[Chimera-users] Docking box

George Tzotzos gtzotzos at me.com
Fri Nov 18 10:35:07 PST 2011

Hi Tom / Elaine,

Many thanks for the useful suggestions. I'll certainly try them

Best regards


On Nov 18, 2011, at 7:28 PM, Tom Goddard wrote:

> Hi George,
> Tricky, Elaine!  Another crazy way to do this if your box does not need to be aligned with the PDB model axes is to use menu entry Measure and Color Blobs from the Tools / Surface & Binding Analysis menu, click on the "Show principal axes box" option and then click the CASTp pocket surface.  This will draw a green outline box and the meshmol command can be used as Elaine explained to make that into a PDB containing the box corners as atoms.  This doesn't allow you to manually adjust the box size.  It will be aligned with the principal axes (moment of inertia) of the pocket surface and just bound that surface.  A sticky point is when using the meshmol command you'll need to close the surface model (use Model Panel) because the outline box and the surface are assigned the same model number (matching the PDB model) and there is no way to distinguish those two when using the meshmol command.
>     Tom
> -------- Original Message --------
> Subject: Re: [Chimera-users] Docking box
> From: Elaine Meng 
> To: George Tzotzos
> Date: 11/18/11 10:03 AM
>> Hi George,
>> I can't think of any way to do this directly.  However, here are a couple more circuitous ideas.
>> (1) generate a density map from the structure, just because we have box-drawing capability for density maps.  For example, I tried commands:
>> open 2gbp
>> molmap protein 5 model 2
>> Density map and Volume Viewer will appear. In Volume Viewer:
>> move the vertical bar on the data histogram all the way to the right so that you don't see the density map any more, since you don't care about it.  In Volume Viewer menu choose "Features... Subregion selection."  In the options that appear in the dialog, turn on "Select subregions..."  and try drawing a box in 3D with the mouse as described here (it can be tricky, may take a while to get the hang of it... have to draw initial box, then rotate, then drag faces to make smaller in the dimensions you couldn't see well at first):
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#mouseselect>
>> The box is aligned on the X,Y,Z coordinates of the molecule, which I believe is probably what you want.  It depends on the docking program, of course, but I suspect at least some of them require the boxes to be aligned on the X,Y,Z coordinates rather than oriented any which way.
>> When you get the box how you want it, click the Crop button.  From menu (still in Volume Viewer) choose "Features.. Data display options" and turn on the option to "Show outline box."  If that outline box looks OK, you can click with the box-drawing button (whichever it was set to in the dialog) outside the box to get rid of the original green box you drew.  If not, go back to Full (click the Full button, it's in the same row as the Crop button) and start over with drawing the box.
>> When you have an OK outline box, use the meshmol command to make it a "molecule", for example:
>> meshmol #2 0.25
>> (model 2 was created in the molmap command above, and the 0.25 is just bond thickness for displaying the box)
>> That creates a new "molecule" model #3 that is really the box.  You can write it as a PDB file in the normal ways (Chimera File menu or command "write"), making sure you save it "relative to" your original structure.  If you reopen it some of the bonds may be dashed since they are recognized as being too long to be real bonds.
>> There, wasn't that fun?
>> (2) If you are using DOCK, you could use the small accessory program that comes with it, "showbox," to draw a box centered on and/or enclosing your docking spheres.  
>> <http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Showbox>
>> I haven't forgotten that you are looking at a Castp pocket and might not have any spheres, but now Chimera can be used to create the pheres.  A very new feature in Chimera (daily builds from last couple of days) is that it can read/write the Sphgen sphere format used by DOCK.  You could use the castp dialog option to select the pocket atoms, then save those atoms as DOCK spheres making sure to use the "Save selected atoms only" option.
>> The trick here is that the save spheres option (it's in the Model Panel, "save sphgen" function) is not shown unless you have opened a sphere file.  I attach a small sphere file here solely for the purpose of giving you access to this option.  It can be opened in the usual ways (Chimera File menu etc.).
>> I hope this helps and that you haven't lapsed into a coma while reading this answer,
>> 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 Nov 18, 2011, at 2:33 AM, George Tzotzos wrote:
>>> Hi everybody,
>>> I'm visualising a cavity generated by CASTp. Ideally I'd like to draw and get the coordinates of a box around the cavity to use in docking simulations. Is this possible with Chimera?
>>> Your suggestions would be much appreciated.
>>> Regards
>>> George
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>> Chimera-users at cgl.ucsf.edu
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