Hi Bernhard CCP4bb
The pre-1998 CCP4 Study Weekend Proceedings are available from the
Daresbury Lab e-pubs (electronic publications, for those not familiar
with e-speak) system via:
http://epubs.cclrc.ac.uk/search?st=browse-by-serials=1764
(I checked and the one Ian mentions is there).
1) You dont say whether there is a non crystallographic translation
vector - if that is so the twinning statistics can be misleading.
SFCHECK analyses this or you can just run a native patterson to 4A say
and see if there is an off-origin peak.
2) The twinning tests that use the correlation
Hi,
Any one has topology and parameter files for RNA cap 5'-5' triphosphate
linkage for CNS refinement ? Already get MGT to define the cap, how to
define the 5'-5' linkage from MGT to RNA? Thanks.
Hongmin
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I have a mtz file (output from phenix AutoSol and AutoBuild) where the
FreeR flag for the test set has a value of 1 and and the working set
has value 0. This is opposite to the ccp4 default where the FreeR set
used within refinement is flagged as 0. Is there a way to swap the two
around so
Hi Petra,
You can use sftools, to set the FreeR_flag column
to be the old ((FreeR_flag - 1)*-1 ) e.g.
sftoos eof
read myfile.mtz
calc col FreeR_flag = col FreeR_flag 1 - -1 *
write free-R-swap-1-0.mtz
quit
eof
Regards,
Mitch
-Original Message-
From: CCP4 bulletin board
Hi,
Just to explaine: it is assumed that if you came from using phenix
AutoSol and AutoBuild then for refinement you use phenix.refine
(refinement program in PHENIX). phenix.refine uses 1 for TEST and 0 for
WORK (similar to CNS). It is not clear to me at all why you need to do
the swap.
Dear Petra,
the following shell script should do the job.
best wishes
James
#!/bin/bash
input=input.mtz
oldfreer=FREE
newfreer=NEWFREE
sftools EOF
read
${input}
calc W col ${newfreer} = -1 col ${oldfreer} -1 + *
write
${input%\.mtz}_newfreer.mtz
STOP
EOF
Dr. James Murray
Hi,
The assumption is hard to understand. We are thankful to the community who
are developing the great programs (and teaching), and with limited
experience, I think it is good to have choices. So, thanks also to people
who provide such scripts.
If we have to convert file formats, then whats
You are absolutely right. Although the idea in my message was that if
you are in certain environment and do something in that environment then
it's kind of natural to expect the output features are related to that
environment. Example? I wouldn't be very frustrated if CNS refuses to
read in
