Re: [Chimera-users] Chimera-users Digest, Vol 60, Issue 4
Hello, Is it possible to use Chimera to dock a small ligand into a binding pocket pdb - and if so how is the ligand imported into the protein pdb file ? Yours Sincerely, Joseph Boyle ________________________________ From: chimera-users-bounces@cgl.ucsf.edu on behalf of chimera-users-request@cgl.ucsf.edu Sent: Thu 03/04/2008 8:41 AM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 60, Issue 4 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Smooth Trajectory in MD Movie Tool (Eric Pettersen) 2. Re: Smooth Trajectory in MD Movie Tool (Yan Liang) 3. chimera manual (bala) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Apr 2008 16:37:42 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [Chimera-users] Smooth Trajectory in MD Movie Tool To: Yan Liang <liangyan@cems.umn.edu> Cc: Chimera forum <chimera-users@cgl.ucsf.edu> Message-ID: <7524F1C4-94F1-487C-A67F-FA6A5B4778DB@cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Yan, You _could_ write a script to do the averaging, but you would pretty much have to be an expert on how Chimera handles trajectory data to be able to write it in any reasonable amount of time. Since I am such an expert, I've written the script for you and attached it to this message. To do the averaging, simply have your trajectory open and then open the script (either with the File...Open menu or with the "open" command). Note that the script rewrites the coordinates of the trajectory. The only way to restore the trajectory to the "unaveraged" state is by reopening the original files. The main parameter in the script you might want to change is the "window" variable, which controls how many adjacent frames contribute to the averaging. The value in the script right now is 2, which means that the two frames to each side of a frame contribute to the average (with further-away frames contributing less). --Eric ? On Apr 2, 2008, at 2:36 PM, Yan Liang wrote:
Thank you very much Eric. I have tried "Hold selection steady" function, and it helps a lot to reduce the overall movement of the large molecule. But as for the residuals, they are still very shaky.
I am thinking about writing a script to average the movement of each atom, but I have no experience in Chimera scripting. Do you think it is possible to write such scripts in Chimera? Thanks.
Sincerely,
Yan Liang Graduate Student Department of Chemical Engineering and Materials Science University of Minnesota
On Apr 2, 2008, at 1:42 PM, Eric Pettersen wrote:
Hi Yan, Chimera doesn't yet support smoothing per se. What you can do is use "Hold selection steady" in MD Movie's Actions menu to hold one or more atoms (possibly all atoms) as steady as possible across the trajectory -- which will mostly eliminate the translational component of the "shakiness". This "holding steady" is most useful for small-molecule trajectories and replica-exchange trajectories.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/>
On Apr 2, 2008, at 10:44 AM, Yan Liang wrote:
Hi
I am using Chimera to make a MD movie. The problem is the movie is too shaky. Is it possible to smooth the trajectory by writing a Per- Frame script in MD Movie tool?
Thanks,
Yan Liang _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Joseph, Chimera does not do automated docking, but you can position the structures manually. Normally you would open the protein and ligand from two separate files. Then in the Model Panel (in Favorites menu), there will be a line for each file. You can check/uncheck the "Active" box to control which are movable with the mouse. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef Several other tools may be useful during this process: FindHBond, Find Clashes/Contacts, Distances (under Tools... Structure Analysis), Rotamers, Adjust Torsions (under Tools... Structure Editing). http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc... Once you have the ligand positioned how you want it relative to the protein, you can save PDB. You can save two separate PDB files or both structures in one PDB file. If you didn't change the structure of the protein part (for example, by rotating bonds), you could save a file of just the ligand as long as you save it "relative" to the protein structure. Then, later opening the original protein file and that new ligand file regenerates your docking. It doesn't matter which file-saving approach you take, if you will be using the file(s) later in Chimera. If you intend to use the PDB file(s) as input to another program, however, it all depends on what that other program expects and you may need to do some manual editing. If you are starting with both in one file and the Model Panel only shows one line, you would need to get the protein and ligand on separate lines to allow separate motion. You could do that by text- editing to create to files, or by simply opening that file twice and then (in Chimera) deleting the ligand part of one copy and deleting the protein part of the other. For automated docking rather than doing it yourself, you would have to use a separate program such as DOCK. Then you can view the output in Chimera. 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 On Apr 3, 2008, at 7:58 AM, Boyle, Joseph J wrote:
Hello, Is it possible to use Chimera to dock a small ligand into a binding pocket pdb - and if so how is the ligand imported into the protein pdb file ? Yours Sincerely, Joseph Boyle
participants (2)
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Boyle, Joseph J -
Elaine Meng