[Chimera-users] Non-alphanumeric character in keyword
mpi566 at gmail.com
Tue Oct 27 08:51:32 PDT 2015
Dear Eric and Elaine,
Thanks for the solution.
It works but one of result files ( say, mytest.pdbqt if mytest is
prefix) will NOT come out if the command of vina is provided in a
script instead of GUI.
I guess that the main output ( mytest.pdbqt) will directly be given
into viewdock in GUI mode and it will be saved but not in a script.
I wonder if there is a way to save the main output (mytest.pdbqt) in
a script so that I can view the result of mytest.pdbqt later.
On 10/26/15, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> The file to be modified is <your Chimera
> installation>/share/Midas/midas_text.py. Here’s the diff:
> @@ -3352,9 +3353,9 @@
> raise MidasError, "No value provided for keyword
> '%s'" \
> - if not keyword.isalnum():
> - raise MidasError, "Non-alphanumeric character in" \
> - " keyword '%s'" % keyword
> + if not keyword.replace('_', '').isalnum():
> + raise MidasError, "Non-alphanumeric or underscore "
> + " character in keyword '%s'" % keyword
> if keyword.isdigit():
> raise MidasError, "Leading digit in keyword '%s'" %
> Eric Pettersen
> UCSF Computer Graphics Lab
>> On Oct 26, 2015, at 6:43 PM, MPI <mpi566 at gmail.com> wrote:
>> Dear Elaine,
>> Thanks for your kind help ! Would you please let me know which
>> file is to be modified in old ver. if a single file is responsible
>> for that keywords ? because I have mulitple manchines. I'll
>> download a daily build and update that modifiled file if this would
>> On 10/26/15, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> Dear Dwey,
>>> Sorry about that — it was a bug that keywords with underscores in them
>>> not work.
>>> You can get the fix in the next successful daily build (probably
>>> Check for daily build dated Oct 22, 2015 or later:
>>> Thanks for reporting the problem!
>>> Elaine C. Meng, Ph.D.
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>>> On Oct 25, 2015, at 7:38 AM, MPI <mpi566 at gmail.com> wrote:
>>>> Dear users,
>>>> In Chimera, I tried to run a vina docking in command line like
>>>> vina docking receptor #0 ligand #1 output mytest search_center 10,20,30
>>>> There is an error:
>>>> Non-alphanumeric character in keyword 'search_center'
>>>> I have tried tweaking the keyword 'search_center' in different ways
>>>> but the error won't go.
>>>> Dose anyone know how to fix it ? or is this format correct ?
>>>> Many thanks,
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
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