Search found 66 matches

by zcx@umich.edu
Sun Feb 25, 2024 2:09 am
Forum: Main Forum
Topic: US Align - superimposition of all proteins
Replies: 1
Views: 54

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: 4263

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: 2456

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: 4263

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: 4263

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: 6199

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: 14800

Re: USalign: Multiple Sequence Alignment withous superpostion

No, -se is not implemented for multiple alignment.
by zcx@umich.edu
Wed Oct 25, 2023 12:51 am
Forum: Main Forum
Topic: BioLiP Has Fewer Entries Than Before
Replies: 2
Views: 15595

Re: BioLiP Has Fewer Entries Than Before

Yes, some entries are removed due to correction of van deer Waals radius calculation.
https://github.com/kad-ecoli/mmCIF2BioL ... d9349c02c9
by zcx@umich.edu
Mon Oct 09, 2023 8:37 pm
Forum: Main Forum
Topic: Deprecated Biolip File Downloads
Replies: 7
Views: 24885

Re: Deprecated Biolip File Downloads

Dear user, To address your request, I have uploaded all BioLiP (version 1) webserver data to https://doi.org/10.5281/zenodo.8407896 and https://zenodo.org/record/8407920 You may concatenate the two files and decompress them by: $ cat BioLiP1aa BioLiP1ab > BioLiP.tar.bz2 $ tar -xvf BioLiP.tar.bz2 You...
by zcx@umich.edu
Tue Oct 03, 2023 1:03 am
Forum: Main Forum
Topic: BioLiP mismatch with updated PDB atom records (ligand residue name & identifier)
Replies: 2
Views: 15725

Re: BioLiP mismatch with updated PDB atom records (ligand residue name & identifier)

Most likely we will not update PDB records that are changed after initial release, as regenerating the full database for every weekly release is a huge undertake. By the way, for the cases you mentioned where the ligand name is changed, it is not entirely true that the ligand is not present in the c...