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" <[email protected]> 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
>> <[email protected]> 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:[email protected]] On Behalf Of Ian Tickle Sent:
>>> Thursday, March 05, 2015 14:04 To: [email protected] 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-
>>> [email protected]> 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
>
>GPG Key ID = A46BEE1A
>
>-----BEGIN PGP SIGNATURE-----
>Version: GnuPG v1
>
>iD8DBQFU+V2jUxlJ7aRr7hoRApjyAKCwUB2lXaXFEoFievrLgJ+YDPZg+gCcDF6x
>IkBOMnu3OH/gjJknjvPWP+I=
>=K7G9
>-----END PGP SIGNATURE-----
