Search found 69 matches

by zcx@umich.edu
Fri Mar 15, 2024 12:17 pm
Forum: Main Forum
Topic: BioLip column names clarification
Replies: 5
Views: 479

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: 479

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: 479

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: 2
Views: 370

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: 5859

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.
by zcx@umich.edu
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...
by zcx@umich.edu
Sun Jan 21, 2024 2:15 am
Forum: Main Forum
Topic: BindProfX Linux tool set-up (2024)
Replies: 6
Views: 5859

Re: BindProfX Linux tool set-up (2024)

No, BindProfX is single threaded.
by zcx@umich.edu
Wed Jan 10, 2024 2:37 am
Forum: Main Forum
Topic: BindProfX Linux tool set-up (2024)
Replies: 6
Views: 5859

Re: BindProfX Linux tool set-up (2024)

The BindProfX tool was last updated in 2017 but its standalone tool should still work fine.
by zcx@umich.edu
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/
by zcx@umich.edu
Wed Oct 25, 2023 12:53 am
Forum: Main Forum
Topic: USalign: Multiple Sequence Alignment withous superpostion
Replies: 1
Views: 29116

Re: USalign: Multiple Sequence Alignment withous superpostion

No, -se is not implemented for multiple alignment.