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pdb_deinsert #13
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If I understood correctly, the implementation would be: input (from PDB 1IGY):
using:
while an option would select the given insert, using:
is that so? |
No! It's not about deleting insertions but making them part of the regular numbering, i.e.shifting the numbering to accommodate the insertions. The title is |
input:
output:
|
That's it! |
But insertions are there for a reason, I'd see 2 tools for this: delete insertions and select insertion, where the latter would just pick one and then the regular reres or shiftres would do the job? |
They are there because of some old numbering convention of antibodies mainly. And this is messing up things in various software. These are not alternative conformations, but real residues. Again - I don't want to delete the insertion, but rather integrate them smoothly in the sequential residue numbering hence the name |
Following the first message of @amjjbonvin , just to clarify on the behavior of On the above example,
should it be updated to:
if so, I suggest to open a new issue for this matter. |
Ok - so |
I edited Do you think selecting one and reres is a good idea? |
Not sure what you mean here... |
Sorry, I was in a rush yesterday writing these messages. I meant that we should not duplicate functionality that already exists. The insertions are a bit of a problem because they can represent a ton of different things, including antibody loops. I recently changed @joaomcteixeira comments? |
I might be wrong but wouldn't it be simpler to add an option to |
That's too many options.. I really wanted to keep it one option per script :-/ |
I would argue that as long as you are doing "normal" things this is simple, just use the script without any argument. Then we should adopt the most generic and standardized way to handle things. In parallel, you left the possibility for advanced users to tune the behavior. But I fully get your point and that's a decision to make. And anyway, if a combination of scripts can achieve the requested behavior then we should leave it that way but maybe document it (maybe a Recipes section in the documentation? For the tasks that could happen more than once and require some "tricky" pipelines?) |
We do have Those insertions are nasty. Which is why I was advertising a Try finding an advanced scenario with the existing tools to "deinsert" the insertions and preserve the gaps. That's a challenge... |
Following everything said, I would suggest:
|
I agree with this strategy. PS: And |
Definitively |
After thinking about this yesterday for a bit, here's my suggestion for a solution. I wrote a I think this is quite flexible and addresses most of the issues we had here. It does renumber, but I think that's something we have to include for simplicity. Thumbs up for approval and I will merge the code. |
Sounds good. So the default is that all insertions are removed, correct? But I am not convinced by the name - it is confusing since it implies it deletes insertions, which is not the case. So I would still be in favour of |
Closed by commit 50ba6e1 |
Insertions in the residue sequence with a numbering such as
100A
,100B
, ... can be nasty for some programs. It would be nice to have a tool that will detect those and renumber sequentially the PDB file.pdb_reres
will preserve the insertions.The text was updated successfully, but these errors were encountered: