HETATMs in reference structures

[smlewis]

In the 14-17 benchmark, some reference structures (input/structures/14_17_res/rosetta/reference/ folder) have HETATMS:

1r6x
1ra0
1rdq
1s95
2aeb
2b0t
2bwr
2puh
3a3p
3a64
3b40
3cnq
3ea1

These blow up the RMSD step for some ways of calculating RMSD. My use of this benchmark isn't totally "inside" - I'm doing the RMSD in its own separate RosettaScripts step - so it might affect only me. I'm filing the issue because I'm having to remove the heteroatoms to get it to work for my purposes. I can PR fixed structures if it is determined that they are wanted, but I'm not sure that it's relevant for the "official" use of the data.

[kalekundert]

I'd be open to a PR, although @xingjiepan knows more about that benchmark than I do.

[spiderbaby]

Amelie put together some great notes on the Kortemme Lab wiki about the dataset - they should probably be included in some form in the repository since they are currently unavailable to most people. Maybe loop (harhar) her into the conversation if she's not already on the list? I'm on my phone so I can't check her email address easily.

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On Aug 21, 2017, at 7:16 PM, Kale Kundert ***@***.***> wrote: I'd be open to a PR, although @xingjiepan knows more about that benchmark than I do. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[smlewis]

In my local version I did it by sed -i 's/HETATM/REMARK/' *pdb in the 14-17 directory that was interesting to me - this lets Rosetta handle it but also leaves the core data there if you decide you want it later. I leave the decision on whether you want it in your hands; and will set up the PR if you do.

@spiderbaby - send me an email so I have a working address; the only email address I have for you is dead. (the public github one included).

[spiderbaby]

Nearly there, just put @gmail.com onto the end of spiderbaby. I'll check that public GitHub address later, thanks for the heads-up.

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On Aug 22, 2017, at 8:11 AM, Steven Lewis ***@***.***> wrote: In my local version I did it by sed -i 's/HETATM/REMARK/' *pdb in the 14-17 directory that was interesting to me - this lets Rosetta handle it but also leaves the core data there if you decide you want it later. I leave the decision on whether you want it in your hands; and will set up the PR if you do. @spiderbaby - send me an email so I have a working address; the only email address I have for you is dead. (the public github one included). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[amelie-stein]

The comments Shane mentioned are in the Kortemme lab wiki, so I can't access them anymore, but some of you should be able to. I'm happy to revise and elaborate if anything is unclear.