How do you use Pymol?

May 26, 201312 yr

I've got some predcited protein structures, and I want to see how well they match against another one from the Protein Databank.

See the attached files.

I-TASSER and EsyPred3D and predict protein were all used.

What I designed was an ScFv, and now I need to see how similair it is to something else. I have no idea what I;m doing other than that.

The text document is the peptide sequence I designed.

Any help appreciated..

June 21, 201312 yr

Pymol is my favorite about protein structure viewing.

creating a new protein when you have its code ia done easily.

simply open the program and you'll see somethiong tlike this :

click on the "Builder" button at the upper window .

now press and hold "Alt" key on your keyboard and press amino-acids One-letter abbr keys after each other.

example : to attach a Trytophan you should hold Alt and press W.

as W stands for that amino acis.

Important : you should assign the sheets or helix mode just before entering new AAs.

my first test of this program was to simulate a venoum from Black-Widow spider, which had around 1400 Amino acids. any question , i'm here

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