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Focus static View:
Here we will go through the center and focus options capabilities.
The first example will use the pdb code 1CRN (CRAMBIN). Set the title to "1CRN Focus on Cysteine 3" and display the backbone as "Lines". Choose the t_spheresky2 for the background and increase the image size to big (700x700). Now that we defined the overall scene, we will adapt the "center on" option, to center the scene on a particular atom, namely the third cysteine alpha carbon of the crambin. For that, we have to enter the following command in the "center on" fields: " .CYS3.CA". As there is no chain identifier in the crambin, we begin with a blank space, then the residue type and nature, and finally the atom name (as it is described here).
In addition, as we want to center on the cysteine, we have to display it. Thus, we will use a user selection as follow: rname=CYS and aname=CA rendered as Sphere color by ResidueType.
Launch the rendering via the process button. Note that all options are displayed in the waiting page. For comparison the different pictures obtained according to the camera options (simple, wide, ultra-wide and zoom, respectively from right to left) are shown:
As you should notice the effect of changing the "center on" option is to zoom and translate the camera in front of the cysteine 3 alpha carbon.
Now we will present a combination of both center and focus options. The focus option aligns the camera direction with the vector starting from the "center on" coordinates and finishing at the "focus on" position. Here is the form used. Notice that only the "focus on" and the user selection fields are changed to:
" .CYS3.SGA" and selection 1: rname=CYS and aname=CA,SG.
Here is the result. If you compare it to the previous picture, you can observe that the camera is now aligned with the vector CA-SG.
By default, the final picture is zoomed on the selected atom or point coordinates. In order to show a residue or a group of residues you can change the camera angle value. See the above examples showing different angle values for a picture centered on the CYS 3 (the default value of camera angle when "center on" and "focus on" are used is ~20). Notice that we reoriented the molecule according to a rotation around the Yaxis of about 60 degrees. For several angles we also made camera zoom animations (20 frames, ~30mn for each computation).
Here are the options and the results according to the different angles:
- Representation: backbone render as Trace color by white, and user selection 1 rnum=3 render as BallnSticks color by Atom
- Scene: center on .CYS3.CA focus on auto
- Picture: background t_box size 700x700 format png procude simple
- Animation: scenario None with camera simple renderer povray 1 frames
- Option : Radiosity No Reflection No Light Skylight depth-cueing No
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