Hi,
I'm trying to create a rigid.txt file for an antibody PDB file that contains multiple subunits (ie subunit A, subunit B, subunit C, and subunit D). However, the example in the ncmi_2008_files folder only contains a single subunit. Is there any way one can specify subunit as well as residue number in an rigid.txt file?
On 12/10/09 4:01 PM, Robin Zhang wrote: > I'm trying to create a rigid.txt file for an antibody PDB file that > contains multiple subunits (ie subunit A, subunit B, subunit C, and > subunit D). However, the example in the ncmi_2008_files folder only > contains a single subunit. Is there any way one can specify subunit as > well as residue number in an rigid.txt file?
No, not as currently implemented - in fact, FlexEM explicitly removes chain labels, so you'll end up with 4 chains each with no ID. So just specify the residue number with no chain ID. This is only a problem if you have residues in different chains that have the same number. As a workaround until FlexEM properly supports multiple chains, you could renumber your antibody so residue numbers aren't duplicated (e.g. first chain is 1-100, second is 101-200, and so on).
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Robin Zhang