Hi Herman,
That's correct!
- Adam
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update 017 next week in order to
be able to run molecular replacement.
Is this correct?
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von Adam Simpkin
Gesendet: Freitag, 5. November 2021 12:45
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] MrBUMP for cryo-EM
Hi Herman,
A path to a local c
Hi Herman,
A path to a local copy of the PDB will work, although I should caution that
MrBUMP's cryo-EM mode is releasing with ccp4 update 017 next week. This also
corresponds with an update Ronan has made that allows MrBUMP to search the EBI
Alphafold database, so that will also be available
shire
OX11 0DE
From: CCP4 bulletin board on behalf of Schreuder,
Herman /DE
Sent: 04 November 2021 14:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] MrBUMP for cryo-EM
Dear Community,
I just came accross a paper on the use of MrBUMP to fit pdb models to cryo-EM
maps: https://script
Dear Community,
I just came accross a paper on the use of MrBUMP to fit pdb models to cryo-EM
maps: https://scripts.iucr.org/cgi-bin/paper?S2059798321009165
However, it turned out that the program tries to download coordinates directly
from the pdb, which our firewall does not allow. Is there a
Hi Christian,
Thanks for pointing out that option. I will definitely try it out. Perhaps my
tutorial can be adapted to this way of making the models.
/Derek
On 16 Oct 2020, at 10:26, Christian Roth
mailto:christianroth...@gmail.com>> wrote:
HI Derek,
I don't know which options you need, but t
HI Derek,
I don't know which options you need, but there is the interactive task of
model preparation with mrbump and ccp4mg in the bioinformatic tasks, which
might allow what you want to do.
Cheers
Christian
On Thu, Oct 15, 2020 at 11:02 PM Derek Logan
wrote:
> Hi all,
>
> I'm looking for some
Hi all,
I'm looking for some advice on MrBUMP. Is it possible to access MrBUMP via
CCP4I2 with all the options it had in CCP4I? The options seem to have been
drastically trimmed in CCP4I2. The reason I ask is that I have a tutorial that
I've put a lot of work into over the years that involves t
Dear Derek and CCP4bb community,
Sorry for not posting the solution. The issue have got solved with the help
from Felix, Ronan and Jens.
Adding # in front of *locale.setlocale(locale.LC_NUMERIC, "") *(near the
top), in
"/Applications/ccp4-7.0/share/mrbump/include/output/MRBUMP_printTable.py"
wor
Dear Nishant,
Did you ever get an answer to your question? I came across it while looking
through old e-mails. This has happened to me on every Mac I have run MrBUMP on
in recent years (always in Sweden). You need to go to
/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/pyth
Dear Crystallographer,
I will be grateful if you help me with what may be a simple problem. While
trying MrBUMP with my mtz file , I am currently getting the following
error. Similar error I am getting while trying AMPLE as well.
"CCP4I VERSION CCP4Interface 7.0.044
#CCP4I SCRIPT LOG mrbump
#CCP4
Yes, Eleanor D. is right. I had a similar experience. MR did not provide me
the solution with monomeric protein. However, when i used dimer as a search
model, it appeared to be a low-hanging fruit afterwards. May be you have a
similar situation, there are very less possibilities to explain othewrwi
With such a lot of molecules, I would check for oligamers. Look at the
MOLREP self rotation - is there anything obvious? Send the*.ps if you like
and I can comment.
And do the models form oligimers? If so search with that..
Eleanor
And as Randy says - try PHASER ..
On 31 October 2016 at 21:30
Dear Alex,
We’ve had very good luck using Phaser to place large numbers of copies of good
models. It’s in this kind of case where the increased sensitivity of the
likelihood approach really helps. I would suggest trying the different choices
of model as alternatives, and you might also want t
Hi All,
I have a protein which contains 72 amino acids. The crystal of this protein
diffracts to 2.5A with SG P31 (CELL Dimension 65.9590 65.9590 164.3900
90. 90. 120.). Pointless indicates no twinning.
Mathew coefficient as below:
For estimated molecular weight 7919.
Nmol/asym Mat
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 but
Dear Crystallographers,
I am trying to get MrBump to complete a partial solution, but on my windows7
machine, the CCP4i interface essentially freezes (cannot see logfiles therein,
nothing responds, although it does not completely die), and those log files
which I think are the correct ones have
Hi Marjolein,
I'm glad to hear that. You may also be interested in the new CCP4 online
service which hosts, among other applications, a MrBUMP service. One of
the main advantages it has is that it uses HHPred to search for MR
search models which can produce better models than the simple Fasta
Hi
I just encountered the same problem as described in the message below. I tried
to search but couldn’t find an answer, but was a solution for this problem
found?
Thanks
Marjolein
On 04 Aug 2014, at 03:59, Eze Chivi
mailto:ezech...@outlook.com.ar>> wrote:
Hello, I have a problem with the
Hello, I have a problem with the update 6.4.0 of ccp4: MrBump does not start,
it freezes in the message "Please wait...drawing task window mrbump" and the
error "expected integer but got """. Sometimes, MrBump starts, but drop-down
menu doesn't work. Same problem in Linux or Windows versions.
Th
Dear Ronan
Thank you!
Happy holidays!
Jie
- Original Message -
From: "Ronan Keegan"
To:
Sent: Monday, December 16, 2013 3:40 AM
Subject: Re: [ccp4bb] MrBUMP not running after update
Dear Jie,
Thanks for spotting this problem. I've made a fix for MrBUMP that shou
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 i
Dear All
I just installed CCP4-6.4 and all the subsequent updates. Now MrBump failed
with the following error message:
The program run with command: /usr/local/ccp4-6.4.0/bin/ccp4-python -u
/usr/local/ccp4-6.4.0/bin/mrbump HKLIN
/home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c.mtz SEQI
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,
Rona
Hello Everyone,
PHASER is returning the following error "Input Error: No Mode Set" when called
from MRBUMP.
CCP4-6.3.0 running on Centos5-x64.
Any help , ideas, comment would be greatly appreciated.
Thanks,
Doug
###
seems to be an
undocumented "QTYPE SGE" keyword. But I can't be sure without trying it.
Cheers
Martyn
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Miguel Ortiz Lombardía
> Sent: 13 May 2011 16:38
> To: CCP4BB@JISCMAIL
Dear all,
I get this unexpected (by me) message from MrBUMP:
Reindex Warning: spacegroup P43212 does not have an enantiomorph
I thought P41212 and P43212 were enantiomorphs...
So, am I wrong ?
(PS: I'm looking for indications on how to use MrBUMP on a cluster with
a SGE queueing system. Any poi
Hi Riya,
You'll need to install at least one of these programs for it to work.
What kind of operating system have you got? Clustalw/2 is about the
easiest to install and is available from here:
ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.11/
Let me know if you need any further help with i
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 to install all these programs and will they need to be in the
CCP4 director
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
Hi all,
We' ve just encountered a problem concerning the installation of MrBump on our
Linux machine. MrBump needs Fasta35 for operation, but during installation
does not recognise the already installed Fasta35, even if Fasta35 is placed in
the ccp4i bin. Under the same location the recognition of
Dear All
I want to run MrBump. We have dynamic internet system in our institute. So I am
not able to locate the proxy address.
Any help please
Sajid
From Chandigarh to Chennai - find friends all over India. Go to
http://in.promos.yahoo.com/groups/citygroups/
Hi all,
I'm having problems to install the ccp4i task for MrBump 0.4.2.
The error message I get is the following
UnpackTaskArchive: uncompress failed to create
"./install_MrBUMP-ccp4i/MrBUMP-ccp4i.tar"
ExamineTaskArchive: failed to unpack temporary copy of
/home/linux/xtal/ccp4-6.0.2-all-packages
8 21:48
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] MrBUMP FASTA
Hello Everyone,
Just to let you know our lab just starting using the MrBUMP program
(v0.4.1), so our problem(s) could definitely be from lack of knowledge.
Anyway, when we try a FASTA search from CCP4i, either over the internet o
Hello Everyone,
Just to let you know our lab just starting using the MrBUMP program
(v0.4.1), so our problem(s) could definitely be from lack of knowledge.
Anyway, when we try a FASTA search from CCP4i, either over the internet or
locally, things just seem to hang at "Getting Template Sequence
Dear all,
I have a couple of questions concerning mrBUMP:
1) I cannot correctly fix E-values for Fasta search, e.g., 6E-11,
actually it seems
it accepts only 4 decimal places like 0.0001. I also tried to edit scripts
by hand ("run & view com file").
2) I would like to use mrBUMP firstly in
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 for
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