Dear all,
First, I am happy that there is am easy solution.
Second, let me clarify that ARP/wARP CCP4i GUI uses standard CCP4i
library functions to read in files etc etc.
I am sorry to get technical, but what I do is simply:
CreateInputFileLine line \ [...lines deleted...]
-setfileparam space_group_name SPACE_GROUP \
thus I am relying to the CCP4i libraries to return to me the correct
space group name when the user reads in a file.
Later on I use the CCP4i library command
set space_group [GetSpaceGroupNumber $array(SPACE_GROUP)]
that is because ARP/wARP programs want to use space group numbers as
input later on.
So, whatever the error is with C121 and P121 is not in ARP/wARP. Very
likely it is in the GetSpaceGroupNumber function of CCP4i.
You can easily check that, since under 'Crystal Parameters' the space
group name should be 'P121', but I suspect that for that
I get a '0' for space group number... (would be good if somebody sends
me such a file so I can check!)
Thus, the 'ARP/wARP people' cannot fix, no matter how willing they
are. However, I would appreciate if
somebody from CCP4 team tells me if there is something wrong in the
code,
or fixes the CCP4i code if it is indeed broken for that function.
Also, yet another solution if anyone runs to this problem, is to run
auto_tracing.sh
from the command line (it will list a choice of needed keywords)
That uses a program by the ARP/wARP team that will figure out the
correct space group number from the symmetry operators of the MTZ file
and it should run in C121 just like C2.
The same is true for the ARP/wARP Hamburg Web Server.
Best -
Tassos
On Dec 1, 2009, at 18:05, Jan Abendroth wrote:
Hi all,
I ran into that several times in the monoclinic space groups. ARP/
wARP does not seem to like the C121 notation, yet likes the C2
notation. Same for P121 vs. P2. Re-assigning the SG eg. in CAD using
the correct notation or the SG number is an easy remedy.
Cheers
Jan
On Tue, Dec 1, 2009 at 8:57 AM, Eleanor Dodson
<c...@ysbl.york.ac.uk> wrote:
One easy suggestion - try buccaneer and refinement!
Eleanor
The Arp/warp people will have to fix this..
Anita Lewit-Bentley wrote:
Dear all,
I have a nice MAD map produced by Sharp and would like to trace a
chain into it using Arp/wArp. When I input the mtz file via the
CCP4i interface, I get the following message:
"Cannot extract ARP/wARP asymmetric unit limits
The job will fail if run"
Well it DOES fail when run!
My space group is C2 (given as C121 in the mtz file header), the mtz
file is a standard structure factor file generated by CAD (adding
Sharp phases to native data which are at a higher resolutino than
the MAD data) and I just don't see what is going wrong.
I am using CCP4 6.1.2 and Arp 7.0.1, with the CCP4Interface version
2.0.5 running on Mac OSX version 10.5.8.
Any advice will be extremely welcome!
Anita
Anita Lewit-Bentley
Unité d'Immunologie Structurale
CNRS URA 2185
Département de Biologie Structurale & Chimie
Institut Pasteur
25 rue du Dr. Roux
75724 Paris cedex 15
FRANCE
Tel: 33- (0)1 45 68 88 95
FAX: 33-(0)1 40 61 30 74
email: ale...@pasteur.fr
--
--
Jan Abendroth
Emerald Biostructures
Seattle / Bainbridge Island, WA, USA
http://www.emeraldbiostructures.com
work: JAbendroth_at_decode.com
home: Jan.Abendroth_at_gmail.com
P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
