[chimerax-users] MOL2 import

[Conrad Huang]

Hi, Marco.

There was indeed another subtle problem with my parsing code.  My test 
data files were all produced by DOCK and did not reveal the issue.

The problem should be fixed in daily builds dated March 15, 2019 or later.

Conrad

On 3/14/2019 3:56 AM, Marco J. Müller wrote:
> Hello Conrad,
> 
> thank you for your reply. Attached is a test file that is causing 
> problems in ChimeraX (see below for the log). This testfile is a 
> cut-down version of the original file (containing informations on 
> docking scores from GOLD suite) that was created in Chimera by saving it 
> as mol2 file /and manually removing the zeros in line 8/, as Chimera was 
> sanitizing this line upon saving. If I add the two zeros in the original 
> file, ChimeraX was loading the structures successfully, still 
> complaining about the metainformations though.
> 
> I'm using version 0.9 (2019-03-12) of Chimera X on Win10 (1809) and was 
> using Chimera 1.13.1 to generate the testfile.
> 
> Thank you and best regards,
> 
> Marco
> 
> 
> open 
> <help:user/commands/open.html>"C:\\Users\\Marco\\Desktop\\benzotriazol\\chimeratest.mol2"
> Summary of feedback from opening 
> C:\Users\Marco\Desktop\benzotriazol\chimeratest.mol2
> /warnings/ 	line 8: bad molecule data
> line 8: ignore unexpected line '57 62 1'
> line 9: ignore unexpected line 'SMALL'
> line 10: ignore unexpected line 'USER_CHARGES'
> 
> 
> Opened chimeratest.mol2 containing 0 structures (0 atoms, 0 bonds)
> 
> 
> Am 14.03.2019 um 00:18 schrieb Conrad Huang:
>> Hi, Marco.
>>
>> Can you send me the file that is causing the problem?  When I change a 
>> working Mol2 file to remove those two fields, I get a few error 
>> messages but the molecules are opened.  I'm concerned that some other 
>> error is preventing import of your file.
>>
>> Conrad
>>
>> On 3/13/2019 2:23 AM, Marco J. Müller wrote:
>>> Dear ChimeraX Team,
>>>
>>> when I try to load structure outputs of docking runs in .mol2 format 
>>> into ChimeraX, it fails to load them, while the same can be imported 
>>> by Chimera successfully. After a bit of playing around I found that 
>>> the following section is relevant and fails in this format:
>>>
>>> @<TRIPOS>MOLECULE
>>> MYCOOLMOLECULE
>>>      57    62     1
>>> SMALL
>>> USER_CHARGES
>>>
>>> The problem seems to be that ChimeraX requires explicit definitions 
>>> of /#features/ and/#sets/ in the third line (apart from /#atoms 
>>> #bonds #substructures/), while they are typically omitted in most 
>>> programs. So the following lines could be imported:
>>>
>>> @<TRIPOS>MOLECULE
>>> MYCOOLMOLECULE
>>>      57    62     1  0  0
>>> SMALL
>>> USER_CHARGES
>>>
>>> Can this case be addressed in a future version of ChimeraX?
>>>
>>> Thank you in advance,
>>>
>>> Marco
>>>
>>> -- 
>>> Marco J. Müller
>>> PhD student
>>>
>>> Technische Universität Braunschweig
>>> Institute of Medicinal and Pharmaceutical Chemistry
>>> https://www.tu-bs.de/pharmchem
>>> Beethovenstr. 55 | 38106 Braunschweig | Germany
>>>
>>>
>>> _______________________________________________
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>>>
> -- 
> Marco J. Müller
> 
> Technische Universität Braunschweig
> Institut für Medizinische und Pharmazeutische Chemie
> https://www.tu-bs.de/pharmchem
> 
> Beethovenstr. 55 | 38106 Braunschweig | Germany
> Tel.: +49 531 391 2768 |marco.mueller at tu-bs.de
>