On Mar 13, 2019, at 9:57 AM, Chakraborty, Joydeep <jc323@njit.edu> wrote:
Hi Elaine I am trying to show the active site space fill model as depicted by the CASTp. However I am having difficulty to generate the same file using chimera. I was wondering if there is any special way we could depict a ribbon diagram of the protein with a space filled active site pocket. Thanks, Joydeep.
Hi Joydeep, A picture would have been helpful, but I’m guessing you mean how it looks at the CASTp website. I looked at the website and see it shows some transparent spheres filling the pocket. However, these spheres are not described in any of the files Chimera gets from CASTp (which are the same as the files you get if you choose “Download” on their website), so we don’t have any way of showing them, sorry. I didn’t see any way to get the spheres from the website… I agree it would be useful! Just to help explain it to everybody else, I attached an image showing left to right: the Chimera CASTp dialog, Chimera window showing PDB structure 3TRG ribbon with molecular surface of biggest pocket from CASTp, and image of the same structure and pocket at the CASTp website <http://sts.bioe.uic.edu/castp/index.html?3trg>, including the transparent spheres: For future reference, it is better to send Chimera questions to chimera-users@cgl.ucsf.edu (CC’d on this message) to ensure you get an answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
In the past, I have made an image showing spheres in a cavity, but this was using the MolAxis server plus an additional step to manually edit the output file to make a BILD file to open in Chimera. See righthand image in this page, and below it, a description of how the image was made: <http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html> It may not be that easy to get the server to put spheres in the same pocket you want to show. Best, Elaine
On Mar 13, 2019, at 11:01 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
On Mar 13, 2019, at 9:57 AM, Chakraborty, Joydeep <jc323@njit.edu> wrote:
Hi Elaine I am trying to show the active site space fill model as depicted by the CASTp. However I am having difficulty to generate the same file using chimera. I was wondering if there is any special way we could depict a ribbon diagram of the protein with a space filled active site pocket. Thanks, Joydeep.
Hi Joydeep, A picture would have been helpful, but I’m guessing you mean how it looks at the CASTp website. I looked at the website and see it shows some transparent spheres filling the pocket. However, these spheres are not described in any of the files Chimera gets from CASTp (which are the same as the files you get if you choose “Download” on their website), so we don’t have any way of showing them, sorry. I didn’t see any way to get the spheres from the website… I agree it would be useful!
Just to help explain it to everybody else, I attached an image showing left to right: the Chimera CASTp dialog, Chimera window showing PDB structure 3TRG ribbon with molecular surface of biggest pocket from CASTp, and image of the same structure and pocket at the CASTp website <http://sts.bioe.uic.edu/castp/index.html?3trg>, including the transparent spheres:
<Screen Shot 2019-03-13 at 10.43.42 AM.png>
For future reference, it is better to send Chimera questions to chimera-users@cgl.ucsf.edu (CC’d on this message) to ensure you get an answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
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Elaine Meng