Hello Byron.
byron delabarre wrote:
I'm looking for an easy way in coot to trim residues back to Cbeta.
There is now.
1) Is there an easy way to do this, other than: click mutate, click
residue, click trim to Cb, click mutate to ?
Bleugh!
2) I wrote a script but couldn't get it
Hi -
I'm looking for an easy way in coot to trim residues back to Cbeta. This is
for regions of the structure where there is no or minimal electron density
for side chain location.
1) Is there an easy way to do this, other than: click mutate, click
residue, click trim to Cb, click mutate to xxx
Hi,
everyone, who has much more experience about the 2-D crystallization of
membrane proteins using the dialysis method.
1) how to avoid the change of whole sample's volume after dialysis?
2) can you tell me some tricks during making grids, that is, when we put
dialysis sample on grids,
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On Wednesday 12 March 2008 18:30, Pavel Afonine wrote:
> Hi Martin,
>
> > 2) in the context of PX, only the total "B factor" contribution to
> > Fcalc needs to be positive definite, the TLS component might not be
> > (though it is satisfying if it is)
Correct (if I understand what you mean).
Hello Serge
Thanks for the clarification - in this case I feel fairly confident that
it has already been addressed for the next test release of CCP4 (due
very soon), however please let me know if turns out I'm wrong.
Best wishes
Peter
Serge Cohen wrote:
> Hello Peter;
>
> The problem I observe
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Hello Peter;
The problem I observed is indeed corresponding to what you say should
be fixed.
To answer Leo, this is a problem of the interface alone, indeed the
'way out' when using the buggy interface is to use the 'Run and See
Batch file' t
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On Wed, 2008-03-12 at 18:30 -0700, Pavel Afonine wrote:
> Hi Martin,
>
> > 2) in the context of PX, only the total "B factor" contribution to Fcalc
> > needs to be positive definite, the TLS component might not be (though it is
> > satisfying if it is)
> >
>
> Please correct me if I'm wrong.
Hi Dale,
to my knowledge, sfcheck calculates the contribution of the bulk
solvent using the double-exponential scaling model (Babinet model),
but not using the mask model that REFMAC applies per default. I
sometimes have to discuss similar R-factor differences with RCSB upon
PDB submissio
Dale,
I have had a similar problem with two of my entries. However, if I take
the TLS information from the PDB header and put it in a "in_tls.tls" file
that I feed into REFMAC (0 cycles, just structure factor computation), I
can reproduce the R-factors within 0.1% or less.
It is just the or
Hello Serge
I have to say that your message wasn't very clear to me, but Leo's email
made me wonder if this isn't related to a bug in CCP4i in the 6.0.99
releases, which meant that only a subset of labels were made available
to the user for things like the weighting.
This was a bug introduced aft
Jan,
Crystals containing haem protein are not necessarily red, the colour
depends on the oxidation state of the haem and on the haem/protein
ratio. A FeIII haem will look yellowish, gold or brown depending on
the haem/protein ratio, while an FeII haem will look more pink or red.
Daniel
Ian
Dear Jan,
I'll try to give you a few explanations that may not involve having
upset the hemes in your protein.
You say your crystals are not red but what about the solution? Could you
have salt or other protein crystals but your target protein be fine but
not crystallized. You can get some o
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