On Jun 5, 2018, at 6:38 PM, Modeller Caretaker <firstname.lastname@example.org:email@example.com> wrote:
On 6/5/18 12:26 PM, Richard E. Gillilan wrote: Trying to hold a range of atoms rigid during optimization.
In most cases it's easier and more efficient to do that by simply excluding the atoms from the optimization, by defining select_atoms as per https://salilab.org/modeller/9.20/manual/node23.html
Nice idea! I can do this for one of the rigid bodies. The other, which isn’t defined yet in the code snip I sent, needs to move relative to the other, so I’m thinking it will have to be defined as a true rigid body.
I get an error message. Can anyone spot what I’m doing wrong here? ... r1 = rigid_body(self.residue_range('152:A','384:A')) rsr.rigid_bodies.append(rigid_body(r1))
Sure, you are trying to make a rigid body containing another rigid body, which isn't supported in Modeller. If you want to go the rigid body route the following should work:
Ah ha! I see I split a line and accidentally duplicated the rigid_body function. Funny how you can stare at something simple and just not see it. Thanks!
r1 = rigid_body(self.residue_range('152:A','384:A')) rsr.rigid_bodies.append(r1)
Ben Webb, Modeller Caretaker -- firstname.lastname@example.org:email@example.com https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage