[Chimera-users] Fw: To add hydrogen atoms for a dataset

Williams, Joanne Joanne.Williams at ucsf.edu
Wed Nov 20 08:56:09 PST 2019


JoAnne Williams | Executive Analyst to:

Matt Jacobson, Professor and Department Chair

Pam England, Professor

Zev Gartner, Professor

Tom Ferrin, Professor

Department of Pharmaceutical Chemistry

Wallace Marshall, Professor

Center for Cellular Construction | Department of Biochemistry & Biophysics

600 16th Street, Room N372 | UCSF MC2200 | San Francisco, CA 94158

Phone: (415) 418-3079 | Email: joanne.williams at ucsf.edu
From: 周盛福 <zhousf at szbl.ac.cn>
Sent: Tuesday, November 19, 2019 1:33 AM
To: chimera <chimera at cgl.ucsf.edu>
Subject: To add hydrogen atoms for a dataset

Hi all,

    I have used UCSF Chimera for several years and find that Chimera has a perfect behavior in adding hydrogen atoms for small molecules. It is easier to add wrong hydrogen atoms onto nitrogen heterocycles groups with other software, including openbabel, MGLTools, PyMol, etc. Now I want to add hydrogen atoms for a dataset, which contains more than 10 thousands ligands for virtual screening. And a great number of compounds in this dataset have nitrogen heterocycle groups.
    So I want to add hydrogen atoms for all these compounds by Chimera.
    When I try to run a script in Favorites > Command line by read a MOL, addh and delete the MOL in cycle. I found that the memory usage of Chimera keep growing although I have delete the previous MOLs.

    My question is:
        How can I avoid this problem while I want to handle numerous molecules with Chimera?
        If there is a way to run Chimera in a real terminal without run Chimera in graphic interface?  Or
        Which bin file in Chimera_HOME can add hydrogen atoms for a molecule?

Sincerely look forward to your reply.

Shengfu Zhou
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