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mittinatten / freesasa

C-library for calculating Solvent Accessible Surface Areas
http://freesasa.github.io/
MIT License
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FreeSasa unable to analyze nmr structures of RNA #24

Closed drjsoundsgood closed 7 years ago

drjsoundsgood commented 7 years ago

I am running the following command:

freesasa xxx.pdb --format=pdb --join-models > xxx.txt, (where xxx = 1anr, 2fey, 2n6x, 2n6w, 2n6t, 2n6s, 2m21, 28sr, 1a51) but the SASA value for nearly everything is 0. Some exceptions are 1elh (I also get a 'nan' error for some) and 1a4d. Not all have SASA values, but a good majority of them do.

The thing that all of these have in common is that they are NMR derived structures.

When I use a pdb file such as 357d.pdb (364d, 354d,1c2x) there are SASA values for nearly every atom. 1c2x is a cryo electron microscopy structure, and the other three are X-ray diffraction derived structures.

Why is SASA unable to gather surface accessibility for NMR structures?

Attached are the outputs for three examples: 1a4d, 1anr, and 357d.

1a4d.txt 1anr.txt 357d.txt

mittinatten commented 7 years ago

Hi, The problem is probably --join-models, if you join NMR models you get a very high density of atoms, and no single atom is very exposed. The best option is to either use one single model (default) or treat them separately using --separate-models.

Simon On Sat, 24 Jun 2017 at 10:26, drjsoundsgood notifications@github.com wrote:

I am running the following command:

freesasa xxx.pdb --format=pdb --join-models > xxx.txt, (where xxx = 1anr, 2fey, 2n6x, 2n6w, 2n6t, 2n6s, 2m21, 28sr, 1a51) but the SASA value for nearly everything is 0. Some exceptions are 1elh and 1a4d.

The thing that all of these have in common is that they are NMR derived structures.

When I use a pdb file such as 357d.pdb (364d, 354d,1c2x) there are SASA values for nearly every atom. 1c2x is a cryo electron microscopy structure, and the other three are X-ray diffraction derived structures.

Why is SASA unable to gather surface accessibility for NMR structures?

Attached are the outputs for three examples: 1a4d, 1anr, and 357d.

1a4d.txt https://github.com/mittinatten/freesasa/files/1099566/1a4d.txt 1anr.txt https://github.com/mittinatten/freesasa/files/1099567/1anr.txt 357d.txt https://github.com/mittinatten/freesasa/files/1099568/357d.txt

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drjsoundsgood commented 7 years ago

Hi Simon,

Yes, this was the solution to the issue.

However, when I try something like:

freesasa --separate-models --format=pdb 1anr.pdb

only the first model's SASA is calculated. Is it not possible to link these two options?

mittinatten commented 7 years ago

It is not possible at the moment, but it makes sense. I don't think it will be difficult to add, but I'm not sure if I'll have time to do it before august.

mittinatten commented 7 years ago

I created a specific issue for this feature (#25). Will close here. Reopen if anything else comes up.