Contact Geospiza
E-mail Geospiza with questions or bug reports: support@geospiza.com.

You can also reach us by phone: 206-633-4403, between 9am and 5 pm Pacific Standard Time.

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FAQs

Cn3D and CD questions

• Trouble opening files
• It's a pain moving between multiple windows. Can I make this easier?
• My structure disappeared. How do I see what I'm supposed to?
• I changed the style and rendering options but now I can't get the structure to look like it did in the beginning. What do I do?
• Why won' t Cn3D show me structures that I retrieved from the Protein Data Bank?

Operating system and platform questions

• Can I run the CD on a Unix computer with Windows emulation software - like Wine?
• Can I run the CD on older Macs?
• Can I install the CD materials on a server and run them on a network?

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Trouble opening files

From the CD menu:

Some files may not open the first time they are selected from the CD menu. If this is the case:

1. Make sure that all relevant software (Adobe Acrobat Reader 7.0 or Cn3D) has been installed.
2. Select a file that is the same type as the file causing problems - i.e. a pdf file, or a .cn3 file. Right-click the file name and change the file opening preferences so that pdf files open with Acrobat Reader 7.0 and .cn3 files open with Cn3D.

When a file is double-clicked

From the pdf document

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It's a pain moving between multiple windows. Can I make this easier?

It is kind of a pain but people who do bioinformatics work typically use many windows at a time and move back and forth between them. Sometimes, they even have multiple monitors hooked up to one computer.

The pain can be minimized a bit by learning how to control the size of your windows so that you can see multiple windows, simultaneously on the screen. If you adjust the window sizes, you can have multiple windows open on a screen and see them at the same time, as well as move between them. On Windows computers, click the icons at the top right hand corner of a window, and then drag the bottom right-hand corner of the window to change the size.

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My structure disappeared. How do I see what I'm supposed to?

This is a bug and will be fixed. For now - open the Style menu and select Edit Global Style. The check boxes in the first column control whether certain types of molecules are visible or not. Check and uncheck boxes for the type of molecule you're viewing. The molecule should appear while you're doing this. Click Done and close the window.

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I changed the style and rendering options but now I can't get the structure to look like it did in the beginning. What do I do?

At this point, it's easiest to open the file again.

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Why won't Cn3D show me structures that I retrieved from the Protein Data Bank?

Cn3D uses files that come from the molecular modeling database at the National Center for Biotechnology Information. These files differ from PDB files in three ways: information content, structure and file format. In other words, PDB files do not contain sufficient information for Cn3D to draw the structures. But that doesn't mean that you can't view a PDB structure in Cn3D. Almost all PDB structure files, in a modified form, are also in the molecular modeling database. So - if you know the PDB ID number, you can get that structure from the NCBI, and view it in Cn3D.

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Can I run the CD on a Unix computer with Windows emulation software - like Wine?

Probably not. We have not tested this and do not guarantee this.

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Can I run the CD on older Macs?

No. Your Mac has to be running OS X.

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Can I install the CD materials on a server and run them on a network?

You will need a network license to do this. Contact Geospiza 206-633-4403 for more details.

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