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
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://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry
...followed by something like sym #1 symmetry #2
... with other options, e.g. "center" like you used before, see the help: https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry
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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry
...followed by something like sym #1 symmetry #2
... with other options, e.g. "center" like you used before, see the help: https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry
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@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
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@cgl.ucsf.edu Sent: Thursday, March 25, 2021 2:44 PM To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Cc: Moustafa, Ibrahim M. ria2@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@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://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%7C9f98a03d18204acbafa908d8efbdfd07%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637522946559299686%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=BTG5hqnpaCaFHv4DTh35NU9v2pHxxMw%2Fiqr%2FGLwjq2c%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://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%7C9f98a03d18204acbafa908d8efbdfd07%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637522946559309681%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jrcV3ZqMQNQtAFd4dRLCv%2F85BgHiWIkRphClgW4tNT4%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@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
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@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@cgl.ucsf.edu Sent: Thursday, March 25, 2021 2:44 PM To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Cc: Moustafa, Ibrahim M. ria2@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@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://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%7C9f98a03d18204acbafa908d8efbdfd07%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637522946559299686%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=BTG5hqnpaCaFHv4DTh35NU9v2pHxxMw%2Fiqr%2FGLwjq2c%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://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%7C9f98a03d18204acbafa908d8efbdfd07%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637522946559309681%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jrcV3ZqMQNQtAFd4dRLCv%2F85BgHiWIkRphClgW4tNT4%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@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
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@cgl.ucsf.edumailto:meng@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@psu.edumailto:ria2@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@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: Thursday, March 25, 2021 2:44 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Cc: Moustafa, Ibrahim M. <ria2@psu.edumailto:ria2@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@cgl.ucsf.edumailto:meng@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
...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
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@psu.edumailto:ria2@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl....
The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
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@crick.ac.uk Sent: Thursday, March 25, 2021 5:41 PM To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Cc: Moustafa, Ibrahim M. ria2@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@cgl.ucsf.edumailto:meng@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@psu.edumailto:ria2@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@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: Thursday, March 25, 2021 2:44 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Cc: Moustafa, Ibrahim M. <ria2@psu.edumailto:ria2@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@cgl.ucsf.edumailto:meng@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....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%7C351d5135a21046d2931608d8efd6c4b5%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637523053003254260%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=IXvfuF56vSlD0zf75pu9sPyXtonEFMX9wfsA56zeKdw%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....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%7C351d5135a21046d2931608d8efd6c4b5%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637523053003264242%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=X2PR2TydySR7fn3fYdEvRO%2Fyx7PzKQkVeAhMRYjM1t4%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@psu.edumailto:ria2@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl....https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimerax-users&data=04%7C01%7Cria2%40psu.edu%7C351d5135a21046d2931608d8efd6c4b5%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637523053003274243%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=F%2FSdcyeqG7Mr7%2Fr0RT7%2F%2BBPzgWx5HXvorP6JLVaXRYI%3D&reserved=0
The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
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@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@crick.ac.uk Sent: Thursday, March 25, 2021 5:41 PM To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Cc: Moustafa, Ibrahim M. ria2@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@cgl.ucsf.edu mailto:meng@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@psu.edu mailto:ria2@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@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> Sent: Thursday, March 25, 2021 2:44 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Cc: Moustafa, Ibrahim M. <ria2@psu.edu mailto:ria2@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@cgl.ucsf.edu mailto:meng@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.... 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%7C351d5135a21046d2931608d8efd6c4b5%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637523053003254260%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=IXvfuF56vSlD0zf75pu9sPyXtonEFMX9wfsA56zeKdw%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.... 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%7C351d5135a21046d2931608d8efd6c4b5%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637523053003264242%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=X2PR2TydySR7fn3fYdEvRO%2Fyx7PzKQkVeAhMRYjM1t4%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@psu.edu mailto:ria2@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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Thank you Tom. I will give it a try.
Ibrahim ________________________________ From: Tom Goddard goddard@sonic.net Sent: Thursday, March 25, 2021 6:17 PM To: Moustafa, Ibrahim M. ria2@psu.edu Cc: Tom Calcraft tom.calcraft@crick.ac.uk; ChimeraX Users Help chimerax-users@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@psu.edumailto:ria2@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@crick.ac.ukmailto:tom.calcraft@crick.ac.uk> Sent: Thursday, March 25, 2021 5:41 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Cc: Moustafa, Ibrahim M. <ria2@psu.edumailto:ria2@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@cgl.ucsf.edumailto:meng@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@psu.edumailto:ria2@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@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: Thursday, March 25, 2021 2:44 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Cc: Moustafa, Ibrahim M. <ria2@psu.edumailto:ria2@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@cgl.ucsf.edumailto:meng@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....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....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@psu.edumailto:ria2@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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participants (4)
-
Elaine Meng -
Moustafa, Ibrahim M. -
Tom Calcraft -
Tom Goddard