Search found 74 matches
- Sun Jan 21, 2024 2:38 am
- Forum: Main Forum
- Topic: itasser model comptability with ucsf chimera strucure minimization
- Replies: 1
- Views: 6892
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: 12030
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: 12030
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: 21548
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: 42010
Re: USalign: Multiple Sequence Alignment withous superpostion
No, -se is not implemented for multiple alignment.
- Wed Oct 25, 2023 12:51 am
- Forum: Main Forum
- Topic: BioLiP Has Fewer Entries Than Before
- Replies: 2
- Views: 43525
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
https://github.com/kad-ecoli/mmCIF2BioL ... d9349c02c9
- Mon Oct 09, 2023 8:37 pm
- Forum: Main Forum
- Topic: Deprecated Biolip File Downloads
- Replies: 7
- Views: 75357
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...
- 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: 43931
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...
- Mon Sep 25, 2023 5:52 pm
- Forum: Main Forum
- Topic: Deprecated Biolip File Downloads
- Replies: 7
- Views: 75357
Re: Deprecated Biolip File Downloads
There is no need to download http://zhanglab.ccmb.med.umich.edu/BioL ... LiP_ax.txt
You can download all current biolip entries from https://zhanggroup.org/BioLiP/download/BioLiP.txt.gz
May I know why you need BioLiP_*.txt?
You can download all current biolip entries from https://zhanggroup.org/BioLiP/download/BioLiP.txt.gz
May I know why you need BioLiP_*.txt?
- Tue Sep 12, 2023 8:33 pm
- Forum: Main Forum
- Topic: US align phylogenetic tree availability
- Replies: 1
- Views: 30419
Re: US align phylogenetic tree availability
US-align does not output the guide tree. Sorry.