Hi Kelly
How about the 'echo-pipe' syntax, e.g.:
echo 'outp xplor\nexcl sigp .01\nlabin FP=F-obs SIGFP=SIGF-obs
FREE=R-free-flags' |mtz2various hklin in.mtz hklout out.mtz
(all on 1 line).
Any CCP4 program can be run from the CL in exactly the same way, i.e.
separate the program input lines wit
Yes, you are correct, mtz_to_cns is calling up mtz2various.
I have tried many alternatives for the label for Rfree flag with no success.
I have also tried just asking for F and SIGF, and the output does not
contain Rfree.
The next step would be to use make_cv.inp to generate a test test.
I want to
When I was using BALBES, I had to download everything manually from the server,
one by one. However, you do have the option of running BALBES from within ccp4,
which will automatically save all of the files to a local folder .
If all you want are the files needed to continue refinement, then yo
mtz_to_cns calls mtz2various as far as I know.
If mtz2various works for you then you can use it directly. It too can be
run from the commandline. Look for the 'View Files from Job' --> 'View
Command Script' in the GUI to get help on syntax or look at the website
under examples (http://www.ccp4.
Is there any way to download all of the files produced by a BALBES run
on YSBL server at once (as opposed to going through every item
individually)?
A related question is what is a minimal set of files I will actually
need to analyze the solution? refmac_final_result.* and summary.log -
is that
Hello all,
I am been unsuccessful in converting my mtz file into cns format and
bringing along my R-free reflections.
The interwebs tells me that the label should be FREE=label
So, on the command line I type:
mtz_to_cns hklin hklout F=F-obs SIGF=SIGF-obs FREE=R-free-flags
Yet I am always returne
Dear All,
Ruben Abagyan & I will be presenting a 2-day workshop in San Diego/La Jolla
June 16-17. Excellent excuse for a trip to Sea World, the Zoo, the USS
Midway,
or the Balboa Park model railroad (my favorite).
http://www.ruppweb.org/workshops/Molsoft_2011.htm
Best, BR
On 27 Apr 2011, at 15:02, Edward A. Berry wrote:
> No, that would be the TABFUN step. You are running SORTFUN which takes your
> experimental data and puts in the the .tab format required by the subsequent
> routines. And with the HKLIN command line variable you are telling it to
> get data from A
Agree with Tim's idea. Generating a composite omit map to see if your
solution is correct (or at least some part is correct if conformational
difference exists between model and your protein).
Bingfa
-邮件原件-
发件人: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] 代
表 Tim Grue
Chris Richardson wrote:
One of our group was having trouble getting AMoRe to use model coordinates as a
trial model. I've replicated this using the data from the tutorial at
http://www.ccp4.ac.uk/dist/examples/tutorial/html/mr-tutorial-amore.html
It fails using CCP4 6.1.13 on OS 10.6.7 (com
You could try the stand-alone version of AMoRe from Jorge Navaza's web site.
http://mem.ibs.fr/JORGE/index.html
Stefano TRAPANI
Maître de Conférences
Centre de Biochimie Structurale (CBS)
CNRS UMR 5048; UM1; UM2; INSERM UMR 554
29 rue de Navacelles 34090
MONTPELLIER Cedex - France
Tel : +33 (0
One of our group was having trouble getting AMoRe to use model coordinates as a
trial model. I've replicated this using the data from the tutorial at
http://www.ccp4.ac.uk/dist/examples/tutorial/html/mr-tutorial-amore.html
It fails using CCP4 6.1.13 on OS 10.6.7 (compiled from Fink) and Ubuntu
Dear all:
I am dealing with a SHELXL/ BAVERAGE issue.
I have refined a few structures in SHELXL but I think I am not converting
properly the coordinates into the .pdb format. I am trying to use Baverage but
I get an error
The program run with command: baverage XYZIN "C:/datasets/34_MolP.pdb"
Dear Jashin,
do you see any extra density in the map, of unexplained features?
An easy and quick test is to remove some part of the search model, e.g. an
alpha-helix, and recalculate the map. If you do see density for the missing
helix, it is a very promising sign that your solution is correct.
I
Dear all:
A phase ambiguity problem.
After rotation/translation/refinement, the free value junk >0.5.
It seems no significant solution from rf file. INTERESTING, the density map
seems to fit the template very well.
In this case, is the phase still ambiguity or not?
Thank you very much. Any co
> Dear All:
> What does it mean when I get negative values under Anomalous Corr
> column after running XDS? I set the Friedel Law=False even though I
> suspect that my signal is very very weak.
> Thanks
> Subbu
Hi Subbu,
it means that in resolution shells with negative Anomalous Corr the
anomal
Dear Subbu,
it means that you do not have anomalous signal at the corresponding resolution
shell and the correlation between the Bijvoet pairs is rather random.
Cheers, Tim
On Tue, Apr 26, 2011 at 01:24:42PM -0400, Narayanan Ramasubbu wrote:
> Dear All:
> What does it mean when I get negative va
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