Dear Niu,
To me, it looks like random density. Since coot contours are based on sigma
levels, you will always see features. I do not think you can do anything with
your current map. As others have said, it is always a good idea to test ALL
possible space groups, even if you are convinced it is
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Dear all,
I am sorry about this 'double' post, but I had no reply on ccp4bb-dev
within about three weeks.
I wonder if I was the only one using the ccp4 man-pages. They were
available until ccp4-6.3 but seem to be absent in the latest version.
I
The 95% off-origin peak in the Patterson might be telling you that the true
space group has a centering operation that was missed, or the cell was doubled,
in the indexing step (i.e. systematically absent spots are being indexed and
integrated). If the zeros for systematically absent spots are
Dear Niu,
I had an interesting pseudo-translation case recently where my off-origin peak
was located near the centre of the unit cell (fractions a=0.5, b=0.46, c=0.5)
of a P222 symmetry. Processing and phasing in P222 looked reasonable and the
model could be built. I had background density
I agree completely with Tim: I use 'man' (or 'info' for gfortran the
like) all the time - but then I'm a die-hard command-liner/shell-scripter
who never uses ccp4i! I haven't got around to installing 6.4 yet but if
when I do I find the man pages missing as Tim says I'll probably copy
over the
Dear CCP4 users,
After last update of CCP4 package for Windows (I work on Win8.1) I found
some error during use of aimless with ctruncate. The output from log looks
like this:
***
* Information from CCP4Interface script
(assuming of course the .doc files aren't also missing).
CDOC: Undefined variable.
[berry@sbserv ~]$ ls $CCP4/doc
ls: cannot access /sw/lnx/ccp4-6.4.0/doc: No such file or directory
I second the request for continued man pages and .doc files
Ian Tickle wrote:
I agree completely with Tim: I
AFAICS the .doc files look as if they were auto-generated from the .html files
in 6.3.0. Certainly the only documentation I have written for Pointless and
Aimless is in html
Phil
On 15 Nov 2013, at 14:33, Edward A. Berry ber...@upstate.edu wrote:
(assuming of course the .doc files aren't
Many, many years ago, the man pages used to be nroff-formatted .1 files. We
converted these to html files, and used lynx to automatically generate ASCII
.doc files which could be used as man pages. AFAIK this is still the case.
I mention this in case anyone wants to get nostalgic about
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Dear Martyn,
thanks for the hint about lynx. I could create the 'man'-pages with
# cd $CHTML
# mkdir ../doc
# for i in *.html; do lynx -dump $i ../doc/${i%html}doc; done
# bash makeman.sh
That's good enough for me.
Regards,
Tim
On 11/15/2013
Yes, that's more or less what we do/did. It was in a makefile somewhere.
Cheers
Martyn
-Original Message-
From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de]
Sent: 15 November 2013 15:00
To: Winn, Martyn (STFC,DL,SC)
Cc: ccp4bb
Subject: Re: [ccp4bb] ccp4 man-pages
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It may be helpful to add some information during index. HKL2000 could find
four reasonable solutions:
40, 32, 101, 90, 101, 90 for P1 and P2
200, 40, 32, 90, 90, 90 for C2 and C222
It looks very strange to me since these two unit cells look differently,
but during refinement the predicated spots
Hi Folks,
As many of you may know, Andy Torelli and I have been co-chairing sessions at
the yearly American Crystallographic Association meetings that deal with the
nuts and bolts about how to determine crystal structures. Next May in
Albuquerque, NM, we are hosting a session called
The 47th Course of the International School of Crystallography: Structural
Basis of Pharmacology: Deeper Understanding of Drug Discovery through
Crystallography will be held in Erice (Italy) May 30 - June 8, 2014. More
details are available below. An up-to-date program can be found in the
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