Hi all, I am trying to colour with coulombing potential only a portion of the surface I generated, and show it together with the rest of the surface, coloured in grey. The way I've done it is to create a duplicate of the pdb model, generate surface1 from the full model, and surface2 from the selected area, and colour with coulombic potential only surface2. The issue is that sometimes surface1 is "in front" of surface2, and the only way to see surface2 is to hide surface1. This is not related to the order I create the surfaces apparently, but rather to the order I created the models. Is there a way to "bring to front" or " send to back" surfaces or models for display purposes, rather than copying models (and re-doing the selection for the residues that I want coloured?). Or a way to colour with potential only the selected area of a surface? Thanks! Giulia
Hi Giulia, Sorry, there is no "bring to front" option or ability to color only part of a surface by Coulombic ESP. As you found out, the workaround to get partial Coulombic coloring is to use two copies of surface. Instructions are given in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-November/008168.html> I would recommend first experimenting to see which copy of the surface "wins" display, then using that copy for the Coulombic coloring. 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 Jan 17, 2013, at 7:51 AM, giulia zanetti wrote:
Hi all, I am trying to colour with coulombing potential only a portion of the surface I generated, and show it together with the rest of the surface, coloured in grey. The way I've done it is to create a duplicate of the pdb model, generate surface1 from the full model, and surface2 from the selected area, and colour with coulombic potential only surface2. The issue is that sometimes surface1 is "in front" of surface2, and the only way to see surface2 is to hide surface1. This is not related to the order I create the surfaces apparently, but rather to the order I created the models.
Is there a way to "bring to front" or " send to back" surfaces or models for display purposes, rather than copying models (and re-doing the selection for the residues that I want coloured?). Or a way to colour with potential only the selected area of a surface? Thanks! Giulia
Thank you Elaine, then maybe there is a way to copy/transfer a selection of residues from one model to its copy? Giulia On Thu, Jan 17, 2013 at 6:37 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Giulia, Sorry, there is no "bring to front" option or ability to color only part of a surface by Coulombic ESP.
As you found out, the workaround to get partial Coulombic coloring is to use two copies of surface. Instructions are given in this previous post:
< http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-November/008168.html
I would recommend first experimenting to see which copy of the surface "wins" display, then using that copy for the Coulombic coloring. 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 Jan 17, 2013, at 7:51 AM, giulia zanetti wrote:
Hi all, I am trying to colour with coulombing potential only a portion of the surface I generated, and show it together with the rest of the surface, coloured in grey. The way I've done it is to create a duplicate of the pdb model, generate surface1 from the full model, and surface2 from the selected area, and colour with coulombic potential only surface2. The issue is that sometimes surface1 is "in front" of surface2, and the only way to see surface2 is to hide surface1. This is not related to the order I create the surfaces apparently, but rather to the order I created the models.
Is there a way to "bring to front" or " send to back" surfaces or models for display purposes, rather than copying models (and re-doing the selection for the residues that I want coloured?). Or a way to colour with potential only the selected area of a surface? Thanks! Giulia
Hi Giulia, Unfortunately I don't know of a way to do that either, but here is way to make the other surface "win" the display: - start Model Panel (under Favorites in menu) - in Model Panel, close (delete) the currently "winning" surface - re-create that surface For example, I used the following commands to open 2 copies of 1gcn and show surfaces on both: open 1gcn open 1gcn surf I can tell the #0 surface is winning because it is tan (#1 is light blue). Using Model Panel, I closed surface #0. Then I re-created surface #0 with command: surf #0 Now surface #1 is winning because it is light blue. It is necessary to actually close (delete) the first surface #0 because simply hiding and reshowing (~surf #0; surf #0) will not reverse the "winning" display. 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 Jan 17, 2013, at 12:58 PM, giulia zanetti wrote:
Thank you Elaine, then maybe there is a way to copy/transfer a selection of residues from one model to its copy? Giulia
Oh, yes, it works! That's an easy fix, thanks! Giulia On Thu, Jan 17, 2013 at 10:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Giulia, Unfortunately I don't know of a way to do that either, but here is way to make the other surface "win" the display:
- start Model Panel (under Favorites in menu) - in Model Panel, close (delete) the currently "winning" surface - re-create that surface
For example, I used the following commands to open 2 copies of 1gcn and show surfaces on both:
open 1gcn open 1gcn surf
I can tell the #0 surface is winning because it is tan (#1 is light blue). Using Model Panel, I closed surface #0. Then I re-created surface #0 with command:
surf #0
Now surface #1 is winning because it is light blue.
It is necessary to actually close (delete) the first surface #0 because simply hiding and reshowing (~surf #0; surf #0) will not reverse the "winning" display. 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 Jan 17, 2013, at 12:58 PM, giulia zanetti wrote:
Thank you Elaine, then maybe there is a way to copy/transfer a selection of residues from one model to its copy? Giulia
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