Hi James,
I think what you want to do is to load your data to the b-factor column of
the pdb file and then ask PyMol to color the protein according to the
b-factor values. Try with this
<http://www.pymolwiki.org/index.php/Color#B-Factors> example from the PyMol
wiki and let us know if you find some trouble.
Regards,
Osvaldo.
On Wed, Apr 8, 2015 at 1:47 PM, James Starlight <jmsstarli...@gmail.com>
wrote:
Dear Pymol users!
>
> For better visualization of the MMGBSA outputs from MD performed for 10
> ligands
> agains 1 receptor-target I wonder to map per-residue decomposition
> data from each of the systems onto the receptor's 3D structure.
> Eventually I'd like to produce 10 cartoon diagrams which would differs
> in the coloring according to the difference in the contribution of
> residues from the receptor's cavity to binding for different ligands.
> I will be very thankful if someone provide me with ideas of how such
> visualization could be done using receptors structure, decomposition
> logs as the inputs and/or pymol. Here some general idea whig came in
> mind- import column from the mmgbsa.log directly (with number of
> rows= number of receptors residues) to the receptor.pdb B-factors
> column (for instance making meaningful value for C-alpha atom and 0
> for the rest). Will be very thankful for some examples of how it could
> be achieved e.g using combination of awk_sed if more trivial way is
> not exist.
>
>
> Thanks for help!!
>
> James
>
>
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