[Chimera-users] Docking box

Fri Nov 18 10:45:09 PST 2011

Okay, third crazy idea.  Make sure that one of your CASTp options is  
to select the pocket atoms, and with those atoms selected do the  
following:

1) open IDLE (in Tools->General Controls)

2) type (or paste):
bbox = chimera.BBox([a.coord() for a in  
chimera.selection.currentAtoms()])

3) then type:
bbox.llf
	to see the lower-left-front coordinate of the bounding box, and:
bbox.urb
	to see the upper-right-back coordinate

(also, "bbox.center()" will show the center if you care)

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Nov 18, 2011, at 10:28 AM, 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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>
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