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

Eric Pettersen pett at cgl.ucsf.edu
Thu Nov 21 10:38:49 PST 2019

Glad it works!  Happy I could help.


> On Nov 21, 2019, at 12:51 AM, 周盛福 <zhousf at szbl.ac.cn> wrote:
> Hi Eric,
>     Thanks for your advice.
>     I have tried to run chimera with --nogui option, then I can run almost all commands smoothly.  Thank you for your contribution to share us a perfect package.
> Best,
> Shengfu Zhou,
> 2019.11.21
> ------------------------------------------------------------------
> 发件人:Eric Pettersen <pett at cgl.ucsf.edu>
> 发送时间:2019年11月21日(星期四) 07:19
> 收件人:周盛福 <zhousf at szbl.ac.cn>
> 抄 送:Chimera User Help <chimera-users at cgl.ucsf.edu>
> 主 题:Re: [Chimera-users] Fw: To add hydrogen atoms for a dataset
> Hi Shengfu,
> Glad to hear that Chimera does a good job of hydrogen addition relative to other packages.  It can still get things wrong with extremely complex ring systems or poor starting coordinates, but seems pretty reliable otherwise.  I’m glad you like it!
> One problem here is that Python memory consumption may not go down when in the middle of script execution.  You can in fact run Chimera from a terminal with no graphical interface by giving the --nogui option, as described here: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html> .  Therefore you could break your computation into batches of 500 or 1000 molecules and possibly work around the memory problem that way.
> There is no standalone binary for adding hydrogens within Chimera.  There is a Python module (AddH), but it relies heavily on Chimera’s built-in atom typing, and which is therefore difficult to run outside the context of Chimera.
> —Eric
> Eric Pettersen
> UCSF Computer Graphics Lab
> On Nov 20, 2019, at 8:56 AM, Williams, Joanne <Joanne.Williams at ucsf.edu <mailto:Joanne.Williams at ucsf.edu>> wrote:
> --  <x-msg://3/#this>
> 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 <mailto:joanne.williams at ucsf.edu>
> From: 周盛福 <zhousf at szbl.ac.cn <mailto:zhousf at szbl.ac.cn>>
> Sent: Tuesday, November 19, 2019 1:33 AM
> To: chimera <chimera at cgl.ucsf.edu <mailto: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.
> Thanks
> Best
> Shengfu Zhou
> 2019.11.19
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