Update VDW Dots During Torsion Rotation
Hello, If I am displaying atomic dots using the “vdw” command, is there any way to get the dots to update as structural changes are made? For example, if I am adjusting torsions in the Adjust Torsion box, is there a way to get the dots to follow along as the structure changes? Thanks, Brian --- Brian E. Coggins, Ph.D. Assistant Research Professor of Biochemistry Duke University, Durham, NC
Hi Brian, This is not a direct answer to your question, but alternatives to showing VDW dots are: (A) show sphere representation (VDW spheres) instead of stick representation of atoms (B) show molecular surface, which will update as bonds are rotated. You could make it transparent and/or show it as mesh, e.g. commands: surftrans 75 surftrans 0 surfrep mesh There is also a “dot” style (as opposed to mesh and solid) but then you’d want to crank up the vertex density to put the dots closer together… e.g. select the surface with Ctrl-click and then use the Selection Inspector (open by clicking green magnifying glass icon), inspect: MSMS surface, increase “vertex density” and maybe dot size. Depending on the structure, however, molecular surface calculation may be slow and/or fail as you change the structure by rotating bonds. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 23, 2019, at 1:29 PM, Brian E Coggins <bec2@duke.edu> wrote:
Hello,
If I am displaying atomic dots using the “vdw” command, is there any way to get the dots to update as structural changes are made? For example, if I am adjusting torsions in the Adjust Torsion box, is there a way to get the dots to follow along as the structure changes?
Thanks, Brian
--- Brian E. Coggins, Ph.D. Assistant Research Professor of Biochemistry Duke University, Durham, NC
Hi Brian, It seems the vdw command caches the computed surface points and that therefore various tricks with ~vdw/vdw don’t update the surface. However changing the dot density does clear the cache and cause a recomputation, so you can use this awful hack to get the vdw surface to update as you adjust torsions: perframe “vdwdens 5.1; vdwdens 5” Every frame, the density will be changed to 5.1 and then back to the (default) 5. You might want to use different numbers. I prefer not to be “credited” with this idea. :-) not Eric Pettersen not from the UCSF Computer Graphics Lab
On Jan 23, 2019, at 3:14 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Brian, This is not a direct answer to your question, but alternatives to showing VDW dots are:
(A) show sphere representation (VDW spheres) instead of stick representation of atoms
(B) show molecular surface, which will update as bonds are rotated. You could make it transparent and/or show it as mesh, e.g. commands:
surftrans 75 surftrans 0 surfrep mesh
There is also a “dot” style (as opposed to mesh and solid) but then you’d want to crank up the vertex density to put the dots closer together… e.g. select the surface with Ctrl-click and then use the Selection Inspector (open by clicking green magnifying glass icon), inspect: MSMS surface, increase “vertex density” and maybe dot size.
Depending on the structure, however, molecular surface calculation may be slow and/or fail as you change the structure by rotating bonds.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 23, 2019, at 1:29 PM, Brian E Coggins <bec2@duke.edu> wrote:
Hello,
If I am displaying atomic dots using the “vdw” command, is there any way to get the dots to update as structural changes are made? For example, if I am adjusting torsions in the Adjust Torsion box, is there a way to get the dots to follow along as the structure changes?
Thanks, Brian
--- Brian E. Coggins, Ph.D. Assistant Research Professor of Biochemistry Duke University, Durham, NC
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participants (3)
-
Brian E Coggins -
Elaine Meng -
Eric Pettersen