[Chimera-users] APBS mobile ion option

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 11 12:36:26 PDT 2016

In case anybody else on the list was interested, this bug will be fixed in the next Chimera daily build, which should be available by tomorrow from:



> On Aug 11, 2016, at 9:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Eita,
> This appears to be a bug… when I tried it I got a traceback.  Normally I’d suggest you file a bug report (menu: Help… Report a Bug), but since I was able to reproduce the problem myself, I will file the report and include your email address for notification of a fix.  Thanks for letting us know about the problem, and sorry for the inconvenience.  Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Aug 11, 2016, at 6:43 AM, Eita Sasaki <sasaki at org.chem.ethz.ch> wrote:
>> Hi,
>> I'd like to run APBS command with mobile ions (150 mM NaCl).
>> I tried the following command, but it did not work.
>> apbs molecule #1 ion true _posion 1,0.15,1.16 _negion -1,0.15,1.67
>> If I typed just "apbs molecule #1" it works (without mobile ions).
>> I am wondering my command was perhaps wrong but don't know the right one.
>> I hope you could help me to solve the problem
>> Thank you in advance.
>> Eita

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