Re: [PyMOL] Using API to select resi, and return some information within a certain distance

When debugging, it is good to stop running pymol as a command line app and just run your script in a pymol gui and see what it is going on. In this case, you would find your selections have zero atoms. Why? Because you are basing them on something like "resn 102" , which is using the residue name

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

Thank you. I made a few mistakes in my code. I wasn't paying attention to the commented code because I was only trying stuff there. I still get: 1) a bunch of 3 kb black png's 2) I still have no idea what the command cmd.get_pdbstr do 3) can you give me a line using iterate to get the residue

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

Hi Ahmad - Please see below for some suggestions on getting your script to do what I understand you would like to do. Cheers, Jared > On May 1, 2017, at 4:54 PM, Ahmad Abdelzaher wrote: > > OK I finally tried some of Jared suggestions, I'm not sure why > util.cnc

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

I forgot to ask, how to retrieve residues within my selection to a list or something. Also, what does cmd.get_pdbstr do? On Mon, May 1, 2017 at 10:54 PM, Ahmad Abdelzaher wrote: > OK I finally tried some of Jared suggestions, I'm not sure why > util.cnc doesn't work I get

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

Thanks Jared. A lot of fantastic tips there. Much appreciated. Regards. On Sat, Apr 29, 2017 at 6:03 AM, Jared Sampson wrote: > Hi Ahmad - > > Here are a few suggestions: > > I'm still a bit new to the API so I'm not sure which commands to use. > At least I know I

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

Hi Ahmad - Here are a few suggestions: > I'm still a bit new to the API so I'm not sure which commands to use. > At least I know I will start with cmd.select(string name, string > selection). > > How can I tell Pymol to: > > 1) look within a certain radius distance, and return resi's within >