4 update which
will go out tomorrow (Tuesday 17th of December) all being well.
Best wishes,
Ronan
On 10/12/13 01:34, jie liu wrote:
Dear All
I just
Dear Colleagues,
This is a reminder about the second CeBEM/CCP4 South American School in
Macromolecular Crystallography. The closing date for applications is
Monday the 10th of February.
This year's school will take place at Sao Carlos University in Brazil.
Full details including the
Hi Robert,
Thanks for your interest in AMPLE and reporting this bug. There is a
small bug that has come about as a result of the latest MRBUMP update
last week that causes this problem. We're preparing a fix for it which
should be in the next ccp4 update towards the end of this week or early
Dear Jan,
There will be a Windows version of Aimless in the upcoming 6.3.0 release of
CCP4 which is due very soon. We'll announce it on the bb when it's ready.
Best wishes,
Ronan
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jan
Gebauer
Hi Nate,
The fasta licencing doesn't allow us to distribute it with the suite so it
needs to be downloaded separately. For MrBUMP to find it you should have it
somewhere in your system PATH. The easiest thing to do is to put the fasta3?
.exe executable into your $CCP4/bin directory. However,
, if
you have not done so already. Note that auto-updates will work correctly only
with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to
c...@stfc.ac.uk.
Many thanks for using CCP4,
-- Ronan Keegan
--
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Dear All,
A quick reminder to you all about this coming January's CCP4 Study Weekend
entitled Molecular Replacements (January 3rd-5th 2010). As the title
suggests, the meeting will be all about the latest developments in molecular
replacement with many leading crystallographers and software
Dear All again,
DoH! Minor typo in my previous email. The dates are January 3rd-5th 2013! (not
2010).
Best wishes,
Ronan
-Original Message-
From: Keegan, Ronan (STFC,RAL,SC)
Sent: 08 November 2012 18:06
To: ccp4bb
Cc: Miller, Shirley (STFC,DL,SC)
Subject: CCP4 Study Weekend 2013
...@stfc.ac.uk.
Many thanks for using CCP4,
-- Ronan Keegan
--
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Dear All,
A quick reminder that these next few days are the last chance to register for
next month's CCP4 Study Weekend. Registration will close next Monday the 10th
of December. The meeting will take place at the East Midlands Conference Centre
in Nottingham, UK from the 3rd to the 5th of
Dear All,
I repost this message on behalf of Dr. Jia-huai Wang, as this position needs to
be filled as soon as possible. For inquiries please contact Dr. Wang directly
at jw...@red.dfci.harvard.edu
Postdoctoral Position in Structural Biology of Immune Receptors:
There is an immediate opening
Dear Jiawei,
Thanks for spotting this and bringing it to our attention. It is a serious bug
in the interface when using the default protocol for Acorn. When running Acorn
to determine heavy atoms the default is to truncate the resolution to 3.5
Angstroms. However this default is there for all
Hi Huw,
Well spotted! We originally gave structure factors to SHELXE in our testing as
for most of our test cases we only had F/SIGF available. We were advised to
change to intensities but somehow in the released version the -f flag
remained. I'll make the change and put it in a CCP4 update.
...@stfc.ac.uk
Many thanks for using CCP4.
Ronan Keegan
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Hi Eugene,
Yes we should do this post-haste. First day that we are all present in RAL next
week.
Ronan
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
eugene.krissi...@stfc.ac.uk
Sent: 01 February 2013 09:42
To: ccp4bb
Subject: Re: [ccp4bb]
Dear Jilliu,
If you contact us here at the ccp4 help desk
(c...@ccp4.ac.ukmailto:c...@ccp4.ac.uk) we can remove the advert from the
CCP4 vacancies website. However, we can't remove it from the various archives
of the mailing list that exist around the web.
Let me know which advert you want
Dear All,
We're pleased to announce the latest release of MrBUMP. Pre-release
version 0.4.0 is now available from the MrBUMP website:
http://www.ccp4.ac.uk/MrBUMP
The new features include:
- The inclusion of the new CCP4i DBviewer, a graphical interface for
viewing CCP4i jobs. This will
Hi Harry,
Might not be the problem but does this machine have its ccp4 scratch
space ($CCP4_SCR) mounted from another machine by nfs across a network?
Refmac writes a lot of temporary files to CCP4_SCR and if this is across
a busy network it can really slow Refmac's progress.
Ronan
Harry
---BeginMessage---
Hi,
I had a very curious result when doing a round of isotropic B factor
refinement on Refmac5.
After iso B my R is 19.2 and Rf 24.3. My resolution is 1.95, what does
not justify anisotropic b-factor refinement. However I did it by mistake
and it dropped my R to 17.8
Dear Colleagues,
Within the framework of the SAXIER European Contract, we are developing
at SOLEIL, and in collaboration with an NMR team of the ICSN at Gif sur
Yvette (CNRS), a piece of software to refine protein 3D structures
against NMR Residual Dipole Couplings and solution SAXS
Hi Jerry,
I've not got a whole lot of experience with docking programs but I have
used 3D-dock (http://www.sbg.bio.ic.ac.uk/docking/) to do docking trials
between two proteins and found it to be easy to set up and use. It uses
an algorithm that mainly looks at surface complimentarity between
Hi Daniel,
Sorry to hear about your problem with mrbump. You say that you put the
Fasta35 executable in the ccp4i bin directory(note the i). This
directory is probably not in your system PATH. I would recommend that
you put it into the $CCP4/bin which should be in your system path
provided
*MRC PROTEIN PHOSPHORYLATION UNIT*
*COLLEGE OF LIFE SCIENCES*
*UNIVERSITY OF DUNDEE, SCOTLAND*
*PROGRAMME LEADER *
The Unit invites applications for the above position from scientists
with exciting research programmes aimed at understanding the role of
protein phosphorylation in cell
Hi Stephen,
Have you a project set up in CCP4i? Make sure that your CCP4i project
directory is set before you try to start Imosflm. When run through
CCP4i, Imosflm uses this directory to write it's output files.
You can set the project directory by clicking on the
DirectoriesProjectsDir
that you
install the official Graphviz distribution available from:
http://www.graphviz.org/
This includes the missing fonts and should work for you. Make sure that
the new executables for Graphviz precede the CCP4 versions in your PATH.
Let me know if this works for you.
Kind regards,
Ronan
Database
Configuration and un-check the radio button that sets the option to
connect to the database server on start up. Then have all your users
restart CCP4i.
Kind regards,
Ronan Keegan
CCP4 Group
Jun Dong wrote:
Dear CCP4 developers,
I just wonder if there will be a fix for this problem
,
Ronan
Ronan Keegan
CCP4 Group
Dear All,
A final reminder about next month's CCP4 Study Weekend entitled Model
Building and Refinement and Validation. The meeting will run from the
5th to the 7th of January and will be held at the University of Warwick
in the UK. We have a limited number of places left and the deadline for
an update as
soon as it's available. Our apologies for the inconvenience.
Best wishes,
Ronan
Ronan Keegan
CCP4 Group
won't be available for the first part of the
meeting. We're hoping to fix it as soon as possible and we'll send an update as
soon as it's available. Our apologies for the inconvenience.
Best wishes,
Ronan
Ronan Keegan
CCP4 Group
contributed to CCP4 6.2.0 and
all of those who have helped in testing it. See you in Madrid!
Kind regards,
Ronan
Ronan Keegan
CCP4 Group
Dear All,
This is a reminder about this coming January's CCP4 Study Weekend taking place
from the 4th - 6th of January at Warwick University in the UK. The topic for
the 2012 meeting will be Data Collection and Processing and a provisional
programme is now available. The meeting will cover all
Dear all,
There's just one week remaining to register at the reduced rate for the
upcoming CCP4 Study Weekend in January entitled Data Collection and
Processing. The meeting is taking place at the University of Warwick, UK, from
the 4th-6th of January 2012. For more details about the meeting
Dear All,
This a final reminder about next month's CCP4 Study Weekend taking place at
Warwick University in the UK from January 4th to 6th. The topic of this meeting
will be Data collection and processing. There are still a few registration
places remaining but the registration deadline is
Dear Raja,
This is a known bug in version 6.1.1. There is a fix for it available
from the CCP4 problems pages. See item no. 7 in the following page:
http://www.ccp4.ac.uk/problems.php#6.1.1-ccp4i
You'll need to download import_scaled.script and replace the version
that you have in:
an
older python such as python 2.6.
Kind regards,
Ronan
Ronan Keegan
CCP4 Group
Victor Alves wrote:
Dear BB
Balbes (run from within CCP4i) gave me one MR solution but stopped with
this error.
I am now using the Balbes WWW server, but could some of you
knowledgeable guys have some ideas of might
with it.
Best wishes,
Ronan
Ronan Keegan
CCP4 Group
riya doreen wrote:
Hi everyone,
I am trying to run MrBUMP through the CCP4 6.1.1 but the program is
complaining that no multiple alignment programs like mafft, clustalw,
clustalw2, probcons, or t_coffee were found on the system.
Will I need
://www.cse.scitech.ac.uk/events/CCP4_2010/
We hope to see you there.
Best wishes,
Ronan
Ronan Keegan
CCP4 Group
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tried and it works!
Thanks!
Marjolein
On 19 Aug 2014, at 12:28, Ronan Keegan ronan.kee...@stfc.ac.uk
mailto:ronan.kee...@stfc.ac.uk wrote:
Hi Marjolein,
Thanks for your email and sorry to hear about your problems with
MrBUMP. Can you please tell me what OS you are using (Linux, Mac
etc
*The CCP4 Study Weekend (7 - 9 January 2015)*
*East Midlands Conference Centre, University of Nottingham*
**
*Wednesday 7 - MX User Meeting*
*Thursday 8 / Friday 9 - CCP4 Study Weekend*
**
*Advances in Experimental Phasing*
**
*We cordially invite you to participate in the 2015 CCP4 Study Weekend
Dear Pietro,
Tim's solution should work for you. If not please let me know.
From CCP4 6.5.0 (due very soon), the default sequence search tool in
MrBUMP will be Phmmer which will be included in the suite on all
supported operating systems. So there won't be the need to download
fasta
Dear Jacob,
Thanks for reporting this problem. Can you tell me what version of CCP4
you are using?
As an alternative, you can use MrBUMP via the CCP4-online service which
is available from here:
www.ccp4.ac.uk/ccp4online
It's still in development and only goes as far as the Refmac step
Dear All,
The webcast for this year's CCP4 Study Weekend on Advances in
Experimental Phasing taking place on the 8/9 of January will be
available from the STFC Webinars page:
http://www.stfc.ac.uk/webinars
A programme for the meeting can be found here:
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