[Chimera-users] 3D dashed pseudobond styles?

Oliver Clarke olibclarke at gmail.com
Fri Nov 6 10:06:13 PST 2015

It does indeed Elaine, very much looking forward to trying out Chimera 2!

Yes, I am aware of the pseudobond reader, and it’s great for scripting or when extensive per bond customization is required, but a single command allowing addition of a pseudo bond between two atoms would be handy in cases when one doesn’t need all the options that are available in the pseudobond reader.

You know, that would actually also solve the third point - if I could create a single pseudobond easily, then I could associate dummy atoms (using ac mc) with the 3D labels and use pseudobonds as arrows.


> On Nov 6, 2015, at 12:59 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Oliver,
> You will be happy to hear that the nextgen program Chimera2 has 3D dashed pseudobonds!
> In the current Chimera, you can add custom pseudobonds by listing the pairs of atoms or markers in a text file and reading it in with the Pseudobond Reader tool.  It also allows for labels, individual coloring, etc.  See the manpage for file description and other details:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html>
> Although there is nothing like the arrows/pointers that you mention for the 3D labels in current Chimera, you can specify 3D offsets in the label command, and (probably much friendlier) move them around in 3D with the mouse.  You would just have to reassign one of the mouse buttons from its normal function to 3D label movement using the Preferences (in Favorites menu), category: Mouse.  See “label-dragging” function:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse>
> 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 Nov 6, 2015, at 9:03 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> Hi all,
>> Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful.
>> Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds.
>> Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues.
>> One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great  to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do.
>> Cheers,
>> Oliver.

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