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
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@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@tu-bs.de
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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@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@tu-bs.de
participants (2)
-
Conrad Huang -
Marco J. Müller