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Google Chrome seems to replace the MIME type and file extension of exported files (you can download the source file of the current 3D model using the _Tools > Export_ menu) In Google Chrome 40.0.2214.…
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Given `CC(=O)[C@@]1(O)CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C`, the babel-generated 3d molecules differ at two stereocenters from the Schrodinger Ligprep-generated molecule.
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The source distribution for vmd 1.9.1 includes `plugins/molfile_plugin/src/dtrplugin.cxx` which is licensed under the BSD 3-clause, and would be suitable for inclusion in MDTraj. Note that inclusion o…
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I should be able to support more or less all of the Accelrys CTfile formats. All information gathered from http://download.accelrys.com/freeware/ctfile-formats/ctfile-formats.zip
### molfiles
Molecu…
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Subtask for #252:
We want to make frame numbering start from 0 so that indexing with, say:
``` python
u = mda.Universe(GRO, XTC)
u.trajectory[0]
```
gives frame 0 instead of frame 1. This change wi…
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If the Babel dir in the settings is incorrect, this currently results in an error at mbWorkflow Step 6 (generate molfiles) - whereas if _no_ babel dir is given, we can still produce structures. We sho…
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It's a bit annoying that we can't use driver to compute quantities depending on electrostatic charge (e.g. DHENERGY). For masses the situation is even worst: in the driver they are set to 1. Thus, COM…
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It seems to want to clean all compounds, regardless of whether they need it or not. This can be misleading.
I pasted a simple benzene ring from the templates (perfectly drawn) and when I went to sav…
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I often copy the molfile from the database and paste it into the marvinSketch window on my desktop for editing. It would be useful to have this feature in this marvin version.
(This would also be goo…
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```
Hello,
As discussed in the mailling list
(https://groups.google.com/forum/#!msg/mdnalysis-discussion/C5TbkZLB2Eo/vyzcafrF
1AkJ), alpha and gamma angles are swapped between VMD and MDAnalysis whe…