Comments (2)
Dear koyurion,
currently PLIP handles only the first model it sees in a PDB file and ignores the rest:
plip/plip/structure/preparation.py
Line 60 in c8d4c8d
I will consider to implement a command line flag that allows to select the desired model for the next release. For now, could you please use PyMol to isolate your models into separate structures with the split_states
command (see https://pymolwiki.org/index.php/Split_states)? Then you could analyze all models with a simple bash script or you use a specific one.
from plip.
Thank you for your help !~
from plip.
Related Issues (20)
- Interpretation of results HOT 3
- XML filename shouldn't be `report.xml` HOT 2
- Openbabel package name conflict HOT 2
- python module stuck in loop with some pdb files
- Traceback (most recent call last): File "/plip/plip/plipcmd.py", line 16, in <module> from plip.basic import config, logger ModuleNotFoundError: No module named 'plip' HOT 1
- How to go about finding interacting Amino Acid Residues of ~1 billion compounds (In PDBQT) HOT 1
- Batch mode for protein-peptide
- pymol.CmdException: Error: Object not found
- << PLIP took forever >>
- Segmentation error with pdb files: HOT 1
- Calculate and report interactions for just one amino acid residue
- Generated RST file missing blank line after section titles
- Option not to add whitespace after trimming
- supplemental.py:90: RuntimeWarning: invalid value encountered in arccos
- The ligand structure is not visible.
- conf.NOHYDRO and aromatics
- MmCIF support HOT 1
- Extract interaction specifically for RNA-small molecule ligand and exclude other interactions in the output
- Incorrectly indexed interacting residues HOT 2
- Is there any parameters which can control the report results only include the lig interaction within protein instead of some residue interaction in protein? HOT 10
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from plip.