CTFFIND3 executable location

[cg20...@gmail.com]

I am trying to use ctffind3 in relion. It seems that I should tell relion the location of ctffind3. What is the location in the cloud?

Thanks.

Jerry

[Michael Cianfrocco]

Hi Jerry,

All of the EM software packages are found within the directory: 

/home/EM_Packages/

And, for CTFFIND3, there are single processor and multi-processor executables: 

/home/EM_Packages/ctf/ctffind3_mp.exe
/home/EM_Packages/ctf/ctffind3.exe

Thanks,

Mike

[cg20...@gmail.com]

Hi Mike,
I try to run ctffind3 with your suggested location. It shows some error:

Estimating CTF parameters using Niko Grigorieff's CTFFIND3 ...
000/??? sec ~~(,_,">                                                          [oo]sh: 1: csh: not found
   0/   0 sec ...~~(,_,">sh: 1: csh: not found
 ......
CtffindRunner::joinCtffind3Results ERROR; cannot get CTF values for
File: src/ctffind_runner.cpp line: 166

Can you help out?

Thanks a lot.

Jerry

[Michael Cianfrocco]

Hi Jerry,

How are you running the command ? Is it within a c-shell script? If it is, this may be the problem because the default shell is bash for the Amazon ec2 AMI.

You have two choices:
1. Change the shell into csh by typing 'sudo chsh /bin/csh'
2. Update your script to accommodate the bash language. (Pretty easy to do)

What script are you using? Or is this through Relion?

Mike

[cg20...@gmail.com]

HI Mike,

I run it through relion. And my system is ubuntu.

Thanks.

Jerry

[Michael Cianfrocco]

Hey Jerry,

Then the best way will be to change the shell to csh using the change shell command in Linux. Otherwise we'd have to change the way relion runs ctffind from the source code.

I also have a script that will run ctffind3 and output files that are compatible with relion for particle extraction.

Mike

[cg20...@gmail.com]

Hi Mike,

It works now by installing  csh in the cloud. Thanks once more.

Jerry