On Nov 20, 2019, at 8:56 AM, Williams, Joanne <Joanne.Williams@ucsf.edu> wrote:_______________________________________________JoAnne Williams | Executive Analyst to:
Matt Jacobson, Professor and Department ChairPam England, ProfessorZev Gartner, ProfessorTom Ferrin, ProfessorDepartment of Pharmaceutical Chemistry
Wallace Marshall, ProfessorCenter for Cellular Construction | Department of Biochemistry & Biophysics
600 16th Street, Room N372 | UCSF MC2200 | San Francisco, CA 94158Phone: (415) 418-3079 | Email: joanne.williams@ucsf.eduFrom: 周盛福 <zhousf@szbl.ac.cn>
Sent: Tuesday, November 19, 2019 1:33 AM
To: chimera <chimera@cgl.ucsf.edu>
Subject: To add hydrogen atoms for a datasetHi 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? OrWhich bin file in Chimera_HOME can add hydrogen atoms for a molecule?Sincerely look forward to your reply.ThanksBestShengfu Zhou2019.11.19
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