Dear All, I am working with a glycoprotein structure and I want to visualize the protein surface as a continuum with the glycans sticking out as sticks. If I visualize the surface of the whole molecule (including sugars), and then I select the sugars only and visualize them as sticks, the surface of the amino acids immediately connected to the sugar (Asn) appear to be clipped. One solution could be to the following: 1. save the model with a different name 2. load the 2 identical structures and align them 3. remove the sugars from one structure only and use it to visualize the protein 4. the second structure is used for visualizing the sugars and not the protein. I used to do something similar with Pymol, and it should work with Chimera as well, but I am sure there is a better/simpler solution. Any suggestion? Thank you for your help. Carlo
Hi Carlo, Chimera tries to automatically figure out which atoms should be grouped together in surfaces, but when the default is not what you want, you can define the groupings ("surface categories") yourself with the command surfcat. It is not necessary to edit your files or open multiple copies. Without knowing which structure you are using, I can't give the exact commands that will work for it, but here is an example. If you want the surface to go around only chain A's protein part and not the attached sugars, the commands could be something like: surfcat myprot :.a & protein surf myprot where "myprot" is just the name you give the category. Or, if there are multiple chains of protein and you want them all inside the surface, you would omit the ":.a &" part (the intersection with chain A). Here is the surfcat description and more examples: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html> 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 Feb 24, 2010, at 7:31 PM, Zambonelli, Carlo wrote:
Dear All, I am working with a glycoprotein structure and I want to visualize the protein surface as a continuum with the glycans sticking out as sticks. If I visualize the surface of the whole molecule (including sugars), and then I select the sugars only and visualize them as sticks, the surface of the amino acids immediately connected to the sugar (Asn) appear to be clipped. One solution could be to the following: 1. save the model with a different name 2. load the 2 identical structures and align them 3. remove the sugars from one structure only and use it to visualize the protein 4. the second structure is used for visualizing the sugars and not the protein. I used to do something similar with Pymol, and it should work with Chimera as well, but I am sure there is a better/simpler solution. Any suggestion? Thank you for your help. Carlo
Hi Elaine, Your suggestion worked quite well and it gave me a better general understanding of groupings and surfcat. Thank you! Carlo -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Thursday, February 25, 2010 1:25 PM To: Zambonelli, Carlo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] variable surface visualization Hi Carlo, Chimera tries to automatically figure out which atoms should be grouped together in surfaces, but when the default is not what you want, you can define the groupings ("surface categories") yourself with the command surfcat. It is not necessary to edit your files or open multiple copies. Without knowing which structure you are using, I can't give the exact commands that will work for it, but here is an example. If you want the surface to go around only chain A's protein part and not the attached sugars, the commands could be something like: surfcat myprot :.a & protein surf myprot where "myprot" is just the name you give the category. Or, if there are multiple chains of protein and you want them all inside the surface, you would omit the ":.a &" part (the intersection with chain A). Here is the surfcat description and more examples: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html> 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 Feb 24, 2010, at 7:31 PM, Zambonelli, Carlo wrote:
Dear All, I am working with a glycoprotein structure and I want to visualize the
protein surface as a continuum with the glycans sticking out as sticks. If I visualize the surface of the whole molecule (including sugars), and then I select the sugars only and visualize them as sticks, the surface of the amino acids immediately connected to the sugar (Asn) appear to be clipped. One solution could be to the following: 1. save the model with a different name 2. load the 2 identical structures and align them 3. remove the sugars from one structure only
and use it to visualize the protein 4. the second structure is used for visualizing the sugars and not the protein. I used to do something similar with Pymol, and it should work with Chimera as well, but I am sure there is a better/simpler solution. Any suggestion? Thank you for your help. Carlo
participants (2)
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Elaine Meng -
Zambonelli, Carlo