How do you show cartoons on PyMOL?
[PyMOL] cartoon mode
- type “cartoon arrow” in the command line, you will see below.
- cartoon dash,
- cartoon dumbbell.
- cartoon loop,
- cartoon oval,
- cartoon putty (based on b-factor, no color gradient)
- cartoon rectangle (like cartoon arrow, but no “arrow” displayed)
- cartoon tube.
How do you show secondary structure in PyMOL?
Simply type “dss” in the command line, PyMOL automatically calculates, rebuilds and draw the secondary structural regions. If the “all_states” is turned on, all structures will also be displayed properly.
How do you color loops 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 do you display the secondary structure of a protein in PyMOL?
Load the downloaded PDB file into PyMol (Figure 1)….
- Select the object or molecule in internal GUI on the right side.
- Select the molecule or object by clicking left mouse button (in this case 1UBQ).
- Select ‘S’ labeled button, we can select (show →as →stick).
- Similarly for other representations.
What is a protein B-factor?
Abstract. The term B-factor, sometimes called the Debye-Waller factor, temperature factor, or atomic displacement parameter, is used in protein crystallography to describe the attenuation of X-ray or neutron scattering caused by thermal motion.
What is Sele PyMOL?
When you left-click-and-release on an atom using the left button, PyMOL should, by default, select the entire residue: This will create an entry “(sele)” in the control panel which can be acted upon using the pop-up menus. And finally, left-clicking away from any atom should deactivate the selection.
What are the advantages of PyMOL’s cartoon ribbon facility?
One of the advantages of PyMOL’s cartoon ribbon facility is that it is easy to switch between “smoothed” versions of protein secondary structure, and “realistic” renditions which portray actual main chain coordinates.
How to use cartoon_nucleic_acid_as_cylinders in PyMOL?
cartoon_nucleic_acid_as_cylinders (boolean, default: on) controls whether or not PyMOL draws cartoon nucleic acids as high-quality cylinders or low-quality. cartoon_nucleic_acid_color (color, default: -1) controls the control of nucleic acid backbone cartoons. 2 = use P coordinates and terminal 3’ OH (if present)
Is there a way to enable the sausage view in PyMOL?
The familiar sausage representation in PyMOL is called, “putty”. To enable the putty/sausage view simply do, show cartoon cartoon putty unset cartoon_smooth_loops unset cartoon_flat_sheets As of v 0.98 or so, there’s a Putty option. Use this.
How does PyMOL handle helical regions?
Under these conditions, PyMOL will do extra processing to insure that good normals have been calculated for helical regions, and perform smoothing of loops, where desired. Also under such conditions, in automatic mode, cartoon representations will be assigned according to the secondary structure type.