Dear users,
I was trying to process a C2221 data in two different versions
of imosflm (7.0.4 and 7.0.7) using same set of frames, later on
scaled using scala in ccp4 6.1.2. But for m surprise the statistics
were quite different in two cases:
In case of 7.0.4:
Ove
Dear users,
Can the optimization of the X-ray weighing factor
and B-factor (overall wt) as mentioned in the paper
Acta Cryst. (2007). D63, 12741281 by Dr.Ian Tickel,
be used for the refinement of the data sets beyond
the resolution range mentioned in the paper: 1.33 -
2.55 Ang?
Also the structur
bulletin board
Date: 10/14/2011 12:34PM
Subject: Re: [ccp4bb] Optimisation of weights
Hi Kavya
The resolutions of the structures mentioned in the paper were only
examples, the Rfree/-LLfree minimisation method (which are actually
due to Axel Brunger & Gerard Bric
Respected Sir,
For one of the structures that I did optimisation
had values - (resolution of the data - 2.35Ang)
Before optimization- (Bfactor weight=1.0, X-ray Weight - auto)
R factor 0.2362
R free0.2924
-LLfree 7521.8
rmsBOND 0.0160
zBOND 0.660
After optimisation- (B-factor weight
Respected Sir,
Yes, the weight mentioned in the paper was
weight matrix, but the one i used was the
option under "Refinement parameters- weighing
term (when auto weighing is turned off)".
But If I really wasnt to change the weight matrix
where should I change (in the code?)?
No, I dint mean a big
Respected Sir,
I am sorry I wrote it wrongly, its resolution-
independent X-ray weight rather. I use ccp4i
so the input for the weight is what i mentioned
previously-
"Refinement parameters- weighing term (when
auto weighing is turned off)" in refmac.
Thanking you
With Regads
M. Kavyashree
-I
possibility?
Thanking you
With Regards
Kavya
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mpared twinned
structure with those two structures it does not vary much.
> Hope this helps
> cheers
> Padayatti PS
>
With Regards
Kavya
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a dimer in asu which are related by a 2 fold,
so there was no indication of any pseudo translation and protein
is bound to 10-12 cadmiums. Could this off origin peak be due to the
presence of the heavy atoms? how can i rule out the presence of this
pseudotranslation as indicated in sfcheck?
Thanking
> this can screw up your statistics on twinning and this can be due to
> the NCS rotation
> axis (or will be based on what you say) parallel to a crystallographic
> symmetry axis.
> just check that. it should still refine though but this will have
> opposite effect to twinning,
> so it can be probl
Dear users,
I have refined a structure in R3 with cadmium bound to it, which
was present in the crystallization condition. There are 2 chains
in the asu. The structure is twinned. R and Rfree is around 22% and
28%. One of the cadmium has extremely high B-factor of 127, I tried
replacing it with
Dear Sir,
The resolution is 2.35Ang. I was trying to refine Cadmium
occupancy using the option of "SAD data directly" in refmac (as it
cadmium gives anomalous signal at 1.54179 wavelength) and then use
the obtained occupancy of those atoms to refine in usual way. It
used to to refine occupanci
Dear Sir,
I have labeled it rightly. When I was trying to refine
using the method I mentioned it was giving some less than 1
while some more than 1 as occupancy. I am trying to match with
the peaks now.
Thanking you
With regards
M. Kavyashree
> Dear Kavyashree,
>
> Did you properly label the
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