Hi,
I too had a similar error when trying to process very weak
data integrated to the edge of a detector.
The log showed lots of "0.0" and "-nan".
Sometimes the program went into an infinite loop and
tried to consume all the memory of the system.
Applying a reasonable high resolution cutoff by SFTOOLS
solved the problem.
Best regards,
Takanori Nakane
On 2014-06-20 10:49, <Stephen Carr> wrote:
Thanks for the help, the old version of truncate did the trick.
Interestingly running the old version of truncate in either of the
data reduction pipelines (with aimless or scala) produced mtz files
containing no F's but the stand alone version produced an mtz with all
the f's prsent.
cheers,
Steve
Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717
________________________________
From: Parthasarathy Sampathkumar [spart...@gmail.com]
Sent: 19 June 2014 19:55
To: ccp4bb
Subject: Re: [ccp4bb] ctruncate error
Yes.., I too had similar problem with Ctruncate, and used older
truncate to overcome the issue.
Best Wishes,
Partha
On Thu, Jun 19, 2014 at 2:38 PM, jie liu
<jl1...@njms.rutgers.edu<mailto:jl1...@njms.rutgers.edu>> wrote:
Hi
I also encountered the same problem after recent updates (not the most
recent one, but a couple of updates back). Choosing to run
old-truncate will get it around.
Best wishes
Jie
----- Original Message ----- From: "<Stephen Carr>"
<stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk>>
To: <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
Sent: Thursday, June 19, 2014 1:11 PM
Subject: [ccp4bb] ctruncate error
Dear CCP4bb,
I am experiencing an unusual error when running truncate. The program
appears to be converting I's to F's, but then failing to output them
in the resulting mtz file, see mtzdump output below:
Col Sort Min Max Num % Mean Mean Resolution
Type Column
num order Missing complete abs. Low High
label
1 ASC 0 26 0 100.00 12.6 12.6 79.95 3.00
H H
2 NONE 0 15 0 100.00 4.3 4.3 79.95 3.00
H K
3 NONE -42 42 0 100.00 0.7 16.0 79.95 3.00
H L
4 NONE 0.0 19.0 0 100.00 9.56 9.56 79.95 3.00
I FreeR_flag
5 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
F F_delta16
6 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
Q SIGF_delta16
7 BOTH 0.0 0.0 25 99.81 0.00 0.00 42.22 3.00
D DANO_delta16
8 BOTH 0.0 0.0 11253 13.22 0.00 0.00 42.22 3.00
Q SIGDANO_delta16
9 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
G F_delta16(+)
10 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
L SIGF_delta16(+)
11 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
G F_delta16(-)
12 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
L SIGF_delta16(-)
13 BOTH 0 0 25 99.81 0.0 0.0 42.22 3.00
Y ISYM_delta16
14 NONE -8.9 72479.2 25 99.81 198.34 198.44 42.22 3.00
J IMEAN_delta16
15 NONE 0.6 3135.7 25 99.81 5.25 5.25 42.22 3.00
Q SIGIMEAN_delta16
16 NONE -10.8 72479.2 25 99.81 198.18 198.37 42.22 3.00
K I_delta16(+)
17 NONE 0.0 3135.7 25 99.81 6.79 6.79 42.22 3.00
M SIGI_delta16(+)
18 NONE -9.5 72479.2 25 99.81 198.30 198.47 42.22 3.00
K I_delta16(-)
19 NONE 0.0 3135.7 25 99.81 6.70 6.70 42.22 3.00
M SIGI_delta16(-)
No. of reflections used in FILE STATISTICS 12968
The truncate log file shows no obvious errors apart from the
cumulative intensity plot which indicates no reflections, all other
diagnostic indicators for data quality seem to suggest everything is
ok. I get the error with both ctruncate and truncate and also
automatically as part of the scaling/merging pipelines. The data were
processed with imosflm, scaled with aimless with neither flagging any
errors with the data. I am running CCP4 6.4.0 on a linux box (Centos
6) and have installed the latest updates. Any suggestions as to what
the fault might be and how to get around it would be greatly
appreciated.
best wishes,
Steve
Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email
stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk>
tel 01235 567717
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