I found out that the discussion was not posted in ccpem list
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From: Sjors Scheres <[log in to unmask]>
Date: Mon, Dec 2, 2013 at 5:06 PM
Subject: Re: [ccpem] RELION prepocessing using ctffind3
To: [log in to unmask]
Cc: Grigory Sharov <[log in to unmask]>
Oh yes: we discussed this earlier on the list I think: if you use the window of 950, then you should set the FFT window size parameter of CTFFIND3 to less than half of 950, otherwise CTFFIND3 crashes. An alternative is to not window at all: just set that to -1 as Grigory suggests. Both should work fine.
S
On 12/02/2013 04:02 PM, Jenny Barna wrote:
On Mon, 2 Dec 2013, Sjors Scheres wrote:
OK, I forgot I actually shipped a ctffind3 with the tutorial.... OK, replace that one by an older one and all should go OK. Apparently on some systems the new version of CTFFIND3 hangs without the AngAst parameter, while on others (like ours) it works just fine. Sorry about that. As said, the problem will be solved in the next release.
S
and Grigory wrote
"
I just checked the last ctffind version from web-site, it works fine with
tutorial data. Try to set "Estimate CTF on window size" to -1, not to 950
as tutorial says. I remember it caused some segfault errors for me, if I
put any value other than -1.
"
Hmm. Ok looks like I have two issues then. I got the hanging also with v
3.5 (7 Mar 2012) so I will go and look for older versions still.
We did also get seg faults but I was trying to solve one thing at a time
and I had isolated what looked like a basic Fortran/version number issue.
So maybe the tutorial works for some people first time and maybe not
if it always needs -1 not 950 :-\
It also looks as if the version numbering on ctffind3 is odd.
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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