Hi Angelo,
As far as I understand the putty representation takes the values from the
b-factor of the Ca atom. Probably you should store your fluctuation values
either on the Ca (leaving all the others atoms with 0.0 or any other value)
or just set the same b-factor for all the atoms of a given residue. Either
way you should get what you want.
I think the error you are getting is because all the Ca have the same
b-factor value is your error something like "invalid putty settings
(division by zero)"? If you want all the Ca having the same b-factor and
use the putty representation anyway you should do the following:
set cartoon_putty_transform, 2
Cheers,
Osvaldo.
On Mon, May 11, 2015 at 6:35 PM, Angelo Rossi <
angelo.raymond.ro...@gmail.com> wrote:
> Hello:
>
> I am trying to see the effect of side-chain fluctuation on molecular
> permeation through a transmembrane protein channel.
>
> The idea is create a pdb file with a column of B-values related to the
> RMSF values of the MD trajectory.
>
> What I tried was to set the B-values of all heavy atom main-chain atoms to
> 1.0. Then all the B side-chain values were set equal to the RMSF value
> from the trajectory, using the correct formula relating RMSF fluctuation to
> B-value.
>
> But, the above method blows up in pymol when trying to use the Action
> ---> Preset ---> b factor putty option. I think this is probably due to
> the fact that all main-chain atoms are equal to 1, and the algorithm cannot
> handle this.
>
> Can someone please provide me with a way to clearly see the fluctuation of
> sid-chain atoms in the present of the main-chain atoms?
>
> Thanks so much.
>
> Regards,
>
> Angelo
>
>
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