Hello I would like to highlight certain residues of interest in my molecule, preferably by colorizing them in Chimera. Is there a way to do this? Richard Collins Lab Research Project Coordinator Department of Cell Biology Peter Gilgan Centre for Research and Learning Room 199420, bench HH Hospital for Sick Children 686 Bay St. Toronto, ON CANADA M5G 0A4 T (ext): 416 813-8474 T (int): 308474 E: rcollins@sickkids.ca ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
Hi Richard, Of course you can color and show/hide individual residues and atoms in Chimera. Otherwise it would not be very useful!! It is probably the first thing to learn, and there are many different ways depending on your style of working. The two main approaches are: - “select” the residue, which outlines it in green, and then use the Actions menu to do something to your selection - use commands like “color” and “display” specifying the residue directly by residue number and chain (show Command Line from Favorites menu) However, there are many ways to select a residue, including with Ctrl-click in the graphics window or a command or in the Sequence window, and conversely, you can act on the current selection with commands too. You should take a look at the “getting started” tutorial, which has two sections with examples of these two general approaches. <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> There are lots of other tutorials too: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.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 Apr 8, 2017, at 2:34 PM, Richard Collins <rcollins@sickkids.ca> wrote:
Hello I would like to highlight certain residues of interest in my molecule, preferably by colorizing them in Chimera. Is there a way to do this? Richard Collins
Hi Elaine Yes this helps, thanks. I used control-click to select residues. Is there a way to adjust the transparency of ribbons, helices and amino acids? What I am trying to do is find all the residues along the tunnel of my molecule. It is a solid protein with a tunnel through the middle. Using the SURFACE function shows only the outer surface. I am wondering if there is a way to show only the tunnel surface and not the outer surface? For now I am using the PER-MODEL CLIPPING to slice through the middle. Richard Collins Lab Research Project Coordinator Department of Cell Biology Peter Gilgan Centre for Research and Learning Room 199420, bench HH Hospital for Sick Children 686 Bay St. Toronto, ON CANADA M5G 0A4 T (ext): 416 813-8474 T (int): 308474 E: rcollins@sickkids.ca ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Sunday, April 09, 2017 12:42 PM To: Richard Collins Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question about Chimera Hi Richard, Of course you can color and show/hide individual residues and atoms in Chimera. Otherwise it would not be very useful!! It is probably the first thing to learn, and there are many different ways depending on your style of working. The two main approaches are: - “select” the residue, which outlines it in green, and then use the Actions menu to do something to your selection - use commands like “color” and “display” specifying the residue directly by residue number and chain (show Command Line from Favorites menu) However, there are many ways to select a residue, including with Ctrl-click in the graphics window or a command or in the Sequence window, and conversely, you can act on the current selection with commands too. You should take a look at the “getting started” tutorial, which has two sections with examples of these two general approaches. <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> There are lots of other tutorials too: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.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 Apr 8, 2017, at 2:34 PM, Richard Collins <rcollins@sickkids.ca> wrote:
Hello I would like to highlight certain residues of interest in my molecule, preferably by colorizing them in Chimera. Is there a way to do this? Richard Collins
________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
Hi Richard, You can change transparency of anything, see the “transparency” command and for an example, the “similar binding sites” image tutorial… <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html> However, general advice re tunnel surfaces (I changed the e-mail subject line to be more useful): It can be difficult to show the tunnel surface only. Often people will use some separate plugin or program to calculate a tunnel surface rather than trying to specify which atoms’ molecular surface to show, since (as you may have observed) it is hard to figure out which atoms line that tunnel. Some alternatives you can try with Chimera: (1) CASTp has pre-calculated pocket and tunnels for structures in the PDB, and if you are using some already-deposited structure from there, you can fetch the structure and results from CASTp by using menu: File… Fetch by ID (specifying PDB ID in the CASTp option), or a command something like: open castp:2gbp … if your structure were PDB entry 2GBP. That would bring up a dialog listing the various pockets and tunnels, and you can click on each to show its surface. Or, if you are using a structure that is not in the PDB database (or it is, but for some reason CASTp doesn’t have results for it already) you can upload it to the CASTp webserver and get results back by email and then show them in Chimera as described in this page. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html> However, this still uses the molecular surface atomic patches, so sometimes you will get raggedy edges. The other ways I mention avoid that problem. (2) 3V calculation. The 3V webserver calculates a “density map” that fills pockets and tunnels, and then you can open this map and show its isosurface in Chimera. It’s been a while since I tried this, but the “channel finder” sounds the most promising unless you already know the X,Y,Z coordinates of the tunnel of interest. (3) A long time ago I also tried something called MolAxis, with some minor reformatting of its output required to show in Chimera. Example results and description here in our Image Gallery, along with CASTp results for the same structure: <http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html> Finally, if you use Pymol, I know people often use a plugin called “HOLE” with Pymol for this purpose. 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 Apr 9, 2017, at 12:56 PM, Richard Collins <rcollins@sickkids.ca> wrote:
Hi Elaine
Yes this helps, thanks. I used control-click to select residues.
Is there a way to adjust the transparency of ribbons, helices and amino acids?
What I am trying to do is find all the residues along the tunnel of my molecule. It is a solid protein with a tunnel through the middle. Using the SURFACE function shows only the outer surface.
I am wondering if there is a way to show only the tunnel surface and not the outer surface? For now I am using the PER-MODEL CLIPPING to slice through the middle.
participants (2)
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Elaine Meng -
Richard Collins