files we got from the client - TechnionYP5779/SimuMole GitHub Wiki

I talked with our client through the emil.

She sent me two pdb files and 1 mol2 file and wrote that this files can be opened by the USCF Cimera software.

Each protein has his pdb file , that we can retrieve from this website : https://www.rcsb.org/

In order to see a visualization of the protein in the Cimera, you can choose one of this option:

  1. donwload a pdb file from the website we already mentioned and do the following : File-> Open and then choose the pdb file you got from the website

  2. figure out the pdb id of the protein , from this website or Wikipedia and do the following: File ->Fetch by ID and then insert the id in the text box near PDB.

Because of the second option the files she gave us are unnecessary if the protein is known by the Protein Data Bank.

In addition , she gave us an example of what she expect from our website in the next semester: https://www.youtube.com/watch?v=fggqPtaZj8g&feature=youtu.be

Very Important thing: as we can understand from the client, she want the dynamic movement of the molecular and not of the fourth structure of the protein as we can get from the Cimera software.

You can download Cimera from here : https://www.cgl.ucsf.edu/chimera/download.html