Thanks Ian. I got it from the bin folder you mentioned. A moment ago I have
failed to localize it from the CCP4 graphical interface.
Smith
At 2015-03-07 21:13:58, "Ian Tickle" <ianj...@gmail.com> wrote:
Hi Smith
Not sure what you mean, the current version of CCP4 (as have all previous
versions) certainly does contain mtzdump:
> which mtzdump
/software/CCP4-6.5.0/ccp4-6.5/bin/mtzdump
The "limited output" is intentional: mtzdump by default only lists the first 10
reflexions, and you have exactly 10 in your list. If you want more then supply
an NREF value, e.g.
echo nref 99999 |mtzdump HKLIN my.mtz |less
But mtzdump (or any MTZ utility for that matter) is not going to help you with
a corrupted file, since the MTZ read routines assume that the file has a
strictly defined format which has most likely been modified when it was
transferred from the damaged disk, and is therefore now unreadable by any
program that assumes the defined format.
What does the technician who transferred the data have to say about it? He is
the only person who can possibly tell you how the file has been corrupted.
What you need is a hex dump of the file (e.g. using 'hexdump') and someone who
understands a) the correct format and b) exactly how it was corrupted. Then it
may be possible to write a bespoke program tor recover your data. But that is
not going to be easy: it will require someone with some expertise in
programming.
Attempting to read the file with random programs has even less chance of
working than I have of winning the lottery! As others have suggested there are
much easier ways of recovering your data (such as reprocessing the images).
Cheers
-- Ian
On 7 March 2015 at 06:29, Smith Liu <smith_liu...@163.com> wrote:
Dear All,
The current version of CCP4 does not contain mtzdump. I use UCLA MBI — mtzdump
to process it. For a mtz file, the output says there was no valid reflection
data. For another mtz file, it only gave about 50 lines information (not a new
mtz file). As for the original mtz is very large, I think at least some message
in the mtz file has been missing or has not been recovered by UCLA MBI —
mtzdump.
Please feel free for further advise.
Smith
Follwing: output from the UCLAMBI-mtzdump
mtzdump - dump data from an MTZ reflection data file. A CCP4 program
Your mtzdump Results
Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
130.3260 130.3260 360.3400 90.0000 90.0000 90.0000
* Resolution Range :
0.00003 0.22676 ( 180.170 - 2.100 A )
* Sort Order :
1 2 3 0 0
* Space group = 'I 4 2 2' (number 97)
| |
|
1 ASC 0 62 0 100.00 32.5 32.5 180.17 2.10 H H
| |
|
2 NONE 0 43 0 100.00 13.4 13.4 180.17 2.10 H K
| |
|
3 NONE 0 171 0 100.00 64.4 64.4 180.17 2.10 H L
| |
|
4 NONE 0.0 19.0 0 100.00 9.51 9.51 180.17 2.10 I
FreeR_flag
| |
|
5 NONE 65.8466807.5 47890 47.08 14985.84 14985.84 41.21 2.10 J IMEAN
| |
|
6 NONE 22.7 37273.6 47890 47.08 1161.73 1161.73 41.21 2.10 Q
SIGIMEAN
| |
|
7 NONE 65.8466807.5 50197 44.54 15601.05 15601.05 41.21 2.10 K I(+)
| |
|
8 NONE 36.9 37273.6 50197 44.54 1723.38 1723.38 41.21 2.10 M SIGI(+)
| |
|
9 NONE 65.8466807.5 53778 40.58 16626.28 16626.28 41.21 2.10 K I(-)
| |
|
10 NONE 36.9 37273.6 53778 40.58 1568.40 1568.40 41.21 2.10 M
SIGI(-)
| |
|
11 NONE 67.3 6770.8 47890 47.08 1006.23 1006.23 41.21 2.10 F F
| |
|
12 NONE 5.6 446.6 47890 47.08 76.69 76.69 41.21 2.10 Q SIGF
| |
|
13 NONE -514.8 537.4 56085 38.03 0.21 87.57 41.21 2.10 D DANO
| |
|
14 NONE 0.0 380.1 56085 38.03 91.63 91.63 41.21 2.10 Q
SIGDANO
| |
|
15 NONE 67.3 6770.8 50197 44.54 1032.56 1032.56 41.21 2.10 G F(+)
| |
|
16 NONE 8.2 446.6 50197 44.54 90.13 90.13 41.21 2.10 L
SIGF(+)
| |
|
17 NONE 67.3 6770.8 53778 40.58 1075.89 1075.89 41.21 2.10 G F(-)
| |
|
18 NONE 7.6 446.6 53778 40.58 78.67 78.67 41.21 2.10 L
SIGF(-)
| |
|
19 NONE 0 2 47890 47.08 0.4 0.4 41.21 2.10 Y ISYM
| |
|
| |
LIST OF REPLECTIONS
===================
0 0 2 8.00 ? ? ? ? ?
? ? ? ? ? ?
? ? ? ?
0 0 4 10.00 ? ? ? ? ?
? ? ? ? ? ?
? ? ? ?
0 0 6 9.00 ? ? ? ? ?
? ? ? ? ? ?
? ? ? ?
0 0 8 18.00 ? ? ? ? ?
? ? ? ? ? ?
? ? ? ?
0 0 10 3.00 ? ? ? ? ?
? ? ? ? ? ?
? ? ? ?
0 0 12 17.00 3090.57 268.91 3090.57 268.91 3090.57
268.91 554.30 24.36 0.00 0.00 554.30
24.36 554.30 24.36 1.00
0 0 14 9.00 23242.80 1362.28 23242.80 1362.28 23242.80
1362.28 1522.33 44.83 0.00 0.00 1522.33
44.83 1522.33 44.83 1.00
0 0 16 5.00 29139.17 1697.95 29139.17 1697.95 29139.17
1697.95 1704.50 49.90 0.00 0.00 1704.50
49.90 1704.50 49.90 1.00
0 0 18 12.00 478.99 57.42 478.99 57.42 478.99
57.42 217.65 13.29 0.00 0.00 217.65
13.29 217.65 13.29 1.00
0 0 20 3.00 113229.90 6443.99 113229.90 6443.99 113229.90
6443.99 3358.69 96.10 0.00 0.00 3358.69
96.10 3358.69 96.10 1.00
-------- end, thus very limited information output
At 2015-03-06 15:56:19, "Tim Gruene" <t...@shelx.uni-ac.gwdg.de> wrote:
>-----BEGIN PGP SIGNED MESSAGE-----
>Hash: SHA1
>
>Dear Smith,
>
>an mtz-file is a binary file and none of the programs you list is
>suitable to open it in a meaningful manner.
>
>Why don't you follow the advice you were already given?
>mtzdump from ccp4 would be the first program to try and see if any
>information can be retrieved from the mtz-file.
>
>Regards,
>Tim
>
>On 03/06/2015 08:20 AM, Smith Lee wrote:
>> Dear All, For the issue of the recovery of the mtz file, I have
>> tried randomly to use excel to open one specific mtz file, however
>> in this way all the mtz files in the computer will have a excel
>> icon (X), although the file extension is still .mtz. If I tried
>> further to open one specific mtz file (with excel icon) with the
>> notepad, all the mtz files will have the notepad icon. If I tried
>> further to open one specific mtz file (with notepad icon) with the
>> wordpad, all the mtz files will have the wordpad icon. I hope
>> these cluses can be helpful for you to give me the advise on
>> recovery of mtz files. Smith
>>
>> On Thursday, March 5, 2015 11:51 PM, Robbie Joosten
>> <robbie_joos...@hotmail.com> wrote:
>>
>>
>> Hi Smith,
>>
>> If this is really the problem Ian describes, you can try the Linux
>> programs unix2dos and dos2unix the change the line endings. A
>> potential source of the problem might be copying the file with
>> certain (S)FTP clients: in 'text-mode' they change the line endings
>> to your OS default to be user friendly.
>>
>> Cheers, Robbie
>>
>>> -----Original Message----- From: CCP4 bulletin board
>>> [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent:
>>> Thursday, March 05, 2015 14:04 To: CCP4BB@JISCMAIL.AC.UK Subject:
>>> Re: [ccp4bb] how to recover my data
>>>
>>> Hi Smith
>>>
>>>
>>> I sympathise with your plight - I have had to do similar things
>>> in the past for other people! I think your most fruitful course
>>> of action would be to talk to the technician who recovered your
>>> data because only he knows what he actually did to recover it.
>>>
>>>
>>> From your description of your recovery of the PDB file it looks
>>> to me like a line terminator issue, i.e. was the original file
>>> created in Linux, Windows or Mac? This is relevant because the
>>> line terminators are different and it sounds like the technician
>>> didn't simply copy the file, he changed the line terminators. If
>>> he did the same with the MTZ file thinking it was a text file the
>>> additional line terminators would corrupt the binary data making
>>> it impossible to read with any of the CCP4 MTZ utilities. If you
>>> can understand exactly what the technician did you may be able to
>>> reverse it and recover the binary data.
>>>
>>>
>>> Hope this helps!
>>>
>>>
>>> Cheers
>>>
>>>
>>> -- Ian
>>>
>>>
>>> On 5 March 2015 at 05:36, Smith Lee <00000459ef8548d5-dmarc-
>>> requ...@jiscmail.ac.uk> wrote:
>>>
>>>
>>>
>>> Dear All,
>>>
>>> Recently my computer hardware has been broken and all the data
>>> has been recovered to movable hardware by technician. However I
>>> find the recovered PDB file and the MTZcould not be openned by
>>> Coot. Then I open the revovered PDB file by WordPad, and from
>>> WordPad I copied it to notepad and save it as pdb file. I find
>>> the Coot can open the notepad saved pdb file, thus my pdb files
>>> can be succesfully recovered from the hardware.
>>>
>>> But will you please tell me how to have Coot open my mtz file?
>>> After data recovery by the technicial, the data size of the mtz
>>> file did not decrease, thus I think there is a way to have it
>>> recovered.
>>>
>>> I have not noticed there were similar or identical posts as mine
>>> for recovery data before in the CCP4 mail list.
>>>
>>> Thus I am looking forward to getting a reply from you on how to
>>> recover my mtz file.
>>>
>>>
>>> Smith
>>>
>>>
>>
>>
>>
>
>- --
>- --
>Dr Tim Gruene
>Institut fuer anorganische Chemie
>Tammannstr. 4
>D-37077 Goettingen
>
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