How do I make a background transparent in PyMOL?
There are two ways to set the PyMOL background to be transparent. 1) Open PyMOL your usual way, then turn off the opaque background(default is on) by click in the menue bar on Display -> Background -> Opaque. Now you can ray trace and save your image as a png file.
How do I change the background in PyMOL?
Changing the background color: You can change the background to white to make figures by navigating to the top toolbar under Display, then Background, and choose white.
How do I make the background white in PyMOL?
How do I get a white background? In version 0.61 or later, simply use the bg_color command.
How do you trace ray in PyMOL?
You can ray-trace any Scene in PyMOL by clicking the “Ray Trace” button in the external GUI or using the “ray” command. The built-in raytracer also makes it possible to easily assemble very high-quality movies in a snap.
How do I center in PyMOL?
rendering in PyMol is very intuitive. To center a molecule, you need to make a double tap on the screen (see Figure 4). To rotate a molecule, you need to drag it on the screen; and to zoom in or zoom out a molecule, you need to pinch it on the screen (see Figure 5). …
How do I save an image in PyMOL?
You can save images that you’ve rendered (with Ray) or drawn (with Draw) again using the Save command or by File=>Save Image. You can save in Png, VRML-2 and the POVRay formats. You can save images to disk, through the command line, by using the Png command. PyMOL allows you to save movies you’ve created, too.
How do you highlight specific residues in PyMOL?
Just select the residue you’d like to highlight (either on the graphic interface – clicking on it or displaying the protein sequence on top of the main window- or by using the command line – select “surf-res”, i.
How do you Color a residue in PyMOL?
Once open, go to the command line in PyMOL and enter ‘run colour.py’ (or subbing in whatever you’ve called your file). Hit enter. Then enter ‘ngl’, and hit enter again. The cartoon representation of the protein should now have turned white.
How do you color chains in PyMOL?
Coloring Molecules Any molecule in PyMOL can be assigned a color using the small rightmost buttons in the object list (in the upper right part of the main GUI window. The Color command will do the same. PyMOL has a predefined set of colors that can be edited in the Settings->Colors menu.
How long does ray tracing take PyMOL?
24.50 sec
PyMOL>ray Ray: render time: 24. 50 sec.
What is Ray in PyMOL?
“ray” creates a ray-traced image of the current frame. This can take some time (up to several minutes, depending on image complexity).
How do you move molecules in Pymol?
As Figure 3 shows, dragging with the left mouse button rotates the scene in the Display; dragging with the middle mouse button moves the molecule in the plane of the display; and dragging with the right mouse button zooms in and out. Don’t worry if you get lost.
Is there a way to make the background transparent in PyMOL?
This setting changes how PyMol treats the background. If this option is ON then the background is whatever you specify — like black or white; however, if the setting is OFF, then the background will be treated as a transparent alpha channel. Note: turning this setting off creates the transparent backgrounds.
Can A PyMOL ray tracer generate an image?
The pymol ray tracer can generate an image of any size. For better quality maps with a white background. (This will take quite a while…) You could use the cmd.rotate and cmd.translate to position the labels, but it is likely to be somewhat painful.
Why is the backbone trace sub optimal in PyMOL?
Note that if you only use the cartoon command to explicitly define shapes over a particular region, then your results will be sub-optimal because PyMOL will not be able to properly prepare the geometry of the backbone trace for the corresponding secondary structure. How do I color secondary structure elements?
Can you use PyMOL to interpret sheet records?
PyMOL will interpret HELIX and SHEET records from PDB files if they are available, but you can specify or override these properties by using alter commands: The best PyMOL practice is to start with secondary structure in the PDB as assigned by some reliable program (DSSP, etc.) and then just make minor tweaks using alter.