Bug #520

Editconf with index can not do other things

Added by David van der Spoel over 10 years ago. Updated over 10 years ago.

Target version:
Affected version - extra info:
Affected version:


When one needs to run a debugger to understand the functionality of a basic tool like editconf, something is wrong. In my case I wanted to assign a label and make a selection. This can not be done in one run of editconf due to clumsy implementation. Will fix this soon, but not straight away.


#1 Updated by David van der Spoel over 10 years ago

It is worse than so. If one wants to take a selection from a pdb file using an index file, the label gets discarded. Changing severity to minor.

#2 Updated by Erik Lindahl over 10 years ago

Not sure what you refer to by 'assign a label'?

In general, I would prefer to see the tools move in the opposite direction, so they do fewer things in each run, but make sure each such options really works in every single release, rather than trying to support arbitrary combinations of 20-30 options - the latter is simply too difficult to debug!

#3 Updated by David van der Spoel over 10 years ago

I mean editconf -label "D" to set the chain label to "D". I guess there is an optimum size, but we can not split all tools into hundreds of things. Both for editconf and trjconv we should implement a library of changes which are applied in the order specified on the command line. After 4.5 though.

#4 Updated by Erik Lindahl over 10 years ago

OK - I too have had tons of problems with non-existent chain labels before. This might not help you, but we've improved pdb2gmx as well as the pdb writing a bit in this respect: We now try to write proper TER records for pdb output formats (as well as the original chain labels when we have them), and pdb2gmx can do chain separation with arbitrary combinations of TER and/or chain id. This way you can properly handle multiple chains even if the don't have different labels (and water/protein can now occur in any order you want for multi-chain systems).

#5 Updated by David van der Spoel over 10 years ago

If you read my second comment, there is a real bug: if you have a pdb file with chain labels, and make a selection with an index file, the output file loses the labels. Will fix it tomorrow, but this is not a showstopper.

#6 Updated by Erik Lindahl over 10 years ago

Fixed in commit 3a632b68905c560d5159ce75d5a4b9827f8dfb48.

However, for the record this is a perfect example of a bug that happened because we tried to squeeze in extra functionality which is then difficult to maintain.

The index output option is handled as a separate case, and when other options to handle b-factors and labels were added, those were only added to the default case, not index writing.

Also available in: Atom PDF