[chimerax-users] stretching protein?

[Noriega, Heather]

Thank you for your reply. I have one question to make sure I understand
correctly. *1.5 expands them by 50%, so say I only wanted to do 25% I would
use *1.25 to expand? I do appreciate this.

Thank you,

Heather Noriega
PhD-Pharmaceutical Science student
Howard University
heather.noriega at bison.howard.edu
520-203-1883


On Thu, Nov 10, 2022 at 7:37 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> If you just want to do that unphysical stretching, open the Python Shell
> tool (Tools→General→Shell) and type:
>
> from chimerax.atomic import all_atoms
> atoms = all_atoms(session)
> atoms.coords = atoms.coords * 1.5
>
> … to expand the coordinates by 50%.
>
> —Eric
>
> On Nov 9, 2022, at 6:49 PM, Noriega, Heather via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Hello,
>
> Yes, it does make it arbitrary. The picture was from another study, not
> the family I am working on. It was a request from a colleague, I was just
> seeing if there was an easy way of doing it, instead of manually. Thank you
> though. I hope you have a good evening.
>
> Thank you,
>
> Heather Noriega
> PhD-Pharmaceutical Science student
> Howard University
> heather.noriega at bison.howard.edu
> 520-203-1883
>
>
> On Wed, Nov 9, 2022 at 9:34 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>> Hi Heather,
>> Sorry, there isn't a feature like that. You could imagine expanding all
>> the atomic XYZ coordinates radially from the protomer center but in my
>> opinion it would make the structure ridiculous (unphysical bond lengths
>> etc.)... and even if you wanted to do that, as far as I know you would have
>> to write your own code to do it.  The picture suggests there is already a
>> structure of the bigger one, however.
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>
>> > On Nov 9, 2022, at 6:19 PM, Noriega, Heather via ChimeraX-users <
>> chimerax-users at cgl.ucsf.edu> wrote:
>> >
>> > Hello,
>> >
>> > I hope this email finds everyone well. I was wondering if ChimeraX had
>> a function specific to "stretching" the protein. I am going to attach a
>> picture, for reference. Is it possible to stretch the monomer to build a
>> larger capsid? Thanks in advance.
>> >
>> > Thank you,
>> >
>> > Heather Noriega
>> > PhD-Pharmaceutical Science student
>> > Howard University
>> > heather.noriega at bison.howard.edu
>> > 520-203-1883
>> > <image.png>
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