Menu File

New

Creates new empty project.

Ctrl+N

Open...

Opens project saved as .qcs file.

Ctrl+O

Import...

Imports new external file into current project. Only two file formats are supported: .pdb for importing molecular data and .xvg for importing charts. Aforementioned files can be compressed with gzip, but since archives do not support random access, animation may be significantly slower.

Ctrl+Shift+O

Parameters First and Last represent indices of first and last frame to be imported, respectively. If Last is set to the special value <<undefined>>, then new frames will be read until end of file is reached. Parameter Stride specifies the distance between consecutive simulation frames in the underlying file.

Radio buttons below allow user to specify the caching policy. The first option (which is the default) means that application will scan the underlying file for a next frame just before displaying it. It results in an immediate import, but later the animation may be jerky (especially for large stride). The second option forces application to cache offsets to all frames at the same time. When selecting this option one may have to wait some time to let the application scan the whole file (especially when its size is significantly large), but then the animation will be smooth.

Application accepts the latest version of standard .pdb file format. See Protein Data Bank Contents Guide for details. Each frame must be enclosed between corresponding MODEL and ENDMDL records. Coordinates of each atom are presented by ATOM/HETATM record. The CONECT records specify connectivity between atoms for which coordinates are supplied. All other record types are ignored.

Application accepts also standard .xvg file format generated by various GROMACS analysis utilities. It can be directly used in many graphing software packages including Grace, gnuplot and MS Excel. Each data series must be introduced with Grace command @s<number> legend "<name>". Series enumeration starts from 0. All other lines starting with special characters #@& are ignored. Lines that do not start with a special character are assumed to present data for consecutive simulation frames. Parser ignores therefore the first column, which usually should provide a timestamp.

Save

Saves active project as .qcs file.

Ctrl+S

Save as...

Asks for new file name and saves active project as .qcs file.

Ctrl+Shift+S

Quit

Quits the application. If there are some unsaved changes in any active project, a dialog will ask if you want to save them. Cancel returns to the program.

Alt+F4

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