Search found 71 matches
- Tue Apr 16, 2024 8:15 am
- Forum: Main Forum
- Topic: Restricting TM-align to a given superposition
- Replies: 2
- Views: 88664
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: 48722
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: 68138
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: 68138
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: 68138
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: 48722
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: 11757
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.
- Sun Jan 21, 2024 2:38 am
- Forum: Main Forum
- Topic: itasser model comptability with ucsf chimera strucure minimization
- Replies: 1
- Views: 6643
Re: itasser model comptability with ucsf chimera strucure minimization
Your issue is caused by the inability of UCSF chimera to recognize the hydrogen atoms in the I-TASSER model. In fact, structure minimization runs without any issue if the hydrogen atoms are removed prior to loading the structure into UCSF chimera. I am not familiar with how to remove hydrogens in UC...
- Sun Jan 21, 2024 2:15 am
- Forum: Main Forum
- Topic: BindProfX Linux tool set-up (2024)
- Replies: 6
- Views: 11757
Re: BindProfX Linux tool set-up (2024)
No, BindProfX is single threaded.
- Wed Jan 10, 2024 2:37 am
- Forum: Main Forum
- Topic: BindProfX Linux tool set-up (2024)
- Replies: 6
- Views: 11757
Re: BindProfX Linux tool set-up (2024)
The BindProfX tool was last updated in 2017 but its standalone tool should still work fine.