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Align 2 PDBs using cmd.align(structure1,structure2) #1

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SimengSun01 opened this issue Mar 7, 2023 · 0 comments
Open

Align 2 PDBs using cmd.align(structure1,structure2) #1

SimengSun01 opened this issue Mar 7, 2023 · 0 comments

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@SimengSun01
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Hi All,

I tried to use the command cmd.align(structure1,structure2) to align 2 different structures, and it gave me the following error code:
/usr/local/lib/python3.8/site-packages/pymol/fitting.py in align(mobile, target, cutoff, cycles, gap, extend, max_gap, object, matrix, mobile_state, target_state, quiet, max_skip, transform, reset, _self)
395 finally:
396 _self.unlock(r,_self)
--> 397 if _self._raising(r,_self): raise pymol.CmdException
398 return r
399

CmdException: Error:

My goal is to align multiple protein structures successively (align struc1 to struc2, then align struc2 to struct3); the command "alingto" works though, but it's not essentially what I want to do. How can I fix the code here?

Thank you in advance for your help!

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