Hi community,
I'd like to calculate Ca-RMSD between two related structures without any
structure superposition using a running window of say few amino acids, and
map them onto the mobile structure with color-coding. Does anyone have a
script for the same?
Thanks in advance.
Ashok Nayak
Dear community,
Is it possible to increase the radius of real space refinement while
manually adjusting models in Coot with the sphere refine option?
Thanks in advance,
Ashok Nayak
Post-Doctoral Fellow,
Department of Physiology and Biophysics
VCU Medical Centre,1101 E Marshall ST,
Richmond,VA
>
> Hi Everyone,
> Thank you very much for all your inputs.
> The easiest way that worked for me was to take the coot dot_surface output
> and edit it to a .bild file as per Elaine's suggestion.
>
Coot dot surface output:
>
243.69110 246.85279 354.96833 0.448000.471680.8
>
the dots which appear more than certain radius
limit. I could not control these in sph_process either. Could anyone
suggest me the standard way or fine steps to circumvent this ?
Ashok Nayak
Post-Doctoral Fellow,
Department of Physiology and Biophysics
VCU Medical Centre,1101 E Marshall ST,
Richmond
molecule is elongated you might have diffraction anisotropy and
in that case The R values don't come down.
I would also like to use Refmac along with Phenix; that helped in my case.
So you would like to take them one by one and figure out carefully.
Best Wishes
Ashok Nayak
Post-Doctoral F
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Dear Weifei,
It can also be done manually in Pymol by changing the mouse mode from 3
button viewing to 3 button editing and later moving the envelope onto the
X-ray structure or vice-versa, however the best fit can be achieved in
SUPCOMB.
regards
Ashok Nayak
CSIR-CDRI, Lucknow
India
Hello one and all !!
I have been working on cloning and purification aspects on a Leishmanial
cysteine peptidase (pI= 8.2) for quite some time. I had cloned it in pGEX
expression vector. Expression seemed quite okay when induced with 0.5 and
1mM IPTG, so did the solubility in 4 buffers at differ
