[ccp4bb] MrBUMP

[riya doreen]

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 directory ?
Thanks

[ccp4bb] MRBUMP - PHASER ?

[Bailey, Douglas (NIH/NCI) [E]]

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




#
### CCP4 PROGRAM SUITE: Phaser  
2.5.1 ###
#
User: jacek
Run time: Tue Sep 10 10:02:53 2013
Version:  2.5.1
OS type:  linux
Release Date: Fri Jul  6 07:21:42 2012 (svn )

If you use this software please cite:
$TEXT:Reference1: $$ $$
"Phaser Crystallographic Software"
A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni & R.J. 
Read
J. Appl. Cryst. (2007). 40, 658-674

$$

*
*** Phaser Module: PREPROCESSOR 
2.5.1 ***
*


END


$TEXT:Warning: $$ Baubles Markup $$
-
INPUT ERROR: No MODE set
-
$$

Douglas Bailey
NCI-Frederick
1050 Boyles Street
Frederick, Maryland 21702
301-846-5328

[ccp4bb] MrBUMP FASTA

[Doug Bailey]

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 Sequences and 
Multiple Alignment" . See output from logfile.


Any ideas, directions or suggestions would be greatly appreciated.


Thanks in advance,

Doug





###
### Fasta search###
###

Fasta log message: E value used in Fasta search: 2.00e-02
Fasta log message: Performing Fasta search locally
Fasta log message: Fasta DB set to: 
/people5/bhaumik/.ccp4_mrbump/pdb_ATOMseqs.txt



Number of templates after user specified chains are included: 169

---
Adding chains from local files...
---

Fasta log message: Number of matches: 170


-
Fasta: Getting Template Sequences and Multiple Alignment:
-


Douglas Bailey  Ph: 301-846-5328
NCI-Frederick   Fax: 
301-846-6322

1050 Boyles Street  E-mail: [EMAIL PROTECTED]
Frederick, Maryland 21702

[ccp4bb] MrBUMP error

[Nishant Varshney]

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
#CCP4I DATE 01 Sep 2017  15:58:19
#CCP4I USER apple
#CCP4I PROJECT Josephin
#CCP4I JOB_ID 45
#CCP4I SCRATCH /tmp/apple
#CCP4I HOSTNAME Apples-iMac.local
#CCP4I PID 933

http_proxy not specified in environemnt
***
* Information from CCP4Interface script
***
The program run with command: /Applications/ccp4-7.0/bin/mrbump HKLIN
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1.mtz
SEQIN /Users/apple/Documents/Nishant/Josephin_data/Phenix/Q15040.fasta
HKLOUT
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1_mrbump_soln1.mtz
XYZOUT
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1_mrbump_soln1.pdb
KEYIN /tmp/apple/Josephin_45_1_com.tmp
has failed with error message
Traceback (most recent call last):
  File
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
line 162, in _run_module_as_main
"__main__", fname, loader, pkg_name)
  File
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
line 72, in _run_code
exec code in run_globals
  File "/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in

import MRBUMP_master
  File
"/Applications/ccp4-7.0/share/mrbump/include/initialisation/MRBUMP_master.py",
line 17, in 
import Matches
  File "/Applications/ccp4-7.0/share/mrbump/include/structures/Matches.py",
line 29, in 
import Write_MR_results
  File
"/Applications/ccp4-7.0/share/mrbump/include/output/Write_MR_results.py",
line 20, in 
import printTable
  File "/Applications/ccp4-7.0/share/mrbump/include/output/printTable.py",
line 5, in 
locale.setlocale(locale.LC_NUMERIC, "")
  File
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py",
line 579, in setlocale
return _setlocale(category, locale)
locale.Error: unsupported locale setting
***


#CCP4I TERMINATION STATUS 0 "Traceback (most recent call last):   File
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
line 162, in _run_module_as_main "__main__", fname, loader, pkg_name)
File
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
line 72, in _run_code exec code in run_globals   File
"/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in 
  import MRBUMP_master   File
"/Applications/ccp4-7.0/share/mrbump/include/initialisation/MRBUMP_master.py",
line 17, in  import MatchesFile
"/Applications/ccp4-7.0/share/mrbump/include/structures/Matches.py", line
29, in  import Write_MR_results   File
"/Applications/ccp4-7.0/share/mrbump/include/output/Write_MR_results.py",
line 20, in  import printTable   File
"/Applications/ccp4-7.0/share/mrbump/include/output/printTable.py", line 5,
in  locale.setlocale(locale.LC_NUMERIC, "")   File
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py",
line 579, in setlocale return _setlocale(category, locale)
locale.Error: unsupported locale setting"
#CCP4I TERMINATION TIME 01 Sep 2017  15:58:20
#CCP4I TERMINATION OUTPUT_FILES
/Users/apple/Documents/Nishant/Josephin_data/ccp4/search_45
#CCP4I MESSAGE Task failed


Looking forward for your help

Regards
Nishant

-- 
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477
Mob: 8390564690


45_mrbump.log
Description: Binary data

Re: [ccp4bb] MrBUMP

[Ronan Keegan]

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 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 to install all these programs and will they need to be in 
the CCP4 directory ?

Thanks

Re: [ccp4bb] MRBUMP - PHASER ?

[Ronan Keegan]

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,

Ronan


On 10/09/13 15:44, Bailey, Douglas (NIH/NCI) [E] wrote:


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

#

### CCP4 PROGRAM SUITE: 
Phaser  2.5.1 ###


#

User: jacek

Run time: Tue Sep 10 10:02:53 2013

Version:  2.5.1

OS type:  linux

Release Date: Fri Jul  6 07:21:42 2012 (svn )

If you use this software please cite:

$TEXT:Reference1: $$ $$

"Phaser Crystallographic Software"

A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni 
& R.J. Read


J. Appl. Cryst. (2007). 40, 658-674

$$

*

*** Phaser Module: 
PREPROCESSOR 2.5.1 ***


*

END



$TEXT:Warning: $$ Baubles Markup $$

-

INPUT ERROR: No MODE set

-

$$

Douglas Bailey

NCI-Frederick

1050 Boyles Street

Frederick, Maryland 21702

301-846-5328




--
Scanned by iCritical.

[ccp4bb] MrBUMP in CCP4I2

[Derek Logan]

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 the students solving 
the thaumatin structure using two different search models with higher and lower 
sequence identity, which involves specifying them individually. The advantage 
of using MrBUMP is that the students don't have to do a separate step with 
Chainsaw or Sculptor. What's more, we do one run with and one run without 
automated model building and refinement for each model to compare the final 
results. CCP4I2 doesn't seem to offer any of these options.

Of course I can run the tutorial using CCP4I but I was trying to "modernise" it 
a bit.

Any advice is welcome
Derek


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[ccp4bb] MrBump Behaves Strangely

[Keller, Jacob]

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 ceased changing. Nevertheless, the 
process continues on 2 cores and 800 MB RAM as phaser.exe.

Is something broken here, maybe phaser has gone incognito mode, or something 
else? It's happened the last few days any time I've tried to run MrBump. Any 
thoughts?

...And please spare me any parathyrophobia--we don't need to beat that dead 
horse!

JPK



***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

[ccp4bb] mrBUMP 0.4.1 questions

[Ricardo Aparicio]

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 the "model search only" option 
and then
restart/continue the job (in this case, off-line) to do molecular 
replacement with the previously selected models.

Is there a way to do it without having to enter the selected models by hand?

3) I also would like to enter pre-determined pdb files for molecular 
replacement but I cannot understand

very well the "User specified search models" session in ccp4i.
What I understand is that I need to specify BOTH the pdb file AND the chain.
Thus, if I have a pdb with many chains, I need to define many lines to 
refer to only one
pdb file. Is there a way to only specify the path of the pdb files and 
left to mrBUMP the decision

of whether or not to select a particular chain?

4) ccp4i dbviewer is launched automatically when mrBUMP starts to run.
A task button at the bottom of the "Program List" was created but it does
not work (message:   "sh: bltwish: command not found").
Maybe problems with my installation?
Is there a way to launch dbviewer by command line?


Thank you very much in advance,

Ricardo


#CCP4I VERSION CCP4Interface 1.4.4.2
#CCP4I SCRIPT LOG mrbump
#CCP4I DATE 31 Aug 2007  16:13:17
#CCP4I USER aparicio
#CCP4I PROJECT PRS
#CCP4I JOB_ID 18
#CCP4I SCRATCH /tmp/aparicio
#CCP4I HOSTNAME minerva.iqm.unicamp.br
#CCP4I PID 27340

http_proxy not specified in environemnt

#
#
#
#  CCP4: MRBUMP - Automated Bulk Molecular Replacement (version 0.4.1)  #
#

Re: [ccp4bb] MrBUMP FASTA

[Keegan, RM (Ronan)]

Hi Doug,

The problem could be one of two things. Do you need to set a proxy to access 
the internet? Alternatively, it might just be that the multiple alignment step 
is taking a long time to run. We've noticed this if you chose probcons to do 
the multiple alignment step.

A useful thing to do is turn the debug option on. It will give more feedback 
about what's happening. Please send me the output from this if it still gives 
you a problem.

Hope this helps.

Regards,

Ronan


-Original Message-
From: CCP4 bulletin board on behalf of Doug Bailey
Sent: Mon 14/01/2008 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 or 
locally, things just seem to hang at "Getting Template Sequences and 
Multiple Alignment" . See output from logfile.

Any ideas, directions or suggestions would be greatly appreciated.


Thanks in advance,

Doug





###
### Fasta search###
###

Fasta log message: E value used in Fasta search: 2.00e-02
Fasta log message: Performing Fasta search locally
Fasta log message: Fasta DB set to: 
/people5/bhaumik/.ccp4_mrbump/pdb_ATOMseqs.txt


Number of templates after user specified chains are included: 169

---
Adding chains from local files...
---

Fasta log message: Number of matches: 170


-
Fasta: Getting Template Sequences and Multiple Alignment:
-


Douglas Bailey  Ph: 301-846-5328
NCI-Frederick   Fax: 
301-846-6322
1050 Boyles Street  E-mail: [EMAIL PROTECTED]
Frederick, Maryland 21702

[ccp4bb] MrBump CCP4i task

[Bossi, Roberto [Nervianoms]]

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/ccp4-6.0.2/ccp4i/MrBUMP-ccp4i.t
ar.gz
 
I've checked I can unpack that archive by tar -xvzf, and I think I've no
permission issues.
I'm running CCP4 6.0.2 with CCP4 interface 1.4.4.2 on a Red Hat 4.0
64bit machine.
Any help would be appreciated,
 
Thanks
Roberto
 

--- 
Roberto T. Bossi 
tel.: +39 0331 58 1914 
fax.: +39 0331 58 1360 
E-Mail: [EMAIL PROTECTED] 
Structural Chemistry 
Department of Chemistry 
NERVIANO MEDICAL SCIENCES 
Viale Pasteur 10 
20014 Nerviano (MI) - Italy 
Web: www.nervianoms.com 
 



 
 

[ccp4bb] MrBump Installation ccp4

[Daniel Wohlwend]

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 ClustalW did not
oppose a problem.  Can anybody help us? Where do we have to put Fasta35 in
order to continue the installation of MrBump? Or is something possibly wrong
with the permissions (global or local)?
If anyone has an idea, please let us know!
Thanks a lot in advance!

Daniel

Daniel Wohlwend
GZMB Abt. für molekulare Strukturbiologie
Georg-August-Universitaet Goettingen
Justus-von-Liebig-Weg 11
37077 Goettingen

phone: 0551-39-14074
e-mail: [EMAIL PROTECTED]

Re: [ccp4bb] MrBUMP error

[Derek Logan]

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/python2.7/locale.py

and comment out lines 576-579, i.e.

#if locale and type(locale) is not type(""):
## convert to string
#locale = normalize(_build_localename(locale))
#return _setlocale(category, locale)

 I don't know if this is the most elegant solution, but it works and it doesn't 
seem to break anything else.

/Derek

On 5 Sep 2017, at 13:17, Nishant Varshney 
mailto:nik...@gmail.com>> wrote:

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
#CCP4I DATE 01 Sep 2017  15:58:19
#CCP4I USER apple
#CCP4I PROJECT Josephin
#CCP4I JOB_ID 45
#CCP4I SCRATCH /tmp/apple
#CCP4I HOSTNAME Apples-iMac.local
#CCP4I PID 933

http_proxy not specified in environemnt
***
* Information from CCP4Interface script
***
The program run with command: /Applications/ccp4-7.0/bin/mrbump HKLIN 
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1.mtz SEQIN 
/Users/apple/Documents/Nishant/Josephin_data/Phenix/Q15040.fasta HKLOUT 
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1_mrbump_soln1.mtz
 XYZOUT 
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1_mrbump_soln1.pdb
 KEYIN /tmp/apple/Josephin_45_1_com.tmp
has failed with error message
Traceback (most recent call last):
  File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 162, in _run_module_as_main
"__main__", fname, loader, pkg_name)
  File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 72, in _run_code
exec code in run_globals
  File "/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in 
import MRBUMP_master
  File 
"/Applications/ccp4-7.0/share/mrbump/include/initialisation/MRBUMP_master.py", 
line 17, in 
import Matches
  File "/Applications/ccp4-7.0/share/mrbump/include/structures/Matches.py", 
line 29, in 
import Write_MR_results
  File 
"/Applications/ccp4-7.0/share/mrbump/include/output/Write_MR_results.py", line 
20, in 
import printTable
  File "/Applications/ccp4-7.0/share/mrbump/include/output/printTable.py", line 
5, in 
locale.setlocale(locale.LC_NUMERIC, "")
  File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py",
 line 579, in setlocale
return _setlocale(category, locale)
locale.Error: unsupported locale setting
***


#CCP4I TERMINATION STATUS 0 "Traceback (most recent call last):   File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 162, in _run_module_as_main "__main__", fname, loader, pkg_name)   
File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 72, in _run_code exec code in run_globals   File 
"/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in  
import MRBUMP_master   File 
"/Applications/ccp4-7.0/share/mrbump/include/initialisation/MRBUMP_master.py", 
line 17, in  import MatchesFile 
"/Applications/ccp4-7.0/share/mrbump/include/structures/Matches.py", line 29, 
in  import Write_MR_results   File 
"/Applications/ccp4-7.0/share/mrbump/include/output/Write_MR_results.py", line 
20, in  import printTable   File 
"/Applications/ccp4-7.0/share/mrbump/include/output/printTable.py", line 5, in 
 locale.setlocale(locale.LC_NUMERIC, "")   File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py",
 line 579, in setlocale return _setlocale(category, locale) locale.Error: 
unsupported locale setting"
#CCP4I TERMINATION TIME 01 Sep 2017  15:58:20
#CCP4I TERMINATION OUTPUT_FILES   
/Users/apple/Documents/Nishant/Josephin_data/ccp4/search_45
#CCP4I MESSAGE Task failed


Looking forward for your help

Regards
Nishant

--
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477
Mob: 8390564690
<45_mrbump.log>

Re: [ccp4bb] MrBUMP error

[Nishant Varshney]

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"
worked for me.


many thanks

Nishant



On Wed, Oct 25, 2017 at 1:23 PM, Derek Logan  wrote:

> 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/python2.7/locale.py
>
> and comment out lines 576-579, i.e.
>
> #if locale and type(locale) is not type(""):
> ## convert to string
> #locale = normalize(_build_localename(locale))
> #return _setlocale(category, locale)
>
>  I don't know if this is the most elegant solution, but it works and it
> doesn't seem to break anything else.
>
> /Derek
>
> On 5 Sep 2017, at 13:17, Nishant Varshney  wrote:
>
> 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
> #CCP4I DATE 01 Sep 2017  15:58:19
> #CCP4I USER apple
> #CCP4I PROJECT Josephin
> #CCP4I JOB_ID 45
> #CCP4I SCRATCH /tmp/apple
> #CCP4I HOSTNAME Apples-iMac.local
> #CCP4I PID 933
>
> http_proxy not specified in environemnt
> 
> ***
> * Information from CCP4Interface script
> 
> ***
> The program run with command: /Applications/ccp4-7.0/bin/mrbump HKLIN
> /Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1.mtz
> SEQIN /Users/apple/Documents/Nishant/Josephin_data/Phenix/Q15040.fasta
> HKLOUT /Users/apple/Documents/Nishant/Josephin_data/ccp4/
> XDS_ASCII_scaled1_mrbump_soln1.mtz XYZOUT /Users/apple/Documents/
> Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1_mrbump_soln1.pdb KEYIN
> /tmp/apple/Josephin_45_1_com.tmp
> has failed with error message
> Traceback (most recent call last):
>   File "/Applications/ccp4-7.0/Frameworks/Python.framework/
> Versions/2.7/lib/python2.7/runpy.py", line 162, in _run_module_as_main
> "__main__", fname, loader, pkg_name)
>   File "/Applications/ccp4-7.0/Frameworks/Python.framework/
> Versions/2.7/lib/python2.7/runpy.py", line 72, in _run_code
> exec code in run_globals
>   File "/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in
> 
> import MRBUMP_master
>   File 
> "/Applications/ccp4-7.0/share/mrbump/include/initialisation/MRBUMP_master.py",
> line 17, in 
> import Matches
>   File "/Applications/ccp4-7.0/share/mrbump/include/structures/Matches.py",
> line 29, in 
> import Write_MR_results
>   File 
> "/Applications/ccp4-7.0/share/mrbump/include/output/Write_MR_results.py",
> line 20, in 
> import printTable
>   File "/Applications/ccp4-7.0/share/mrbump/include/output/printTable.py",
> line 5, in 
> locale.setlocale(locale.LC_NUMERIC, "")
>   File "/Applications/ccp4-7.0/Frameworks/Python.framework/
> Versions/2.7/lib/python2.7/locale.py", line 579, in setlocale
> return _setlocale(category, locale)
> locale.Error: unsupported locale setting
> 
> ***
>
>
> #CCP4I TERMINATION STATUS 0 "Traceback (most recent call last):   File
> "/Applications/ccp4-7.0/Frameworks/Python.framework/
> Versions/2.7/lib/python2.7/runpy.py", line 162, in _run_module_as_main
>   "__main__", fname, loader, pkg_name)   File "/Applications/ccp4-7.0/
> Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line
> 72, in _run_code exec code in run_globals   File
> "/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in 
> import MRBUMP_master   File "/Applications/ccp4-7.0/share/
> mrbump/include/initialisation/MRBUMP_master.py", line 17, in 
> import MatchesFile "/Applications/ccp4-7.0/share/
> mrbump/include/structures/Matches.py", line 29, in  import
> Write_MR_results   File "/Applications/ccp4-7.0/share/
> mrbump/include/output/Write_MR_results.py", line 20, in 
> import printTable   File "/Applications/ccp4-7.0/share/
> mrbump/include/output/printTable.py", line 5, in 
> locale.setlocale(locale.LC_NUMERIC, "")   File "/Applications/ccp4-7.0/
> Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py", line
> 579, in setlocale return _setlocale(category, locale) locale.Error:
> unsupported locale setting"
> #CCP4I TERMINATION TIME 01 Sep 2017  15:58:20
> #CCP4I TERMINATION OUTPUT_FILES   /Users/apple/Documents/
> Nishant/Josephin_data/ccp4/search_45
> #CCP4I MESSAGE Task fai

Re: [ccp4bb] MrBUMP in CCP4I2

[Christian Roth]

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 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 the students
> solving the thaumatin structure using two different search models with
> higher and lower sequence identity, which involves specifying them
> individually. The advantage of using MrBUMP is that the students don't have
> to do a separate step with Chainsaw or Sculptor. What's more, we do one run
> with and one run without automated model building and refinement for each
> model to compare the final results. CCP4I2 doesn't seem to offer any of
> these options.
>
> Of course I can run the tutorial using CCP4I but I was trying to
> "modernise" it a bit.
>
> Any advice is welcome
> Derek
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] MrBUMP in CCP4I2

[Derek Logan]

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 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 
mailto:derek.lo...@biochemistry.lu.se>> wrote:
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 the students solving 
the thaumatin structure using two different search models with higher and lower 
sequence identity, which involves specifying them individually. The advantage 
of using MrBUMP is that the students don't have to do a separate step with 
Chainsaw or Sculptor. What's more, we do one run with and one run without 
automated model building and refinement for each model to compare the final 
results. CCP4I2 doesn't seem to offer any of these options.

Of course I can run the tutorial using CCP4I but I was trying to "modernise" it 
a bit.

Any advice is welcome
Derek


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[ccp4bb] MrBUMP for cryo-EM

[Schreuder, Herman /DE]

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 way to point MrBUMP 
to an internal mirror of the pdb?

Thank you for your help,
Herman




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Re: [ccp4bb] MrBump Behaves Strangely

[Ronan Keegan]

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 it 
does process the search models in parallel so it can be a lot quicker 
than running MrBUMP locally.


Best wishes,

Ronan


On 03/02/15 17:22, Keller, Jacob wrote:

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 ceased changing. Nevertheless, the 
process continues on 2 cores and 800 MB RAM as phaser.exe.

Is something broken here, maybe phaser has gone incognito mode, or something 
else? It's happened the last few days any time I've tried to run MrBump. Any 
thoughts?

...And please spare me any parathyrophobia--we don't need to beat that dead 
horse!

JPK



***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

[ccp4bb] MrBUMP version 0.4.0 release

[Ronan Keegan]

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 form part of the upcoming 6.1 release of 
CCP4. We are grateful to Wanjuan (Wendy)Yang and Peter Briggs for 
letting us include it in MrBUMP.

- Support for installing the scripts on Windows.
- Removed the requirement for inputting an MTZ file when running in 
"Model generation only" mode. Sequence file is all that is required now.


Kind regards,

Ronan and Martyn

[ccp4bb] MrBUMP, P43212 and P41212

[Miguel Ortiz Lombardía]

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 pointers?)

Thank you!


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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[ccp4bb] mrBUMP - proxy to internet

[sajid akthar]

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/

Re: [ccp4bb] MrBump Installation ccp4

[Ronan Keegan]

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 that CCP4 is set up correctly.


Kind regards,

Ronan


Daniel Wohlwend wrote:

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 ClustalW did not
oppose a problem.  Can anybody help us? Where do we have to put Fasta35 in
order to continue the installation of MrBump? Or is something possibly wrong
with the permissions (global or local)?
If anyone has an idea, please let us know!
Thanks a lot in advance!

Daniel

Daniel Wohlwend
GZMB Abt. für molekulare Strukturbiologie
Georg-August-Universitaet Goettingen
Justus-von-Liebig-Weg 11
37077 Goettingen

phone: 0551-39-14074
e-mail: [EMAIL PROTECTED]

  

[ccp4bb] MrBUMP not running after update

[jie liu]

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 SEQIN
/home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/seq.seq HKLOUT
/home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c_mrbump_soln1.mtz
XYZOUT
/home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c_mrbump_soln1.pdb
has failed with error message
Traceback (most recent call last):
 File "/usr/local/ccp4-6.4.0/bin/mrbump", line 107, in 
   queue = master.fast_search_MR(init, target_info, mstat)
 File
"/usr/local/ccp4-6.4.0/share/mrbump/include/initialisation/MRBUMP_master.py",
line 482, in fast_search_MR
   ps.get_top_hit(mstat.sorted_MR_list, init, mstat)
 File "/usr/local/ccp4-6.4.0/share/mrbump/include/structures/Matches.py",
line 1431, in get_top_hit
   CHAIN=mstat.chain_list[chain]
KeyError: '1e6j_p2'

It was running fine with CCP4-6.3. Could someone help please?

Thanks!

Jie

[ccp4bb] MrBump doesn't work (6.4.0 update)

[Eze Chivi]

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.
Thank you
 
Ezequiel
  

Re: [ccp4bb] MrBUMP for cryo-EM

[Gildea, Richard (DLSLtd,RAL,LSCI)]

"PDBLOCAL " should do exactly what you want:

https://www.ccp4.ac.uk/html/mrbump.html#pdblocal-directory

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
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://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 way to point MrBUMP 
to an internal mirror of the pdb?



Thank you for your help,

Herman





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Re: [ccp4bb] MrBUMP for cryo-EM

[Adam Simpkin]

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 in the cryo-EM mode. 

Best wishes, 

Adam



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Re: [ccp4bb] MrBUMP, P43212 and P41212

[martyn . winn]

I thought so too  It seems to me that there is a typo in the spacegroup 
name in the code. I'll send you some fixed files offline.

Ronan is the expert on queueing systems, but I though the keyword "CLUSTER" 
should be enough. It is supposed to work with SGE. There also 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.AC.UK
> Subject: [ccp4bb] MrBUMP, P43212 and P41212
> 
> 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 pointers?)
> 
> Thank you!
> 
> 
> --
> Miguel
> 
> Architecture et Fonction des Macromolécules Biologiques (UMR6098)
> CNRS, Universités d'Aix-Marseille I & II
> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
> Tel: +33(0) 491 82 55 93
> Fax: +33(0) 491 26 67 20
> mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
> http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
> 
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.

Re: [ccp4bb] MrBUMP not running after update

[Ronan Keegan]

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 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 SEQIN
/home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/seq.seq HKLOUT
/home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c_mrbump_soln1.mtz 


XYZOUT
/home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c_mrbump_soln1.pdb 


has failed with error message
Traceback (most recent call last):
 File "/usr/local/ccp4-6.4.0/bin/mrbump", line 107, in 
   queue = master.fast_search_MR(init, target_info, mstat)
 File
"/usr/local/ccp4-6.4.0/share/mrbump/include/initialisation/MRBUMP_master.py", 


line 482, in fast_search_MR
   ps.get_top_hit(mstat.sorted_MR_list, init, mstat)
 File "/usr/local/ccp4-6.4.0/share/mrbump/include/structures/Matches.py",
line 1431, in get_top_hit
   CHAIN=mstat.chain_list[chain]
KeyError: '1e6j_p2'

It was running fine with CCP4-6.3. Could someone help please?

Thanks!

Jie




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Re: [ccp4bb] MrBUMP not running after update

[jie liu]

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 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 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 SEQIN
/home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/seq.seq HKLOUT
/home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c_mrbump_soln1.mtz
XYZOUT
/home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c_mrbump_soln1.pdb
has failed with error message
Traceback (most recent call last):
 File "/usr/local/ccp4-6.4.0/bin/mrbump", line 107, in 
   queue = master.fast_search_MR(init, target_info, mstat)
 File
"/usr/local/ccp4-6.4.0/share/mrbump/include/initialisation/MRBUMP_master.py",
line 482, in fast_search_MR
   ps.get_top_hit(mstat.sorted_MR_list, init, mstat)
 File "/usr/local/ccp4-6.4.0/share/mrbump/include/structures/Matches.py",
line 1431, in get_top_hit
   CHAIN=mstat.chain_list[chain]
KeyError: '1e6j_p2'

It was running fine with CCP4-6.3. Could someone help please?

Thanks!

Jie




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Re: [ccp4bb] MrBump doesn't work (6.4.0 update)

[Marjolein Thunnissen]

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 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.
Thank you

Ezequiel

[cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC]




Marjolein Thunnissen
Science Coordinator MX

MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Ole Römers väg 1, 223 63 Lund
Telephone: +46 766 32 04 17
www.maxlab.lu.se

Re: [ccp4bb] MrBump doesn't work (6.4.0 update)

[Ronan Keegan]

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 
search performed in the older MrBUMP. You can access it here:


www.ccp4.ac.uk/ccp4online

Best wishes,

Ronan

On 19/08/14 12:22, Marjolein Thunnissen wrote:

Hii Ronan,

Hi,

Embarrassingly enough, my problem has disappeared...I guess indeed it 
was the update, as I updated ccp4 today and now I tried and it works!


Thanks!

Marjolein


On 19 Aug 2014, at 12:28, Ronan Keegan > 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.)? Also us your CCP4 installation completely up to date? There 
should 20 updates in total installed. The last one has some important 
fixes for MrBUMP.


Best wishes,

Ronan

On 19/08/14 09:28, Marjolein Thunnissen wrote:

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 > wrote:


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.

Thank you

Ezequiel



*



**Marjolein Thunnissen*
Science Coordinator MX

MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Ole Römers väg 1, 223 63 Lund
Telephone: +46 766 32 04 17
www.maxlab.lu.se 




--
Scanned by iCritical.




*



**Marjolein Thunnissen*
Science Coordinator MX

MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Ole Römers väg 1, 223 63 Lund
Telephone: +46 766 32 04 17
www.maxlab.lu.se 




--
Scanned by iCritical.

[ccp4bb] AW: [ccp4bb] MrBUMP for cryo-EM

[Schreuder, Herman /DE]

Hi Adam,

Thank you for your response. Using the pdblocal keyword, I was able to run 
MrBUMP. Also the cryo keyword was recognized, but then the mode of operation 
was set to "MODELS" and only search models were generated. From your email, I 
understand that I will have to wait for ccp4 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 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 in the cryo-EM mode.

Best wishes,

Adam



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Re: [ccp4bb] AW: [ccp4bb] MrBUMP for cryo-EM

[Adam Simpkin]

Hi Herman, 

That's correct!

- Adam



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[ccp4bb] MrBump and Balbes Molecular Replacement of multiple copies in ASU Failed even with high homology model

[Alex Lee]

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  Matthews Coeff  %solvent   P(2.49) P(tot)

_

  126.0795.29 0.00 0.00

  213.0490.57 0.00 0.00

  3 8.6985.86 0.00 0.00

  4 6.5281.14 0.00 0.00

  5 5.2176.43 0.00 0.00

  6 4.3571.71 0.00 0.01

  7 3.7267.00 0.02 0.02

  8 3.2662.28 0.05 0.05

  9 2.9057.57 0.11 0.11

 10 2.6152.85 0.19 0.19

 11 2.3748.14 0.25 0.25

 12 2.1743.42 0.22 0.22

 13 2.0138.71 0.11 0.12

 14 1.8633.99 0.03 0.03

 15 1.7429.28 0.00 0.00

 16 1.6324.56 0.00 0.00

 17 1.5319.85 0.00 0.00

 18 1.4515.13 0.00 0.00

 19 1.3710.42 0.00 0.00

 20 1.30 5.70 0.00 0.00

 21 1.24 0.99 0.00 0.00

_


I have at least 10 structures in PDB with homology 60% or above.

I tried the CCP4online MrBump and Balbes for automatic molecular
replacement. No solutions at all.

I do not know if this is because that the high number of copies in ASU
(maybe 10 copies as shown by Mathew coefficient) hamper the MrBump and
Balbes to do MR?


Dose anyone experience similar difficulties with high number of copies to
do automatic MR?


Thanks ahead!

Re: [ccp4bb] MrBump and Balbes Molecular Replacement of multiple copies in ASU Failed even with high homology model

[Randy Read]

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 to make an ensemble in which 
loops that deviate among the different models have been trimmed off.

If you need more advice on how to do this, you can get in touch off-line.

Best wishes,

Randy Read

-
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

> On 31 Oct 2016, at 18:16, Alex Lee  wrote:
> 
> 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  Matthews Coeff  %solvent   P(2.49) P(tot)
> _
>   126.0795.29 0.00 0.00
>   213.0490.57 0.00 0.00
>   3 8.6985.86 0.00 0.00
>   4 6.5281.14 0.00 0.00
>   5 5.2176.43 0.00 0.00
>   6 4.3571.71 0.00 0.01
>   7 3.7267.00 0.02 0.02
>   8 3.2662.28 0.05 0.05
>   9 2.9057.57 0.11 0.11
>  10 2.6152.85 0.19 0.19
>  11 2.3748.14 0.25 0.25
>  12 2.1743.42 0.22 0.22
>  13 2.0138.71 0.11 0.12
>  14 1.8633.99 0.03 0.03
>  15 1.7429.28 0.00 0.00
>  16 1.6324.56 0.00 0.00
>  17 1.5319.85 0.00 0.00
>  18 1.4515.13 0.00 0.00
>  19 1.3710.42 0.00 0.00
>  20 1.30 5.70 0.00 0.00
>  21 1.24 0.99 0.00 0.00
> _
> 
> I have at least 10 structures in PDB with homology 60% or above.
> I tried the CCP4online MrBump and Balbes for automatic molecular replacement. 
> No solutions at all.
> I do not know if this is because that the high number of copies in ASU (maybe 
> 10 copies as shown by Mathew coefficient) hamper the MrBump and Balbes to do 
> MR?
> 
> Dose anyone experience similar difficulties with high number of copies to do 
> automatic MR?
> 
> Thanks ahead!

Re: [ccp4bb] MrBump and Balbes Molecular Replacement of multiple copies in ASU Failed even with high homology model

[Eleanor Dodson]

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, Randy Read  wrote:

> 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 to make an
> ensemble in which loops that deviate among the different models have been
> trimmed off.
>
> If you need more advice on how to do this, you can get in touch off-line.
>
> Best wishes,
>
> Randy Read
>
> -
> 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 Road
> E-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> > On 31 Oct 2016, at 18:16, Alex Lee  wrote:
> >
> > 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  Matthews Coeff  %solvent   P(2.49) P(tot)
> > _
> >   126.0795.29 0.00 0.00
> >   213.0490.57 0.00 0.00
> >   3 8.6985.86 0.00 0.00
> >   4 6.5281.14 0.00 0.00
> >   5 5.2176.43 0.00 0.00
> >   6 4.3571.71 0.00 0.01
> >   7 3.7267.00 0.02 0.02
> >   8 3.2662.28 0.05 0.05
> >   9 2.9057.57 0.11 0.11
> >  10 2.6152.85 0.19 0.19
> >  11 2.3748.14 0.25 0.25
> >  12 2.1743.42 0.22 0.22
> >  13 2.0138.71 0.11 0.12
> >  14 1.8633.99 0.03 0.03
> >  15 1.7429.28 0.00 0.00
> >  16 1.6324.56 0.00 0.00
> >  17 1.5319.85 0.00 0.00
> >  18 1.4515.13 0.00 0.00
> >  19 1.3710.42 0.00 0.00
> >  20 1.30 5.70 0.00 0.00
> >  21 1.24 0.99 0.00 0.00
> > _
> >
> > I have at least 10 structures in PDB with homology 60% or above.
> > I tried the CCP4online MrBump and Balbes for automatic molecular
> replacement. No solutions at all.
> > I do not know if this is because that the high number of copies in ASU
> (maybe 10 copies as shown by Mathew coefficient) hamper the MrBump and
> Balbes to do MR?
> >
> > Dose anyone experience similar difficulties with high number of copies
> to do automatic MR?
> >
> > Thanks ahead!
>

Re: [ccp4bb] MrBump and Balbes Molecular Replacement of multiple copies in ASU Failed even with high homology model

[zaigham mahmood khan]

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 othewrwise.
I assume that you considered removing the flexible loops and variable side
chains of the homologous protein before declaring it as a search model.

All the best

Zaigham
On Nov 1, 2016 06:24, "Eleanor Dodson"  wrote:

> 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, Randy Read  wrote:
>
>> 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 to make an
>> ensemble in which loops that deviate among the different models have been
>> trimmed off.
>>
>> If you need more advice on how to do this, you can get in touch off-line.
>>
>> Best wishes,
>>
>> Randy Read
>>
>> -
>> 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 Road
>> E-mail: rj...@cam.ac.uk
>> Cambridge CB2 0XY, U.K.
>> www-structmed.cimr.cam.ac.uk
>>
>> > On 31 Oct 2016, at 18:16, Alex Lee  wrote:
>> >
>> > 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  Matthews Coeff  %solvent   P(2.49) P(tot)
>> > _
>> >   126.0795.29 0.00 0.00
>> >   213.0490.57 0.00 0.00
>> >   3 8.6985.86 0.00 0.00
>> >   4 6.5281.14 0.00 0.00
>> >   5 5.2176.43 0.00 0.00
>> >   6 4.3571.71 0.00 0.01
>> >   7 3.7267.00 0.02 0.02
>> >   8 3.2662.28 0.05 0.05
>> >   9 2.9057.57 0.11 0.11
>> >  10 2.6152.85 0.19 0.19
>> >  11 2.3748.14 0.25 0.25
>> >  12 2.1743.42 0.22 0.22
>> >  13 2.0138.71 0.11 0.12
>> >  14 1.8633.99 0.03 0.03
>> >  15 1.7429.28 0.00 0.00
>> >  16 1.6324.56 0.00 0.00
>> >  17 1.5319.85 0.00 0.00
>> >  18 1.4515.13 0.00 0.00
>> >  19 1.3710.42 0.00 0.00
>> >  20 1.30 5.70 0.00 0.00
>> >  21 1.24 0.99 0.00 0.00
>> > _
>> >
>> > I have at least 10 structures in PDB with homology 60% or above.
>> > I tried the CCP4online MrBump and Balbes for automatic molecular
>> replacement. No solutions at all.
>> > I do not know if this is because that the high number of copies in ASU
>> (maybe 10 copies as shown by Mathew coefficient) hamper the MrBump and
>> Balbes to do MR?
>> >
>> > Dose anyone experience similar difficulties with high number of copies
>> to do automatic MR?
>> >
>> > Thanks ahead!
>>
>
>