Typo fix for assigning secondary structure and two new tests for chains of different lengths #13
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
The secondary structure (ss) assignment had a typo that caused problems when the ss was assigned to multi chain models with different chain lengths. When chain.set_ss is run it must either have a input of length one or input length greater than or equal to the length of the chain.
Two new tests on the snare complex 3IPD to justifiy the change to MAIN.py. The chain22ss test outputs a pdb file that is missing a few atoms. With the fix it has the correct number of atoms.
|
I was caught out by this error as well. Without the fix, when given secondary structure with the -SS switch, Martinize reuses the first n secondary structure elements for every chain. If multiple chains have the same number of residues, this will occur silently and won't be caught by GROMPP either. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The secondary structure (ss) assignment had a typo that caused problems when the ss was assigned to multi chain models with different chain lengths. When chain.set_ss is run it must either have a input of length one or input length greater than or equal to the length of the chain.
Two new tests on the snare complex 3IPD to justifiy the change to MAIN.py.
The chain22ss test outputs a pdb file that is missing a few atoms. With the fix it has the correct number of atoms.