[Chimera-users] vina output file misnamed

Conrad Huang conrad at cgl.ucsf.edu
Sat Oct 31 16:23:44 PDT 2015


The problem is that the GUI does a little extra work that the command 
line does not when you use the "Browse" button to select the output 
file, there is a checked check button (in small text) "add .pdbqt suffix 
if none given", so the file name that you supply actually has the .pdbqt 
appended automatically even if you do not type it.  The command line, on 
the other hand, uses the value of the "output" option without 
modification and does NOT add the .pdbqt suffix.  (I think the rationale 
is that you should be able to name your file exactly.  Even the "add 
suffix" check button allows you to turn off that behavior.  I'm not 
saying that's the RIGHT behavior, just that's the reasoning for the 
current behavior.)  In any case, your command:

> vina docking receptor #0 ligand #1 output mytest search_center 10,20,30

creates the output in file "mytest" rather than "mytest.pdbqt".  I'm 
pretty sure if you say:

> vina docking receptor #0 ligand #1 output mytest.pdbqt search_center 10,20,30

you should get the results in a properly named file.

Conrad

On 10/27/2015 8:51 AM, MPI wrote:
> 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.
>
>
> Thanks,
> Dwey
>
>
>
>
>
>
>
>
>
>
>
> 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 @@
>>                  except:
>>                          raise MidasError, "No value provided for keyword
>> '%s'" \
>>                                                                          %
>> typed
>> -               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[0].isdigit():
>>                          raise MidasError, "Leading digit in keyword '%s'" %
>> (
>>
>> keyword)
>>
>> —Eric
>>
>> 	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
>>> work.
>>>
>>> Regards,
>>> Dwey
>>>
>>> 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
>>>> did
>>>> not work.
>>>>
>>>> You can get the fix in the next successful daily build (probably
>>>> tomorrow).
>>>> Check for daily build dated Oct 22, 2015 or later:
>>>> <http://www.rbvi.ucsf.edu/chimera/download.html#daily>
>>>>
>>>> Thanks for reporting the problem!
>>>> 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 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,
>>>>> Dwey
>>>>
>>>>
>>>
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>>
>>
>
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