[chimerax-users] generating icosahedron from pentamer

Thu Mar 25 19:12:16 PDT 2021

Thank you Tom. I will give it a try.

  Ibrahim
________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Thursday, March 25, 2021 6:17 PM
To: Moustafa, Ibrahim M. <ria2 at psu.edu>
Cc: Tom Calcraft <tom.calcraft at crick.ac.uk>; ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] generating icosahedron from pentamer

Hi Ibrahim,

  Since your pentamers are not 5-fold symmetric and you can rotate each of them to 5 different positions along the pentamer axis, and your icosahedron has 12 of them you have about 5**12 possible configurations.  But if you just want one why not use the sym command as you have

  sym #1 i,222 copies true

to make 60 copies and then just delete 48 of the pentamer copies?  It is not hard, could be done in a few minutes.  Just mouse over each of the 12 pentamer facets of the icosahedron.  Each one has 5 copies stacked on top of each other, but mouse over will show the model id of one of them.  Record the model id of one copy at each of the 12 positions then delete the rest, e.g.

close ~#3,15,39,22,46,13,7,32,33,55,61,2

  Tom

On Mar 25, 2021, at 2:46 PM, Moustafa, Ibrahim M. <ria2 at psu.edu<mailto:ria2 at psu.edu>> wrote:

Hi Tom,

  I am interested to build the icosahedral shape with the asymmetric pentamer at each of the 12 5-folds.

  It seems that is not doable since the symmetry is not icosahedral in that case!

  Thanks,
  Ibrahim
________________________________
From: Tom Calcraft <tom.calcraft at crick.ac.uk<mailto:tom.calcraft at crick.ac.uk>>
Sent: Thursday, March 25, 2021 5:41 PM
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Cc: Moustafa, Ibrahim M. <ria2 at psu.edu<mailto:ria2 at psu.edu>>
Subject: Re: [chimerax-users] generating icosahedron from pentamer

Hi Moustafa,

Icosahedral symmetry includes the 5-fold axis of the pentamer, so you can fix your problem by deleting chains B-E and just symmetrising chain A.

Best,
Tom

On 25 Mar 2021, at 19:08, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

External Sender: Use caution.

Sorry no, those were all of my suggestions (I wouldn't hold out on you!).  This is not my area of expertise, however. Maybe somebody who knows more about it can suggest something.
Elaine

On Mar 25, 2021, at 12:04 PM, Moustafa, Ibrahim M. <ria2 at psu.edu<mailto:ria2 at psu.edu>> wrote:

Hi Elaine,

 I tried what you suggested and got the same result. I got 5 copies of icosahedron. At each vertex of the 5-fold copies of chains A-E generated. Difficult to manually delete unwanted copies at each vertex of the icosahedron!

 Any other suggestions?

 Thanks,
 Ibrahim
From: Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>>
Sent: Thursday, March 25, 2021 2:44 PM
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Cc: Moustafa, Ibrahim M. <ria2 at psu.edu<mailto:ria2 at psu.edu>>
Subject: Re: [chimerax-users] generating icosahedron from pentamer

P.S. if you got 5 icosahedra before and any of them is correct, presumably you could just delete the others.  However, you would need to look carefully to decide if it was correct.

Elaine

On Mar 25, 2021, at 11:40 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Ibrahim,
I don't know what symmetry specification is needed to make one icosahedron from your pentamer.  It depends on the specific coordinates of the pentamer, but is not easy to tell from those coordinates (as you can see).  If #2 is a map of the whole icosahedron,  maybe you could try using commands:

measure symmetry #2
...maybe with options, see the help:
<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmeasure.html%23symmetry&data=04%7C01%7C%7Ce002fd8e7e7140dfe7d708d8efc1a166%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637522962217016760%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=uY7dJ228rpsIvVcxE48dF8D9QkaDy9UOTil2yb6oEX4%3D&reserved=0<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmeasure.html%23symmetry&data=04%7C01%7Cria2%40psu.edu%7Cb880c715b5b3404e0f5108d8efdbc12b%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637523074412200856%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6iGMejmouu8ckvIhN0MVPRDwaw1n4yINvNhtuGe9Sx8%3D&reserved=0>>

...followed by something like
sym #1 symmetry #2

... with other options, e.g. "center" like you used before, see the help:
<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fsym.html%23symmetry&data=04%7C01%7C%7Ce002fd8e7e7140dfe7d708d8efc1a166%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637522962217016760%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2%2FkZcnNIW9FL14JJWAeurdIb4fAZeXaa6xIkk%2FYQOOM%3D&reserved=0<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fsym.html%23symmetry&data=04%7C01%7Cria2%40psu.edu%7Cb880c715b5b3404e0f5108d8efdbc12b%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637523074412210850%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Dhw0inuubxejwdmin1fws099iVtzgiIyyljhe23QFh0%3D&reserved=0>>

I don't know if this process would work, however; requires that "measure" is able to detect the needed symmetry from the map.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 25, 2021, at 10:03 AM, Moustafa, Ibrahim M. <ria2 at psu.edu<mailto:ria2 at psu.edu>> wrote:

Dear all,
I want to generate icosahedral structure from a pentamer (chains A-E). When I use the command:

 sym #1 i,222 coordinateSystem #2 center #2

It generated 5 copies, icosahedron for each chain.

What I'd like to build is just 12 copies of the pentamer in an icosahedral sym.

How to do that in ChimeraX?
Thanks,
Ibrahim

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