Search found 69 matches
- Fri Mar 15, 2024 12:17 pm
- Forum: Main Forum
- Topic: BioLip column names clarification
- Replies: 5
- Views: 473
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: 473
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: 473
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: 2
- Views: 369
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: 5857
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: 2656
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: 5857
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: 5857
Re: BindProfX Linux tool set-up (2024)
The BindProfX tool was last updated in 2017 but its standalone tool should still work fine.
- Wed Dec 13, 2023 8:36 pm
- Forum: Main Forum
- Topic: Windows executable for USalign or MMalign
- Replies: 2
- Views: 17457
Re: Windows executable for USalign or MMalign
There is actually precompiled binary at the bottom of https://zhanggroup.org/US-align/
- Wed Oct 25, 2023 12:53 am
- Forum: Main Forum
- Topic: USalign: Multiple Sequence Alignment withous superpostion
- Replies: 1
- Views: 28884
Re: USalign: Multiple Sequence Alignment withous superpostion
No, -se is not implemented for multiple alignment.