UGENE Forum - Ugene v1.33 3D Structure viewer on Linux not working

Oct 13^th, 2024 at 4:03am

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UGENE Forum › General Category › Help and How-to › Ugene v1.33 3D Structure viewer on Linux not working

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Ugene v1.33 3D Structure viewer on Linux not working (Read 5934 times)

Jan 13^th, 2020 at 12:30am

Felcet Offline
YaBB Newbies

Posts: 4

Hi,

I am trying to open a pdb file as in the user manual but 3d structure viewer does not seem to open. I have tried to hide the sequences as per instructions on another post but to no avail. Is there someone who knows how to solve this issue? The linux is running on a virtual machine.

Thanks for the help.

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Reply #1 - Jan 14^th, 2020 at 6:41pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Hi!

Do you use VirtualBox or other software for virtual machine?
What operating systems are on the host and guest machines? Which Linux?
Have you installed the VM guest additions?
What UGENE version do you run?
Which PDB file do you open? Could you please send it to us?
If possible, you might also send us the exported appliance of the virtual machine.
Is "3d" structure object is shown in bold in the Project View?

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Reply #2 - Jan 15^th, 2020 at 1:28am

Felcet Offline
YaBB Newbies

Posts: 4

Do you use VirtualBox or other software for virtual machine?

Yes. I use VirtualBox

What operating systems are on the host and guest machines? Which Linux?

The host machine is Windows 10. The guest machine runs Linux.

Have you installed the VM guest additions?

Yes it should be installed.

What UGENE version do you run?

v33.0

Which PDB file do you open? Could you please send it to us?

These are the sample pdb files provided by ugene. I tried all of them

If possible, you might also send us the exported appliance of the virtual machine.

This would be the .ova file, correct?

Is "3d" structure object is shown in bold in the Project View?

No it's not bold

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Reply #3 - Jan 15^th, 2020 at 1:33am

Olga Golosova Offline
YaBB Administrator

Posts: 338

Yes, the *.ova file (to export select "File > Export Appliance" in the VirtualBox main menu). You might share it e.g. using Google Drive and send us the link by email.

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Reply #4 - Jan 18^th, 2020 at 2:53pm

Felcet Offline
YaBB Newbies

Posts: 4

I am not allowed to post a link. Is there somewhere else I can post it?

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Reply #5 - Jan 19^th, 2020 at 4:25pm

Felcet Offline
YaBB Newbies

Posts: 4

https://drive.google.com/open?id=1i7WVW9ab6umAhW2v1OtHFWYBqLbpBpVF
This is the link to my .ova file

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Reply #6 - Jan 20^th, 2020 at 5:13pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Thank you! We'll check the issue and write you back!

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Reply #7 - Jan 21^st, 2020 at 5:54pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

The issue will be fixed in the next UGENE version 34. For now, please try to use this Linux package: http://ugene.net/downloads/ugene_latest_linux_x11_x86-64_full.html.

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