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@bison.howard.edu 520-203-1883 [image: image.png]
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@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@bison.howard.edu 520-203-1883 <image.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@bison.howard.edu 520-203-1883 On Wed, Nov 9, 2022 at 9:34 PM Elaine Meng <meng@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@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@bison.howard.edu 520-203-1883 <image.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@bison.howard.edu <mailto:heather.noriega@bison.howard.edu> 520-203-1883
On Wed, Nov 9, 2022 at 9:34 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@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@cgl.ucsf.edu <mailto:chimerax-users@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@bison.howard.edu <mailto:heather.noriega@bison.howard.edu> 520-203-1883 <image.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@bison.howard.edu 520-203-1883 On Thu, Nov 10, 2022 at 7:37 PM Eric Pettersen <pett@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@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@bison.howard.edu 520-203-1883
On Wed, Nov 9, 2022 at 9:34 PM Elaine Meng <meng@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@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@bison.howard.edu 520-203-1883 <image.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
That is correct. --Eric
On Nov 14, 2022, at 6:31 AM, Noriega, Heather via ChimeraX-users <chimerax-users@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@bison.howard.edu <mailto:heather.noriega@bison.howard.edu> 520-203-1883
On Thu, Nov 10, 2022 at 7:37 PM Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@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@cgl.ucsf.edu <mailto:chimerax-users@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@bison.howard.edu <mailto:heather.noriega@bison.howard.edu> 520-203-1883
On Wed, Nov 9, 2022 at 9:34 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@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@cgl.ucsf.edu <mailto:chimerax-users@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@bison.howard.edu <mailto:heather.noriega@bison.howard.edu> 520-203-1883 <image.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Noriega, Heather