Comments (4)
Hi,
The correct way is indeed to specify it as ligand_ref='A1'
or ligand_ref='1'
. However, there used to be a small bug regarding regex detection, which I fixed some updates ago. If you update your version of ProtoCaller, it should hopefully fix it, as your example seems to be working for me.
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Hi, How can I install the latest version of protocaller which has the patch you mentioned? I've tried install it by mamba install -c conda-forge -c omnia -c michellab -c essexlab/label/dev protocaller
and mamba install -c conda-forge -c omnia -c michellab -c essexlab protocaller
, no upgrade happened.
My current version of protocaller is:
# Name Version Build Channel
protocaller 1.1.2 40_gf92127e essexlab
Should I clone the dev branch from github and install it manually?
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Since the packages differ only by build numbers, I would uninstall protocaller and clean the cache before installing it again. I think conda
caches the build numbers, so it won't update it, even when it should.
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I have also now released version 1.2.0
, which changes the pdb2pqr
dependency, and uses the latest propka
, so you might want to try it out. It will be easier to update with conda install -c conda-forge -c omnia -c michellab -c essexlab protocaller=1.2.0
as well.
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Related Issues (20)
- Abnormal memory usage in protocaller HOT 13
- Can I use ProtoCaller in protein-protein system? HOT 4
- The merge has opened/closed a ring HOT 12
- An input file contains a line longer than 4095 characters HOT 4
- LINCS warning and structure clash HOT 7
- Can I supply a ligand coordinate file as input? HOT 1
- H bond constraint HOT 1
- How to supply a custom pdb file (without pdb id) for protein? HOT 2
- Memory usage constantly growing with the number of perturbations. HOT 6
- How to restore ligand from parametrised file? HOT 2
- Select chain from polymer HOT 5
- Molecule ID not found HOT 1
- Explicit valence for atom # 37 C greater than permitted HOT 5
- Error while calling command 'antechamber' HOT 1
- minimise not take effect when protonated was set to True HOT 2
- Invalid file format for file HOT 2
- tleap failed for protein HOT 2
- Not all chains are contained in the FASTA sequence
- Installing error
- running error
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