[chimera-dev] Adding a New Atom To AD4 parameter file

[Greg Couch]

Just a reminder that changing the permissions, on an application's 
files, is considered a security risk on Windows.  If you are the only 
user of the computer, then it would be okay.

An alternate, cross-platform solution would be to copy the AutoDockTools 
directory to a directory you control, make the modification, and then 
set the CHIMERAPATH environment variable to that directory.  CHIMERAPATH 
is just like PYTHONPATH but only for Chimera.  That way, Chimera will 
find your version instead of it's built-in version.

On Windows, setting your environment variables is tricky. See How to 
change environment variables on Windows 10 
<https://www.architectryan.com/2018/08/31/how-to-change-environment-variables-on-windows-10/>.  
But create a User variable, not a System one.

     -- Greg

On 8/13/2020 3:30 PM, Eric Pettersen wrote:
> Hi Tram,
> You'll have to change the file/folder permissions for that file and/or 
> containing folder to give yourself "write" permission.  See the "File 
> and Folder Permissions" section of this page for an explanation: How 
> to Set File and Folder Permissions in Windows 
> <https://www.online-tech-tips.com/computer-tips/set-file-folder-permissions-windows/>
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>> On Aug 12, 2020, at 4:47 PM, Tram B. Danh <tbdanh at uci.edu 
>> <mailto:tbdanh at uci.edu>> wrote:
>>
>> To whom it may concern,
>> My name is Tram Danh, a student researcher under the Radiology 
>> Department at UCI. I have encountered problems as I tried to run 
>> AutoDock Vina for a structure with At (Astatine). The system said 
>> that the atom At was not assigned or recognized.
>>
>> I was told by an AutoDock member that At was not in the database so I 
>> would need to derive the parameter for At myself. I followed 
>> instructions, downloaded the default parameter file, and added At 
>> into that file. My current problem is that I am unable to save it in 
>> the "*C:\Program Files\Chimera 
>> 1.14\bin\Lib\site-packages\AutoDockTools*" without administrator's 
>> permission. I've attached the picture below for your reference.
>>
>> Thank you for your assistance! I hope to hear from you soon!
>>
>> Sincerely,
>> Tram Danh
>>
>> <ADA_parameters.PNG>
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