Dear Sangeetha,
what you noticed is a bug that appears under particular circumstances.
Sorry for your inconvenience. From your logfile excerpt I think that
this bug has been observed before and been fixed. The next release will
include the fixed version, however useless this might sound to
Dear Garib
Thank you very much as you suggested, I removed SCALE
card in the pdb file, then it is running smothly.
Rajakumara
--- Garib Murshudov ga...@ysbl.york.ac.uk wrote:
It seems that something may be wrong with your input
file.
Specifically with the SCALE card in the pdb file.
Hi we regularly update our intel mac refmac5 ( and ccp4) installs from W.G
. Scotts fink packages
We just add an unusual error with refmac5 v5.5.0066 doing a routine rigid
body refinement.
The program v5.5.0066 seemed to be swapping the beta and gamma angles in the
mtz produced after the
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Hi Sun,
For 2.5A data you can try phenix or arp/warp to autobuild the the model
using the phase form MR ,then you can get the most of model you want if
you are lucky enough or you need more manual bulding or another cycle MR
again .
Good luck!
liu
Sun Tang wrote:
Dear All,
Recently I
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The NIGMS beam line X6A at the National Synchrotron Light Source has recently
replaced its end-station. The beam line now operates a ADSC Q270 CCD detector
and a Crystallogic diffractometer equipped with an air-bearing single rotation
Dear Sun,
if I remember correctly phaser already carries out a rigid body refinement
of its solution.
To avoid and remove as much model bias as possible, I suggest you look at
the solution from phaser and build _as_ _much_ _as_ _possible_ BEFORE you
do any further refinement, i.e., try to
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Dear All,
during processing some mtz files I noted that some programs complete
the reflection list by padding missing reflections.
a) for Refmac (which did not pad reflections automatically) I read that
1) for 2mFo-DFc: Fwt = DFc in case Fo=0
2) for mfo-fc :
I mean *absent* reflections here with fobs=0
Dear All,
during processing some mtz files I noted that some programs complete
the reflection list by padding missing reflections.
a) for Refmac (which did not pad reflections automatically) I read that
1)
On 18 Mar 2009, at 01:47, Bernhard Rupp wrote:
I mean *absent* reflections here with fobs=0
Dear All,
during processing some mtz files I noted that some programs complete
the reflection list by padding missing reflections.
a) for Refmac (which did not pad
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Hi Bernhard,
b) how does PHENIX/refine handle the fobs = 0 reflections in
either case?
phenix.refine outputs two series of maps:
- one pair of (2mFo-DFc, mFo-DFc) maps is computed using original
untouched Fobs;
- and the other pair of (2mFo-DFc, mFo-DFc) maps is computed using
I've found CNS's simulated annealing composite omit maps to be
very useful in situations like this to avoid phase bias. RESOLVE's
prime and switch offers similar functionality, but I've had less
experience with it.
ho
UC Berkeley
Dear All,
Thank you very much for all your suggestions. They are very helpful in my
further refinements. I am adding some more information about the problem:
1) The Z-score is 11.2 and LLG is 125.
2) The model has 390 aa while my structure has about 440 aa.
Please let me know of any further
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