Question about atom selection in prody

[obasekigit]

Good day all, is it possible to select atom by segid in prody?

[jamesmkrieger]

It should be. Any property should be usable. Please try it and let us know if it isn’t

[obasekigit]

Sorry, I never answered this question. it did not work when I tried it

[jamesmkrieger]

Try segname

[obasekigit]

I got an error

[obasekigit]

invalid selection

[obasekigit]

i discovered segment worked and not segname

[jamesmkrieger]

ok, good to know. Thanks. Perhaps we can add these extra things

[ThaNikkitz]

Hello, I'm tagging along on this issue.
Indeed segname as used in VMD doesn't work, and throws the following error:
prody_segname_error.txt

I actually changed a portion of my code to include the segment selection by indexing an atomgroup (pdb['PROA']), but it's cumbersome for a user on my level (beginner-medium at most) and it has a ton of limitations.

I still want to thank the devs, as the prody package has been incredibly useful 😃

[jamesmkrieger]

Ok. I guess we can add extra things to the selection algebra

indexing atomgroups by segment, etc. is documented on our website along with a lot of other helpful things

[jamesmkrieger]

segname actually should be in the synonyms already. I'll have to figure out what's wrong there

[jamesmkrieger]

ok, this is fixed once I merge the pull request. Then you'll be able to select using segname is you update prody from github