[chimerax-users] MOL2 import

[Marco J. Müller]

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
>>
>>
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu
>> Manage subscription:
>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>>
-- 
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20190314/46f69287/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: chimeratest.mol2
Type: chemical/x-mol2
Size: 5773 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20190314/46f69287/attachment.bin>