Leginon

Hi, Arne,

Thanks for using the forum. It will be good for next person with the same problem.

Your specific configuration of camera computer being separated from the scope computer
creates a situation more like what is on JEOL scope where gatan CCD is on a separate computer.

There are two solutions:

1. Copy tecnaiccd.dll from your microscope PC and register it on the camera computer. However,
there might be one there already with gatan software, just not registered for general use. Do a file search first.

2. Install SerialEMCCD.dll and use dmsem.GatanUltraScan instead of gatan.Gatan as instrument class.
This option is especially good if you have already SerialEM installed there.

Anchi

By the way, you only need camera instrument class on camera computer. Therefore missing TEM/TOM/etc. microscope components are not important for this.

Many thanks Anchi,

this seems to be the right track - we went with solution 2 and also modified instruments.cfg as suggested

however there was no template dmsem.cfg.template on our myami 3.2 svn version - so we copied the one from the K2
as on the Wiki

http://emg.nysbc.org/projects/leginon/wiki/Gatan_K2_installation_and_setup

this is K2 - but it should work for Ultrascan?

we can now connect to Leginon and the camera can be selected as client (scope not yet configured) but when we connect in an application we get an error message on the launcher

no interface could be initialized

any idea?

cheers,

Arne and Juan

What is your dm version ?

Do a basic test on the camera computer, it will show the error when loading the module etc.

import pyscope.dmsem
k = pyscope.dmsem.GatanUltraScan()
k.getImage()

Hey Anchi - cant check today but because of the time difference between europe and USA - my question:

what would do we have to look for
we tried to install the files according to our DM version - if this was the case would that be ok?

thanks
Arne

Regarding version. I am not sure what DM version UltraScan runs on if it was installed a while ago. It is possible that
the socket connection version of SerialEMCCD was not yet developed for. We will just have to try and see and perhaps consult David Mastronarde.

Regarding the pyscope test. You will probably find an error message. If it just says something can not be found, then it is just a matter of install the required module. I can not predict it.

ok - we were not yet able to figure out what is wrong with this scope

we have now tried to install everything (in an identical manner) on the second spirit - in this case the camera and scope PC are the same - and there Leginon is working fine.

on the first scope (with two computers) we get an error message that likely indicates a firewall problem - but this remains when we turn the firewall off - so its a bit confusing..

Resolved the problem through an Skype session.

Resolving socket connection issue¶

pyscope test does not use external network, just local sockets. The "error message that likely indicates a firewall problem" is "No connection could be made because the target machine actively refused it". Similar to dmsem.py fails to open local connection on K2 computer. Since we know it is not a firewall issue, we checked for processes that might block the SEMCCD.dll socket connection specified in environment variable SERIALEMCCD_PORT. We found one revealed by Windows Task Manager with a name like SEMCCD even after DigitalMicrograph was closed. Therefore, we removed it.

I added some instruction in Trouble_shooting_semccd_socket_connection

Adding ultrascan module to dmsem.cfg¶

The next problem in running pyscope test is that upon the last command of getting a test image, got an error ended with

Attribute Error: 'GatnUltraScan' object has no attribute 'cameraid'

This error came from missing ultrascan section of dmsem.cfg
See Gatan_on_Windows-32_with_semccddll

After that, the result of the test is normal, as shown in pyscope test result array