Beta_Testing_2013

ACCESS THE BETA TESTING QUESTIONNAIRE

To perform Beta testing you must complete the steps on this page.

To provide your feedback you must access the Beta Testing Questionnaire.

We suggest that you open the Beta Testing Questionnaire on a separate browser windows so you can record your results as you complete each section.

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OPEN SOURCE SUPPORT

1. Access the MOLMOL website and check.
2. Access the source code repository and check.
3. Access the issue logging feature and check.
4. Complete the Beta Testing Questionnaire for this section.

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ACCESSABILITY

1. Download, install and run the latest MOLMOL application executable following the installation procedure.
2. Complete the Beta Testing Questionnaire for this section.

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FEATURES AND BUG FIXES

1. Ability to display amino acid sequence/domain/chain in main window and select regions by mouse click.

Delete all existing molecular data via menu path "Edit→Init All...".
You should see:
![MOLMOL_Initialise] (http://molmol.sourceforge.net/Documentation/Beta_Testing_2013/MOLMOL_Initialise.gif)
Load the standard sample test PDB file from the folder "data" via menu path "File→Read Mol→Old PDB...".
You should see:

Click on the Mol and Res buttons found on the right hand menu. Then there are 3 radio buttons at the top of both windows change both to display then by clicking the sequences in the residue window you can display individual or sequences of residues.
Verify the results:

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2. Atom display labels/read PDB properly. This is kind of a bug in that the atom labeling nomenclature has changed and MOLMOL gets confused reading new atom coordinate information (PDB files), so won't display certain atoms.

Delete all existing molecular data via menu path "Edit→Init All...".
You should see:

Load the sample test PDB file from the folder "data/TestCases_2013" via menu path "File→Read Mol→PDB..." .
You should see:

Acknowledge the warning message:

Run the sample test macro from the folder "data/TestCases_2013" via menu path "File→Macro→Execute user...".
You should see:

Close the "CalcSecondary.txt" information window:

Verify the results:

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3. Ability to generate constraints of molecules lists and run a comparison to identify missing NOEs.

Delete all existing molecular data via menu path "Edit→Init All...".
You should see:

Load the standard sample test PDB file from the folder "data" via menu path "File→Read Mol→Old PDB..." .
You should see:

and then:

To generate a constraint list navigate your mouse to "Opts→AddNoe".
You should see:

The formats for this is @Atom Name, i.e. @CA or a wild card could be used like @*
Press "OK" and verify the results:

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4. Ability to quickly select and correctly display disulfide bonds.

Delete all existing molecular data via menu path "Edit→Init All...".
You should see:

Load the standard sample test PDB file from the folder "data" via menu path "File→Read Mol→Old PDB..." .
You should see:

Click "Open" and you should see:

Activate the Molecule selection dialog via "Mol" on the right hand menu and select the first molecule and you should see:

Select the "display" option and then the first molecule and you should see:

The main windows should also display:

Run the "ribbon" command from the right hand menu and you should see:

Select close and you should see:

Use the menu path "Opt→DisulfideBond" and you should see.

Select close and verify the results:

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5. Fix the colour palette bug and add a colour wheel/colour field box for choosing colours.

Click on the "Color" button on the right hand bar.
Select "Green" from the list of available colors.
You should see:

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6. Ability to display cyclic backbone of peptides correctly and to display a ribbon with no N- or C-terminus, which should allow the CO-NH bond to display correctly.

Delete all existing molecular data via menu path "Edit→Init All...".
You should see:

Load the test PDB file "kalatab1.pdb" from the folder "data/TestCases_2013" via menu path "File→Read Mol→Old PDB..." .
You should see:

Click "Open" and you should see:

Activate the Molecule selection dialog via "Mol" on the right hand menu and select the first molecule and you should see:

Select the "display" option and then the first molecule and you should see:

The main windows should also display:

Run the "MakeMolCyclic" command via menu path "Edit→Molecule→Make Cyclic..." .

Run the "ribbon" command from the right hand menu and you should see:

Select close and verify the results:

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7. Fix the ability to export to TIFF.

Delete all existing molecular data via menu path "Edit→Init All...".
You should see:
![MOLMOL_Initialise] (http://molmol.sourceforge.net/Documentation/Beta_Testing_2013/MOLMOL_Initialise.gif)
Load the standard sample test PDB file from the folder "data" via menu path "File→Read Mol->Old PDB...".
You should see:

and then:

Click on the "ribbon" button on the right hand menu and you should see:

Use the menu path "File→Plot→TIFF...".
You should see:

Specify a file name and click "OK".
Create another TIFF image plot.
Confirm that you can open both TIFF files created using an external application.

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8. Ability to render in MOLMOL which will help with display of transparent surfaces.

Not implemented at this stage.

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9. Ability to scroll through the molecule’s in a window.

Delete all existing molecular data via menu path "Edit→Init All...".
You should see:
![MOLMOL_Initialise] (http://molmol.sourceforge.net/Documentation/Beta_Testing_2013/MOLMOL_Initialise.gif)
Load the standard sample test PDB file from the folder "data" via menu path "File→Read Mol→Old PDB...".
You should see:

Click on the Mol and Res buttons found on the right hand menu. Then there are 3 radio buttons at the top of both windows change both to display then by clicking the sequences in the residue window you can display individual or sequences of residues.
You should see:

Verify you can scroll using the mouse scroll wheel in the "Residue Dialog" window.

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10. Ability to easily create/export animations through using macro scripts.

Not implemented at this stage.

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11. Skin the display windows to make it look somewhat post-1950s software.

Not implemented at this stage.

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12. Add additional display levels/types for the ribbon display.

Not implemented at this stage.

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13. Complete the Beta Testing Questionnaire for this section.

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OPERATION

1. Complete the Beta Testing Questionnaire for this section.

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COMMENTS

1. Complete the Beta Testing Questionnaire for this section.