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Phenix.reduce Adding spurious hydrogens #52

Open russell-taylor opened 3 years ago

russell-taylor commented 3 years ago

Dorothee forwarded a message from the PHENIX bug list:

From: Wankowicz, Stephanie Stephanie.Wankowicz@ucsf.edu Date: Mon, Jan 4, 2021 at 11:55 AM Subject: Phenix.reduce Adding spurious hydrogens To: bugs@phenix-online.org bugs@phenix-online.org

Hello,

I am getting errors when using certain flags with phenix.reduce. I am trying to get hydrogens to be added to PDB 6fm7.pdb.

The following command works: phenix.reduce 6fm7.pdb

However, using this command:Â phenix.reduce -FLIP 6fm7.pdb > test.pdb causes an extra hydrogen to be added to the ligand NXL.I have also tried to add NXL.cif into the command but get the same result

PDBs (input: 6fm7.pdb, output: test.pdb) and cif files are attached.

Thanks, Stephanie

https://app.zenhub.com/files/298923894/e0006d62-c8b3-4711-bd13-1ee251ef8af1/download

chrissciwilliams commented 3 years ago

There is a discrepancy between the chemical components entry/Reduce het dict (which contain H13 attached to OAD) and the restraint file generated by Elbow (which does not contain H13). I'm currently talking with Nigel about whether this is a group that should be deprotonated (and presumably charged). I'll update the het dict accordingly if so.

-Christopher Williams ---Richardson Lab, Duke University

On Tue, Jan 5, 2021 at 8:05 AM Russell Taylor notifications@github.com wrote:

Dorothee forwarded a message from the PHENIX bug list:

From: Wankowicz, Stephanie Stephanie.Wankowicz@ucsf.edu Date: Mon, Jan 4, 2021 at 11:55 AM Subject: Phenix.reduce Adding spurious hydrogens To: bugs@phenix-online.org bugs@phenix-online.org

Hello,

I am getting errors when using certain flags with phenix.reduce. I am trying to get hydrogens to be added to PDB 6fm7.pdb.

The following command works: phenix.reduce 6fm7.pdb

However, using this command:Â phenix.reduce -FLIP 6fm7.pdb > test.pdb causes an extra hydrogen to be added to the ligand NXL.I have also tried to add NXL.cif into the command but get the same result

PDBs (input: 6fm7.pdb, output: test.pdb) and cif files are attached.

Thanks, Stephanie

https://app.zenhub.com/files/298923894/e0006d62-c8b3-4711-bd13-1ee251ef8af1/download

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russell-taylor commented 3 years ago

Thanks! Go ahead and close this issue when you resolve it.