[chimerax-users] stretching protein?

[Eric Pettersen]

That is correct.

--Eric

> On Nov 14, 2022, at 6:31 AM, Noriega, Heather via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:heather.noriega at bison.howard.edu>
>> > 520-203-1883
>> > <image.png>
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