Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli
Hi Zongli, I believe you can use “vop cover” to expand the map if you can supply the needed symmetry information and box size. Please see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009654.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2017, at 8:01 PM, Li, Zongli <Zongli_Li@hms.harvard.edu> wrote:
Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli
Hi Elaine, Thank you so much for the help. I look up the original post answered by Tom, as he pointed out, "The tricky part will be to assign the correct center of symmetry and icosahedron orientation for the asymmetric piece using the origin and symmetry options of the volume command". He is very right and I could not figured out the way to assign the correct center of the symmetry and icosahedron orientation for asymmetric piece with volume command while I am using "cop cover". The map I tried is EMD-5199 (rotavirus). Could you please help me out? Thanks again, Zongli ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, March 27, 2017 12:49:58 PM To: Li, Zongli Cc: chimera-users@cgl.ucsf.edu Mailing List Subject: Re: [Chimera-users] Create an entire virus from Octant Hi Zongli, I believe you can use “vop cover” to expand the map if you can supply the needed symmetry information and box size. Please see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009654.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2017, at 8:01 PM, Li, Zongli <Zongli_Li@hms.harvard.edu> wrote:
Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli
Hi Zongli, Assign icosahedral symmetry to the map using the BIOMT matrices in the fit PDB coordinates then use vop cover to extend the octant map using that symmetry: open emdbID:5199 open 4v7q volume #0 symmetry #1 vop cover #0 ibox -499,-499,-499,499,499,499 cellsize 2000,2000,2000 The octant map is size 500,500,500 and I assume the 0,0,0 grid point is at the center of symmetry so the vop cover command says to cover grid points -499 to 499. The vop cover command is intended to be used with crystallography so I also tell it the unit cell is bigger than the full map (2000 instead of 1000) so it does not use periodicity of the map. The vop command took about 45 minutes to execute — very slow. The result of this symmetric covering is not ideal because the edges of the octant map could introduce artifacts in the full map. Also it is interpolating the one octant at all symmetry equivalent points and averaging, and this trilinear interpolation is going to introduce a little bit of blurring. Unfortunately because of the symmetry you can’t simply put 8 copies of the octant map together to form a full virus. The x,y,z axes are 2-fold symmetry axes so the given octant can be mapped to 4 of the 8 octants with no grid interpolations, but the other four require other symmetry operators, not just 90 degree rotations. So you can’t reproduce the full virus map with complete fidelity. The only way to avoid the interpolation is to get a full map from the Harrison lab. It is unfortunate that only this inadequate octant map is what is in the EMDB. In the attached image I show the EMDB 5199 octant, and a neighbor octant which obviously is not just a rotated copy since the original octant has 9 spikes while the neighbor octant has only 6. Tom
On Mar 27, 2017, at 9:49 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Zongli, I believe you can use “vop cover” to expand the map if you can supply the needed symmetry information and box size. Please see this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009654.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2017, at 8:01 PM, Li, Zongli <Zongli_Li@hms.harvard.edu> wrote:
Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, Thank you so much for your help, really appreciate. Best, Zongli ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Monday, March 27, 2017 7:42:35 PM To: chimera-users@cgl.ucsf.edu BB Cc: Li, Zongli Subject: Re: [Chimera-users] Create an entire virus from Octant Hi Zongli, Assign icosahedral symmetry to the map using the BIOMT matrices in the fit PDB coordinates then use vop cover to extend the octant map using that symmetry: open emdbID:5199 open 4v7q volume #0 symmetry #1 vop cover #0 ibox -499,-499,-499,499,499,499 cellsize 2000,2000,2000 The octant map is size 500,500,500 and I assume the 0,0,0 grid point is at the center of symmetry so the vop cover command says to cover grid points -499 to 499. The vop cover command is intended to be used with crystallography so I also tell it the unit cell is bigger than the full map (2000 instead of 1000) so it does not use periodicity of the map. The vop command took about 45 minutes to execute — very slow. The result of this symmetric covering is not ideal because the edges of the octant map could introduce artifacts in the full map. Also it is interpolating the one octant at all symmetry equivalent points and averaging, and this trilinear interpolation is going to introduce a little bit of blurring. Unfortunately because of the symmetry you can’t simply put 8 copies of the octant map together to form a full virus. The x,y,z axes are 2-fold symmetry axes so the given octant can be mapped to 4 of the 8 octants with no grid interpolations, but the other four require other symmetry operators, not just 90 degree rotations. So you can’t reproduce the full virus map with complete fidelity. The only way to avoid the interpolation is to get a full map from the Harrison lab. It is unfortunate that only this inadequate octant map is what is in the EMDB. In the attached image I show the EMDB 5199 octant, and a neighbor octant which obviously is not just a rotated copy since the original octant has 9 spikes while the neighbor octant has only 6. Tom [cid:FE798923-04E2-46DF-B9F1-CDE4D99131FF@cgl.ucsf.edu] On Mar 27, 2017, at 9:49 AM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Zongli, I believe you can use “vop cover” to expand the map if you can supply the needed symmetry information and box size. Please see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009654.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipermail_chimera-2Dusers_2014-2DMarch_009654.html&d=CwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=uQMJAWlPEv596kvCdV_ot7YTGNux4AXH5-WfTfSNGmY&m=TWP9dQ8y5W_rjQNWC485ezAUCySJSpaPtdZ3egQr8cM&s=h_KDKzRo42U_dYX9TtJDWSiZn_MDq9oqAk_LCPCXzgs&e=>> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 26, 2017, at 8:01 PM, Li, Zongli <Zongli_Li@hms.harvard.edu<mailto:Zongli_Li@hms.harvard.edu>> wrote: Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Dusers&d=CwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=uQMJAWlPEv596kvCdV_ot7YTGNux4AXH5-WfTfSNGmY&m=TWP9dQ8y5W_rjQNWC485ezAUCySJSpaPtdZ3egQr8cM&s=CcSTrlV8qNq6DP2ofhriXStd-mzFj9JFJid5BX5xTx0&e=>
participants (3)
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Elaine Meng -
Li, Zongli -
Tom Goddard