Search found 74 matches
- Thu May 02, 2024 7:34 pm
- Forum: Main Forum
- Topic: Biolip: pocket - chain relationship
- Replies: 2
- Views: 55601
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.
- Thu May 02, 2024 7:21 pm
- Forum: Main Forum
- Topic: Restricting TM-align to a given superposition
- Replies: 4
- Views: 91609
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.
- Thu May 02, 2024 7:11 pm
- Forum: Main Forum
- Topic: Alignment based on pLDDT
- Replies: 1
- Views: 103670
Re: Alignment based on pLDDT
No, US-align cannot consider pLDDT score.
- Tue Apr 16, 2024 8:15 am
- Forum: Main Forum
- Topic: Restricting TM-align to a given superposition
- Replies: 4
- Views: 91609
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
- Tue Apr 16, 2024 8:13 am
- Forum: Main Forum
- Topic: US Align - superimposition of all proteins
- Replies: 3
- Views: 53666
Re: US Align - superimposition of all proteins
No, -dir1 cannot work with -o.
- Fri Mar 15, 2024 12:17 pm
- Forum: Main Forum
- Topic: BioLip column names clarification
- Replies: 5
- Views: 72754
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 ...
- Wed Mar 06, 2024 5:40 pm
- Forum: Main Forum
- Topic: BioLip column names clarification
- Replies: 5
- Views: 72754
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.
- Wed Mar 06, 2024 5:38 pm
- Forum: Main Forum
- Topic: BioLip column names clarification
- Replies: 5
- Views: 72754
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).
- Sun Feb 25, 2024 2:09 am
- Forum: Main Forum
- Topic: US Align - superimposition of all proteins
- Replies: 3
- Views: 53666
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 ...
- Tue Jan 30, 2024 2:51 pm
- Forum: Main Forum
- Topic: BindProfX Linux tool set-up (2024)
- Replies: 6
- Views: 12092
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.