Search found 74 matches

by zcx@umich.edu
Thu May 02, 2024 7:34 pm
Forum: Main Forum
Topic: Biolip: pocket - chain relationship
Replies: 2
Views: 56906

Re: Biolip: pocket - chain relationship

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.
by zcx@umich.edu
Thu May 02, 2024 7:21 pm
Forum: Main Forum
Topic: Restricting TM-align to a given superposition
Replies: 4
Views: 94214

Re: Restricting TM-align to a given superposition

I am afraid what you request is not implementable. It is not possible to implement rotation but no translation.
by zcx@umich.edu
Thu May 02, 2024 7:11 pm
Forum: Main Forum
Topic: Alignment based on pLDDT
Replies: 1
Views: 105248

Re: Alignment based on pLDDT

No, US-align cannot consider pLDDT score.
by zcx@umich.edu
Tue Apr 16, 2024 8:15 am
Forum: Main Forum
Topic: Restricting TM-align to a given superposition
Replies: 4
Views: 94214

Re: Restricting TM-align to a given superposition

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
by zcx@umich.edu
Tue Apr 16, 2024 8:13 am
Forum: Main Forum
Topic: US Align - superimposition of all proteins
Replies: 3
Views: 55873

Re: US Align - superimposition of all proteins

No, -dir1 cannot work with -o.
by zcx@umich.edu
Fri Mar 15, 2024 12:17 pm
Forum: Main Forum
Topic: BioLip column names clarification
Replies: 5
Views: 74072

Re: BioLip column names clarification

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 ...
by zcx@umich.edu
Wed Mar 06, 2024 5:40 pm
Forum: Main Forum
Topic: BioLip column names clarification
Replies: 5
Views: 74072

Re: BioLip column names clarification

“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.
by zcx@umich.edu
Wed Mar 06, 2024 5:38 pm
Forum: Main Forum
Topic: BioLip column names clarification
Replies: 5
Views: 74072

Re: BioLip column names clarification

Residue sequence number (i.e., column 23 - 26 in PDB format file or _atom_site.auth_seq_id in mmCIF format).
by zcx@umich.edu
Sun Feb 25, 2024 2:09 am
Forum: Main Forum
Topic: US Align - superimposition of all proteins
Replies: 3
Views: 55873

Re: US Align - superimposition of all proteins

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 ...
by zcx@umich.edu
Tue Jan 30, 2024 2:51 pm
Forum: Main Forum
Topic: BindProfX Linux tool set-up (2024)
Replies: 6
Views: 12693

Re: BindProfX Linux tool set-up (2024)

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