[Chimera-users] Reducing the map to a cubic box
goddard at sonic.net
Wed Apr 15 13:25:25 PDT 2015
In Chimera “atoms” means an atomic model, for example from a PDB file, not a density map. If you want to reduce your map to a cube by cropping and it is size 54,36,51 use command
volume #0 region 0,0,0,35,35,35
That gets the lower left corner. To get the center part
volume #0 region 9,0,7,44,35,42
The 6 numbers are imin,jmin,kmin,imax,jmax,kmax where i,j,k are indices along the 3 map axes. You can also do this with the Volume Viewer dialog menu entry Features / Region Bounds, or interactively with the mouse using Features / Subregion Selection. For more info about map manipulations
> On Apr 15, 2015, at 1:17 PM, Sushree Tripathy wrote:
> Thanks for your prompt reply. What I am trying to do is I have a map which I have loaded in chimera as #0. Now I want to reduce it to cubic size. Since the syntax is "vop boxes <> volume-spec atom-spec <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> size d", so I am choosing #0 for my volume and all the atoms in that volume. so #0 again. Please correct me if I am wrong.
> Sushree Tripathy
> Graduate Student
> Department of Physics
> University at Buffalo
> On Wed, Apr 15, 2015 at 4:13 PM, Tom Goddard wrote:
> Hi Sushree,
> Why does your "vop boxes” command use model #0 for both the map and the markers? That can’t be right. If your marker(s) are in model #1 you would need “vop boxes #0 #1 size 36”. What are you trying to do?
> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes>
>> On Apr 15, 2015, at 1:03 PM, Sushree Tripathy wrote:
>> I went through the chimera user's guide and as per the syntax used "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map.
>> Please help.
>> Sushree Tripathy
>> Graduate Student
>> Department of Physics
>> University at Buffalo
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