VMD-L Mailing List

From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Mon Nov 16 2020 - 21:29:22 CST

I would have to imagine there are more effective ways to specify this - if
the issue is they're residues on different chains, you can use parentheses
to split out different sets of selection, for example: (resid 3 and chain
A) or (resid 15 and chain B).

That being said, I think the issue in your atomselection there is the use
of 'and' - when you say 'and', you have to specify what selection you're
using again. "index 1 to 21 and index 5633 to 5649 and index 5650 to 5671",
and so on.

On Wed, 4 Nov 2020 at 22:46, Francesco Pietra <chiendarret_at_gmail.com> wrote:

> Hello
> I am trying to restrain selected atoms (actually selected residues) with a
> homotrimer, where the residues belong to different chains.
>
> It seems to me that the only route is through the index. However, I was
> unable to set the correct syntax. For example
>
> >Main< (MD) 52 % set restrainsel [atomselect top "index 1 to 21 and 5633
> to 5649 and 5650 to 5671 and 11267 to 11288 and 11289 to 11309 and 16907 to
> 16922"]
> atomselect: cannot parse selection text: index 1 to 21 and 5633 to 5649
> and 5650 to 5671 and 11267 to 11288 and 11289 to 11309 and 16907 to 16922
> >Main< (MD) 53 %
>
> Although wrong, it is clear from the above what I would like to do (the
> residues to restrain are where I cut the system to alleviate the
> calculation)
>
> Thanks for advice
> francesco pietra
>
>
>
>