[Chimera-users] scale problem

Yaowang Li liyaowang2911 at gmail.com
Tue Nov 24 09:12:18 PST 2015


Hi Tom,


I did the reconstruction. As you said, there is no relationship between
pixel size of projection and the voxel size of density map?



On Tue, Nov 24, 2015 at 6:08 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Yaowang,
>
>   I don’t know what the correct grid spacing for your density map is,
> although it sounds like by comparing to a PDB model you think it is around
> 2.11 Angstroms.  When Sparky opens the file it reads the grid spacing from
> the file header if the header has the information.  But that value might be
> wrong.  Just because your projection images had 1.055 Angstrom pixel size
> doesn’t mean the 3d reconstruction will use the same pixel size.  You will
> have to get the correct grid spacing from the person who did the
> reconstruction.
>
> Tom
>
>
> On Nov 24, 2015, at 7:17 AM, Yaowang Li <liyaowang2911 at gmail.com> wrote:
>
> Dear Tom,
>
> Yeah, it indeed did not change the intensity, I made a mistake, and did
> not make it clear.
>
> I have a little experience on the this, that is my first time. As I
> stated, the magnitude of projections is 1.055 A/pixel, so I think the
> volume size of density map should be 1.055 A/voxel.
>
> A PDB file should be fitted into the density map theoretically I think,
> while apparently the density map is small compare to PDB.  That is why I
> changed the voxel size to 2.11 A/voxel.
>
> So actually I want to make a confirmation that the grid in the density map
> whether is 1.055 A/voxel or not. if it is right, I guess something is wrong
> during the reconstruction.
>
>
> Regards,
>
>
> yaowang
>
>
>
>
>
> On Mon, Nov 23, 2015 at 7:50 PM, Tom Goddard <goddard at sonic.net> wrote:
>
>> Hi Yaowang,
>>
>>   The Chimera Volume Viewer voxel size setting (menu Features /
>> Coordinates) changes the spacing between grid points.  It does not change
>> the map intensity values.  If it appears to be wrong by a factor of 2 when
>> compared to a PDB file then the voxel size is definitely.   I would not
>> just guess that it is a factor of 2 too small — you should find out from
>> whoever did the reconstruction what the correct value is.  But if 2.11A is
>> the correct size than your fitting is fine.
>>
>> Tom
>>
>>
>> On Nov 23, 2015, at 1:31 AM, Yaowang Li wrote:
>>
>> Dear all,
>>
>>
>> I faced a scale problem when I was trying to fit the density map.
>>
>> A density map was reconstructed from a set of projections which their
>> magnitude are 1.055A/pixel, with a reference model that is 1.055 A/voxel
>> and 5 A in resolution. However the pdb file cannot fit into the map
>> because the map is too much small. So I have to change the voxel size to
>> double and then can be fitted.
>>
>> Here I changed the voxel size, I think it changed the scale for the
>> density. So i just worried about the fitting result.
>>
>> thanks
>>
>>
>>
>
>
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