syntax for creating sidechain pseudoatoms for selected residues

[goji-patai]

Hi, I am hoping you can point me in the right direction. I am reading a PDB as follows:

path = 'TO PATH'
for filename in glob.glob(os.path.join(path, '*.pdb)):
    cmd.load(filename)  # use the name of your pdb file
    stored.residues = []
    cmd.iterate('name ca', 'stored.residues.append((resn))')
    #print (stored.residues)

Then I want to create a sidechain pseudoatom and save its coordinate in an array along the lines ...

    stored_residues_sidechain_PS = []
    for i in stored.residues:
        cmd.select ('resn %s' % i)
        stored_residues_sidechain_PS.append(sidechaincenters [ '(sele)' [2]])

but I am having difficulty with the correct syntax to use for sidechaincenters. Please point me in the right direction. Thank you

[speleo3]

You might find this useful: https://pymolwiki.org/index.php/Sidechaincenters

[goji-patai]

Hi Thomas, Thank you. That was good guidance. I can now calculate the Sidechaincenters. Working on manipulating the scc object.

Best, G

On Tue, Dec 7, 2021 at 4:22 PM Thomas Holder @.***> wrote:

You might find this useful: https://pymolwiki.org/index.php/Sidechaincenters

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