I am also not sure of what your goal is, but you can build a sequence profile
for your sequence and use that profile as input instead of your sequence. You
can do this by aligning a set of sequences homologous to your target sequence,
and use that alignment as input for, for example, HMMER or HH
Dear Shijun,
it is always difficult to answer such questions without very specific
information, like e.g. exact error messages, and exact description what was
done.
In addition to what others wrote, I see two general ways to solve the problem:
a) talk to the beamline people. They should know v
Not sure if I understand the question right, but wouldn't phi-blast do
trick. You supply on too your conserved pattern and blast again.
Christian
Am 20.12.2017 19:37 schrieb "Keller, Jacob" :
> Dear Crystallographer-Bioinformaticians,
>
>
>
> Is anyone aware of a way to tweak BLAST or similar so
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Dear Crystallographer-Bioinformaticians,
Is anyone aware of a way to tweak BLAST or similar software to be able to
specify certain residues to be absolutely required, e.g., active site residues?
I guess one can winnow broad-scale resuts with scripts, but it would seem to be
a pretty common type
This is quite straightforward in any package with a reasonable scripting
interface. In ChimeraX, for example:
-load your model
-make your selection
(https://www.rbvi.ucsf.edu/chimerax/docs/user/selection.html)
-open the shell (Tools/General/Shell), and in it, type:
from chimerax.core.atomic i
Shijun,
I have processed .h5 format data successfully that was collected at NSLS II
AMX (this beamline has a Eiger 9M, not 16M, incidentally, but I don't think
that this matters). I used XDSGUI without converting to .cbf format. To do
so, and without knowing what the error messages are that you ar
Easy with GUI2
Import coordinates and select the part you want
Under validation and analysis
Choose analysis Bs etc and you will get your answer
BAVERAGE will give you Bs for main chain & side chain for each monomer but
there is no selection option - you would have to do that in some other way
Dear all,
Sorry for naive CCP4 question, is there a simple way to calculate average
B-factors (side chain, backbone, all)
for only part of a model, such as a domain, loop, etc…
Thanks,
Amir
Hi Graeme and Shijun
eiger2cbf was indeed used for the conversion - so the metadata should be in the
CBF headers (unless the H5 files produced do not conform to what eiger2cbf
expects). The most recent version of eiger2cbf should be used rather than the
one on the Mosflm website!
My guess is t
Dear Shijun
How did you convert?
If H5ToXDS it throws away all header information - this tool will preserve the
metadata:
https://github.com/biochem-fan/eiger2cbf
which should allow XDSGUI to work. If DIALS can read the data but comes out
with the wrong answer, please could you provide some m
Dear all
When I run dials.index it result me "Sorry: No suitable lattice could be
found", but the other software can give me C2 space group. How could I DO with
this situation
Best Regards
Shijun
Dear all
I just collected some data with Eiger16M whose file format is *.h5. But I
cannot read it with HKL2000, because I don't have the Eiger16M detector license
now, while, I have *.cbf detector license. So I transfered the *.h5 to *.cbf
files, but the problem is XDSGUI still cannot read
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