Re: [scipion-users] eman2 and chimera issues

[Wood, K. <K.W...@wa...>]

Thank you Laura and Pablo,

I have checked my config file and for both eman2 and chimera my version numbers were wrong. I have corrected it now and rebooted scipion, and chimera and eman2 work now! Thanks for your help!

Best wishes,

Katherine

From: Laura <lde...@cn...>
Reply-To: Mailing list for Scipion users <sci...@li...>
Date: Thursday, 13 June 2019 at 14:12
To: "sci...@li..." <sci...@li...>
Subject: Re: [scipion-users] eman2 and chimera issues


Hi Katherine,

it seems that you are trying to use eman-2.12 while scipion automatically installs 2.21.

Could you check your environmental variables opening the plugin manager and then Configuration/Variables on the top menu?

For instance I have:

[cid:par...@cn...]

If you are using eman 2.12 you should add the variable with your version either on your $HOME/.config/scipion/scipion.conf file or on the scipion one (scipion_path/config/scipion.conf)

Regarding chimera, check that whatever is on CHIMERA_HOME variable exists.

any doubt just ask

best regards

Laura
On 13/6/19 13:10, Wood, Katie wrote:
Hello,

I’m having some problems using the eman2 programs in scipion. I put in all the variables the easy refine program asks me for but I end up with the following error whenever I try to execute the program:

Missing Variables:
EMAN2DIR: /home/u1666362/software/scipion/software/em/eman-2.12

I get the same error when trying to run a different eman2 program, but it doesn't happen for relion or xmipp, so I’m assuming I need to alter something eman2 related. I was wondering if anyone knew how to fix this? I couldn't find any answers on the mailing list so far.

Also when I try to use the chimera viewer for 3D volumes it says I haven’t installed the chimera plugin, however, I have installed the plugin so I don’t know what to do to fix this either. I do have chimera installed though on my pc (not the plugin from scipion, so have two chimeras essentially) which works and was there before I installed scipion. Do I need to uninstall that?

Thanks in advance!

Best wishes,

Katherine Wood




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