showing buried pocket
On Apr 17, 2008, at 8:59 AM, Gareth Young wrote:
So I've been trying to make an 'inverted surface'. Basically I have a cavity inside a protein which is almost completely surrounded and so it is hard to illustrate it to others without removing parts of the protein (which I could of course do). Does Chimera have a function to mark the inside of a cavity with a surface, then allowing the user to remove the protein and just leave the surface so as to illustrate the size and shape of the cavity in relation to the protein.
Have I explained that clearly enough???
Hi Gareth, If this is a standard PDB you can fetch the structure from the CASTp database (File->Fetch By ID...) which will bring up an interface that will allow you to browse the pockets of the structure, with only the browsed pocket being surfaced. If you have a non-standard PDB, you will need to identify some residues near the pocket (let's say they were residues 15 to 19) and then use a command like: ~surf :15-19 z>5 to hide surfaces further than 5 angstroms from those residues, which should hide most of the "outside" surface. Then: ~disp will hide the structure. If you don't know the pocket residues, you might clip through the outside surface with the Side View clip planes and then use the mouse-hovering popup balloons to identify some residues. If your pocket has a channel to the outside, you might want to get a clean cut through the channel by using per-model clipping on the surface and orienting the clip plane so that it cuts the channel. The Per-Model Clipping tool is in the Depiction tools category. I'd like to get Chimera to handle CASTp results for non-standard PDBs, but haven't gotten to that yet. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Apr 17, 2008, at 8:59 AM, Gareth Young wrote: So I've been trying to make an 'inverted surface'. Basically I have a cavity inside a protein which is almost completely surrounded and so it is hard to illustrate it to others without removing parts of the protein (which I could of course do). Does Chimera have a function to mark the inside of a cavity with a surface, then allowing the user to remove the protein and just leave the surface so as to illustrate the size and shape of the cavity in relation to the protein.
Hi Gareth, Here is the man page on fetching CASTp data from Chimera: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html Some of what I describe below is newish, so you would need to get a daily build of Chimera to follow along: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Although not all protein PDB entries are in the CASTp database, you can upload a structure to the CASTp server directly (not from Chimera): http://sts-fw.bioengr.uic.edu/castp/calculation.php At least the last time I tried it, if you choose the "E-mail only" output option, one of the files it mails you contains only the atoms that form each pocket. You could look at the text of that file, find the pocket of interest, and then only specify those atoms in the "surface" command in Chimera. (It wouldn't work to just open a file with those atoms and surface them, because the surface would completely enclose the atoms, not just the "real" surface side.) This process is much more tedious than the direct fetch, however. Even if you surface only the pocket atoms, there are other issues. One problem is that Chimera only turns on/off surface patches per atom, and sometimes the same atom has surface on one side that is part of the pocket, but also surface on another side that is part of some different pocket or the protein exterior; when you show the surface for all "pocket atoms" there may be some extra bits. Example: use the command "open castp:2gbp" and in the resulting dialog, make sure the Surface option is turned on and click on the second pocket in the list. It may take a few seconds to compute the surface. That pocket is completely enclosed, but some of the same atoms have additional surface. Extra bits can be clipped away to some extent, but you are limited by the planarity of the clipping plane. Another possibility in Chimera is to use the Surfnet tool. I find it often makes too many small blobs and requires experimentation. Example: open 2gbp, delete ligand (to make the pocket empty), choose Tools... Surface/Binding Analysis... Surfnet - Selected Atoms. Enter Midas Selection: :154 z<5 (I know residue 154 is next to the pocket and include other residues within 5 angstroms), set the color if you want to, click Apply. That gives one extra small blob. Actually I tried 8 angstroms first and that gave several extra small blobs. You can close (delete) the entire Surfnet results in the Model Panel (under Favorites). You can Ctrl-click the Surfnet surface to select it. You still can't control the different blobs independently until you split that surface, however (after selecting the surface, use command "ac Sc"). Then you can Ctrl-click an individual blob, open the Selection Inspector (Actions... Inspect), and change the blob's color, type of display (mesh/dot/filled) and lighting, and whether it is displayed at all - thus you can hide the extra blobs. In fact, several separate programs have been developed to show pocket or tunnel surface or void volume: Hole (can't find a current web page) Mole http://mole.chemi.muni.cz/ Caver http://loschmidt.chemi.muni.cz/caver/ Hollow http://hollow.sourceforge.net/ (you may enjoy the Munch painting in this page!) I haven't had the activation energy to try any of these myself, and unfortunately none have been specifically adapted to work with Chimera (or vice versa). Caver has a Pymol plugin. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
participants (2)
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Elaine Meng -
Eric Pettersen