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@tu-bs.de