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
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@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
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: <http://www.rbvi.ucsf.edu/chimera/download.html#daily> Best, Elaine
On Aug 11, 2016, at 9:33 AM, Elaine Meng <meng@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@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
Hi Elaine, Thank you for fixing the bug! It worked with the daily build! Eita On Thu, Aug 11, 2016 at 9:36 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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:
<http://www.rbvi.ucsf.edu/chimera/download.html#daily>
Best, Elaine
On Aug 11, 2016, at 9:33 AM, Elaine Meng <meng@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@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
Thanks to Conrad -- I’m just the messenger! :-) Elaine On Aug 12, 2016, at 7:51 AM, Eita Sasaki <sasaki@org.chem.ethz.ch> wrote:
Hi Elaine,
Thank you for fixing the bug! It worked with the daily build!
Eita
On Thu, Aug 11, 2016 at 9:36 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: 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:
<http://www.rbvi.ucsf.edu/chimera/download.html#daily>
Best, Elaine
On Aug 11, 2016, at 9:33 AM, Elaine Meng <meng@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@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
participants (2)
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Eita Sasaki -
Elaine Meng