Zhanglab forum

It seems to be solved. For reference, I used the source code from (https://github.com/pylelab/USalign/) with a different version and setup of MinGW (gcc version 9.2.0) and they both compiled successfully.

Is there any way to compile MMalign or USalign source code into a windows executable? This is possible for TMalign, but in USalign and MMalign there are headers that do not exist in Windows and thus the compiling fails. Example: #include <sys/wait.h> // for waitpid() #include <sys/ioctl.h> // for ...

Thank you for the reply. The atom records section you quoted is where I got the hint for the revisions. Unfortunately, these records are not used from molecular visualization applications or parsers (they can only "see" the revised ligand). I understand it is impractical to rebuild the database ...

Hello, I have recently detected a small number of mismatches in i) ligand residue name identifiers and ii) ligand residue index identifiers. This is most likely because PDB has revised the mmCIF atom records between BioLiP releases. I provide here a few examples I came across: pdb_code ligand_chain ...

It looks like the 4th (missing) row in the matrix represents "pre-rotation and post-rotation translation vectors respectively". When the matrix is extended by [0,0,0,1], it will be successfully read by PyMOL and the object will be transformed.

Thank you, this is what I am currently doing. The reason I want to avoid saving the aligned structures is file size. At scale, this will create plenty of data, whereas the matrix alone is much smaller.

Thank you. I have saved the rotation matrix into a separate txt file. My goal is to apply this transformation matrix on the particular structure to recreate the alignment (without having to re-align). I am using PyMOL which supports transformation of objects but seems to expect a 4x4 matrix whereas ...

Hello,
Is there a way to capture and save the rotation matrix for an alignment in TM-align, in a way that can be applied to the two structures later to replicate the exact superposition (without the need to realign them)? I am referring to the last/best alignment.

Thank you!

Does this refer to the fact that a ligand in a single structure could bind two different UniProt IDs, or bind two or more different chains, within that structure? I guess there are multiple perspectives to ligand redundancy, I assume here it is defined on the receptor side, on the level of chains ...