[Chimera-users] Visualising tunnels by MolAxis

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 3 11:22:31 PST 2014

Hi George,
I don't have that problem if I open PDB 1bl8 and then the  BILD file I linked to that cavities page: 
(which has the same coordinates as the pathway file you mentioned <http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/cavities/1bl8.graph_pathway_0_all> ).

Maybe you had somehow separately rotated and translated them.  You could try command "reset" to put both in default orientations, which should then be aligned, or if you didn't want to move your molecular structure, you can use the command "matrixcopy" to make sure the same transform is applied to both.  For example, if the atomic structure is model 0 and the object read from the BILD file is model 1, command:

matrixcopy 0 1

It was a few years ago when I used the MolAxis server.  If you are trying it now (instead of just looking at these example files I have provided), it is possible they changed something, but it seems unlikely that the coordinates of the output would no longer match the input.

I hope this helps,
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 3, 2014, at 10:06 AM, George Tzotzos <gtzotzos at me.com> wrote:

> I’ve tried to visualise protein binding site tunnels to the bulk solvent as detailed in the instructions given in:
> http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html
> The problem I encounter is that I cannot align tunnel produced by _graph_pathway_0_all build file to the receptor. In other words, the coordinates of the receptor and the tunnel are different.
> Is there a way of doing this?  
> Thanks in advance for any help.
> Regards
> George

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