Hi Baptiste -
You can loop through your loaded objects within a Python code block for this.
This works for me with a different set of related structures:
```
python
dihedral = ['N', 'CA', 'CB', 'CG']
for obj in cmd.get_names():
residue = "/{}//A/288/".format(obj)
angle = cmd.get_dihedral(
residue + dihedral[0],
residue + dihedral[1],
residue + dihedral[2],
residue + dihedral[3]
)
print(residue, '-'.join(dihedral), angle)
python end
```
and prints the following output:
```
/3oph//A/288/ N-CA-CB-CG -169.7447509765625
/3opl//A/288/ N-CA-CB-CG -157.88107299804688
/3opp//A/288/ N-CA-CB-CG -76.08760833740234
/3opr//A/288/ N-CA-CB-CG -75.59835815429688
```
Hope that helps.
Cheers,
Jared
On April 4, 2018 at 4:04:25 AM, Baptiste Legrand (bap.legr...@gmail.com) wrote:
Dear all,
I wounder to know about possible ways to measure chi1, chi2 dihedral
angles on a set of structures. For example, I opened 10 pdb files and
the phi_psi command allows us to easily obtain the phi and psi values:
Ex: To obtain the phi and psi values of the residue 288 of the chain A
in the 10 structures,
>phi_psi ///A/288
PHE-288: ( -63.4, -25.1 )
PHE-288: ( -60.1, -35.9 )
PHE-288: ( -65.0, -28.1 )
PHE-288: ( -59.4, -31.0 )
PHE-288: ( -62.6, -34.7 )
PHE-288: ( -80.5, -36.4 )
PHE-288: ( -63.5, -24.7 )
PHE-288: ( -60.5, -31.7 )
PHE-288: ( -63.3, -38.5 )
PHE-288: ( -62.5, -35.2 )
Then, I tried to get the chi1 and chi2 values for the Phe288. It works
for a single structure but not for the entire set (e.g. chi1),
>get_dihedral ///A/288/N, ///A/288/CA, ///A/288/CB, ///A/288/CG
PyMOL>get_dihedral ///A/288/N, ///A/288/CA, ///A/288/CB, ///A/288/CG
GetDihedral-Error: Selection 1 doesn't contain a single atom/vertex.
GetDihedral-Error: Selection 2 doesn't contain a single atom/vertex.
GetDihedral-Error: Selection 3 doesn't contain a single atom/vertex.
GetDihedral-Error: Selection 4 doesn't contain a single atom/vertex.
cmd.get_dihedral: -1.000 degrees.
Is there a simple way to obtain the same results than for phi and psi,
may be tuning the phi_psi command...
Thanks for your help,
Best,
Baptiste
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