Thanks! No error but this (image attached)
bw Dieter
On 2019-10-28 16:03, Takanori Nakane wrote:
> 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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>>>>
>>>
>>
--
Dr. Dieter Blaas
Max F. Perutz Laboratories,
Inst. Med. Biochem.,
Med. Univ. Vienna
Dr. Bohr Gasse 9/3
A-1030 Vienna, Austria
Tel. 0043 1 4277 61630
Fax 0043 1 4277 9616
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