Hi,
N and Z do not matter in most places of RELION
but not in all situations.
> I get somewhat weird results in relion when using big.mrc as a
starting volume
What happened? Did it show any error?
To be on a safer side, you should use a map in XYZ, not XYN.
Best regards,
Takanori Nakane
> Hi Takanori,
>
> ? thanks a lot! That is indeed what I see. So, the starting volume
> created by relion_image_handler is OK :-). However, I initially used a
> starting volume created with:
>
> xmipp_transform_window -i small.mrc:mrc -o big.mrc:mrc --window 900.
>
> whereas image_header for the *relion version* reports:
>
> Dimensions???? : *900 x 1 x 900 x 900*? ((N)Objects x (Z)Slices x
> (Y)Rows x (X)Columns)
>
> for the *xmipp version* it reports:
>
> Dimensions???? : *1 x 900 x 900 x 900*? ((N)Objects x (Z)Slices x
> (Y)Rows x (X)Columns)
>
> does this matter?
>
> bw Dieter
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max F. Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Fax: 0043 1 4277 9616,
> e-mail: [log in to unmask]
> ------------------------------------------------------------------------
>
> Am 28.10.2019 um 15:10 schrieb Takanori Nakane:
>> Hi,
>>
>> Isn't "Plane mode" activated in your Chimera?
>> When the volume is too large, it seems to be automatically activated.
>>
>> In "Volume Viewer", open [Features]-[Planes].
>> Click [All] and select "Surface" as style.
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>>> Hi,
>>>
>>> ?I refined a volume with relion. "xmipp_image_header -i small.mrc"
>>> shows: Please look at the bold values!
>>>
>>> ? --- File information ---
>>> Filename?????? : small.mrc
>>> Endianess????? : Little
>>> Reversed?????? : False
>>> Data type????? : Floating point (4-byte)
>>> Data offset??? : 1024
>>> --- Image information ---
>>> Image type???? : Real-space image
>>> Dimensions???? : *450 x 1 x 450 x 450*? ((N)Objects x (Z)Slices x
>>> (Y)Rows x (X)Columns)
>>> Sampling rate? :
>>> ???????????????? X-rate (Angstrom/pixel) = 0.97
>>> ???????????????? Y-rate (Angstrom/pixel) = 0.97
>>> ???????????????? Z-rate (Angstrom/pixel) = 0.97
>>>
>>> ----------------------------
>>>
>>> I then tried increasing the box size with relion_image_handler:
>>>
>>> relion_image_handler --i small.mrc --o big.mrc --new_box 900
>>>
>>> xmipp_image_header -i big.mrc? shows:
>>>
>>> --- File information ---
>>> Filename?????? : bigr.mrc
>>> Endianess????? : Little
>>> Reversed?????? : False
>>> Data type????? : Floating point (4-byte)
>>> Data offset??? : 1024
>>> --- Image information ---
>>> Image type???? : Real-space image
>>> Dimensions???? :*900 x 1 x 900 x 900*? ((N)Objects x (Z)Slices x
>>> (Y)Rows
>>> x (X)Columns)
>>> Sampling rate? :
>>> ???????????????? X-rate (Angstrom/pixel) = 0.97
>>> ???????????????? Y-rate (Angstrom/pixel) = 0.97
>>> ???????????????? Z-rate (Angstrom/pixel) = 0.97
>>>
>>> so far so good. *But when opening the volumes in Chimera it shows me as
>>> dimensions:*
>>>
>>> *-------------------------------------------------------
>>> *
>>>
>>> *for "small.mrc": 450^3*
>>>
>>> *for "big.mrc": 900 900 1*
>>>
>>> since I get somewhat weird results in relion when using big.mrc as a
>>> starting volume I am wondering what might be wrong with the large
>>> volume!
>>>
>>> Thanks for help, bw Dieter
>>>
>>> ------------------------------------------------------------------------
>>>
>>> Dieter Blaas,
>>> Max F. Perutz Laboratories
>>> Medical University of Vienna,
>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>> Dr. Bohr Gasse 9/3,
>>> A-1030 Vienna, Austria,
>>> Tel: 0043 1 4277 61630,
>>> Fax: 0043 1 4277 9616,
>>> e-mail: [log in to unmask]
>>> ------------------------------------------------------------------------
>>>
>>>
>>> ########################################################################
>>>
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>>>
>>
>
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