Zhanglab forum

8stw is a homo-hexamer, where each chain binds to one PLP and one HEM. Therefore, the full biological assembly has 6 different PLP and 6 different HEM ligands for the 6 different chains. Therefore, it is not true that the same ligand binds to 6 different chains simultaneously.

I am afraid what you request is not implementable. It is not possible to implement rotation but no translation.

No, US-align cannot consider pLDDT score.

I am not exactly sure what you mean. If you want to extract the alignment based on a pair of superimposed structure, you can use the "se" program from https://github.com/pylelab/USalign

No, -dir1 cannot work with -o.

If there are multiple instances of the same type of ligand in the same chain, they will be sequentially labeled as 1,2,3, ... by ligand serial number, For example, PDB 117e chain B has four copies of MN ligands, which have ligand serial number of 1, 2, 3, and 4, respectively. I am afraid you made a ...

“Binding Site Number Code” is the index of ligand binding sites. For example, PDB 10mh chain A has three ligands: two DNAs and one SAH. Their binding sites are sequentially numbered BS01, BS02, BS03, respectively.

Residue sequence number (i.e., column 23 - 26 in PDB format file or _atom_site.auth_seq_id in mmCIF format).

I guess that is two different questions. .1. To have US-align output superimposed structure as seen in TM-align, use either the -o option (for superimposed structure and PyMOL scripts) and the -rasmol option (for RasMol scripts). 2. The equivalent of the "align" command in PyMOL is called ...

The 0.75/0.25 weights are for FoldX3. 0.9/0.4 weights are for FoldX4 or later.