Hi Rezvan,

UCSF Chimera makes it easy to do so.

https://www.cgl.ucsf.edu/chimera/

After selecting a ligand of a complex in UCSF Chimera, do like this:

Select -> Zone... -> ☑ OK.

Rezvan Marjani

Assalam O alaikum

I hope you doing well

first of all you open your complex structure in DS go to analyse structure click on 2D diagram and for distance ligand and receptor with hydrogen bonding click right button of mouse and click on display style at end you have all the required option.

And if you save your time so only enter your complex in ligplot there you will get all.

Dear Rezvan Marjani hope this text finds you well,

I suggest you use RCSB PDB viewer.. it is simple or you can do the same as Waseem Ahmad Ansari said.

good luck

Waseem Ahmad Ansari Thankful . But in the display style option, which is not an option to select amino acids around 6 angstroms of the ligand !!!!!!

Yoshinobu Ishikawa thank you . I went this way but it did not show amino acids after OK !!How do I see amino acids?

Did you open a ligand and a protein in Chimera?

@Yoshinobu Ishikawa

yes Professor

After displaying your ligand and protein and selecting the ligand, you should use the zone command. And you can see the highlighted amino acids around the ligand. You may change the color of the selected amino acids for clarity.

Actions -> Color -> by element

When you want to know the distance between any atoms, try Distances command after selecting two atoms by clicking atom1 with the control key and then clicking atom2 with the control+shift key:

Tools -> Structure Analysis -> Distances

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html

https://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004705.html

@Yoshinobu Ishikawa thank you profeesor

You can modify the script, which selects atoms within 4A.

Go to the ***\BIOVIA\Discovery Studio 20YY\share\Scripts

Open SelectWithin4Angstrom.pl with Script Window and edit the line:

if(SetSelection($document, $selectedObjects)){$document->SelectByRadius(4.0, 'Atom');

Change 4.0 to 6.0 and maybe Atom to Amino Acid, but I didn't check the last option.

Rezvan Marjani

It does work, but type 'Aminoacid' in the command line.