Hello,
I want to study a ligand complex with a WT protein variant and a variant featuring a mutation. For this I use --mutate flag. However, this flag has no effect if the input is in the CIF format. This is because the respective method parse_input_structure in https://github.com/baker-laboratory/PLACER/blob/main/modules/protocol.py does not have the functionality implemented for CIF, only for PDB.
On the other hand, the behaviour of PLACER seems to be significantly different depending on the input file format - when the input is in CIF, the output feels as qualitatively better, at least in this particular case. Thus, using the --mutate feature with PDB input is not possible in my case.
Please advise, is there a possibility to implement the mutate feature with CIF input?
Thank you
Hello,
I want to study a ligand complex with a WT protein variant and a variant featuring a mutation. For this I use
--mutateflag. However, this flag has no effect if the input is in the CIF format. This is because the respective method parse_input_structure in https://github.com/baker-laboratory/PLACER/blob/main/modules/protocol.py does not have the functionality implemented for CIF, only for PDB.On the other hand, the behaviour of PLACER seems to be significantly different depending on the input file format - when the input is in CIF, the output feels as qualitatively better, at least in this particular case. Thus, using the --mutate feature with PDB input is not possible in my case.
Please advise, is there a possibility to implement the mutate feature with CIF input?
Thank you