James Pauff a écrit :
Hello all,
I have a refined structure at 2.6 angstroms that at about 73% completeness at
this resolution. The I/sigma is about 2.0 at 2.6 angstroms, and the omit
density for my ligands is great contoured at 3.0sigma. My Rcryst is 19 or so
and the Rfree is 24.5 or so.
On 20 Aug 2008, at 8:11, Wim Burmeister wrote:
James Pauff a écrit :
Hello all,
I have a refined structure at 2.6 angstroms that at about 73%
completeness at this resolution. The I/sigma is about 2.0 at 2.6
angstroms, and the omit density for my ligands is great contoured
at 3.0sigma.
Thanks to both, in the end I downloaded the new version of refmac and moved the
characters,
Louise
- Messaggio Originale -
Da: Eleanor Dodson [EMAIL PROTECTED]
Data: Martedi', Agosto 19, 2008 6:00 pm
Oggetto: Re: [ccp4bb] Refmac problems on Mac OS X Leopard
A: Louise Gourlay [EMAIL
Hi Folks,
I have an OS X leopard machine which I would really like to get coot
working on, but it appears to involve messing with the X system and / or
fink, neither of which I really fancy. Now I appreciate that there is
something broken about the X window (no idea what though) but I was
James Pauff wrote:
Hello all,
I have a refined structure at 2.6 angstroms that at about 73% completeness at
this resolution. The I/sigma is about 2.0 at 2.6 angstroms, and the omit
density for my ligands is great contoured at 3.0sigma. My Rcryst is 19 or so
and the Rfree is 24.5 or so.
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Hi,
After running VOIDOO, you will get the log file with cavity volume
information. It has the average volume and the sigma volume information,
but along with that If you look at the end of the log file, you will find
the Cavity volume on plot grid (A3) provided separately. This is the
volume
Winter, G (Graeme) wrote:
I have an OS X leopard machine which I would really like to get coot
working on, but it appears to involve messing with the X system and / or
fink, neither of which I really fancy. Now I appreciate that there is
something broken about the X window (no idea what
Hi Manish,
But then volume is biased by the plot grid size one chooses and not the
converged volume. In short, one isn't even using the results of volume
refinement because one'd get the same answer from the same grid size for the
same orientation (given the same probe radius). Using the final
Hi Manish and everyone,
If one uses the volume on the plot grid size, volume is biased by the plot
grid size one chooses and not the converged volume. In short, one isn't even
using the results of volume refinement because one'd get the same answer
from the same grid size for the same orientation
I just recently purchased a Mac Pro Intel with Leopard. I was able to
install, Coot and ccp4. Both were not as straight forward as I would have
hoped but still possible.
For Coot:
Go to:
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Coot-0.5-pre-1-968_for_Intel_10.5_only
Download :
Hello all, thank you for the responses. Just to clear up a couple of things...
1) My dataset was acquired on a synchrotron and scaled/truncated there. To my
knowledge they used the same procedure as for other structures that we have
obtained there...which have had no B factor issues. Granted,
If I've lost my SCALA MTZ, and have only the truncated.mtz for my dataset,
which program is the quickest means of obtaining a Wilson plot?
Thank you again,
Jim
--- On Wed, 8/20/08, Eleanor Dodson [EMAIL PROTECTED] wrote:
From: Eleanor Dodson [EMAIL PROTECTED]
Subject: Re: [ccp4bb] Lower
What is the reason for lower completeness is important.
1) rotation range is not wide enoughyou lost frames? What about
the completeness against
resolution shell?
2) too many rejections?
a) symmetry error
b) really bad crystal (this seems not the case)
c) too many
If I go back to my SCALA mtz and run 'Truncate', I get a completely different B
value at 27.3, which is obviously much better. However, why did I have to do
this, and where would I find this value at the end of my refinement? i.e. did
I miss a line in PROCHECK or my final REFMAC log file?
On 20 Aug 2008, at 18:24, James Pauff wrote:
Hello all, thank you for the responses. Just to clear up a couple
of things...
1) My dataset was acquired on a synchrotron and scaled/truncated
there. To my knowledge they used the same procedure as for other
structures that we have obtained
Hi Jim
You can just run Truncate again, exactly as you did before, but this
time using your truncated.mtz file as input, since it contains the same
IMEAN/SIGIMEAN columns output by Scala. It will also give you another
output mtz file which should be identical to your input mtz (but I
haven't
Ian,
SHELXL users would also be very happy if mtz files routinely
contained F^2 and its esd, but I had long regarded this as a
lost cause.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or
Truncate output does by default contain I (aka F^2) columns
Phil
On 20 Aug 2008, at 20:25, George M. Sheldrick wrote:
Ian,
SHELXL users would also be very happy if mtz files routinely
contained F^2 and its esd, but I had long regarded this as a
lost cause.
George
Prof. George M. Sheldrick
Hi Phil,
My understanding is that the IMEAN/SIGIMEAN columns output by Truncate
are simply copied over from the input columns as output by Scala
(possibly scaled by the Wilson scale to make them absolute), or have I
got this wrong? If so wouldn't it be better to rename the columns (e.g.
IEXP,
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