[3dem] help with volume alignments

[Carlos Oscar S. Sorzano]

Dear Ekaterina,

you may try xmipp_volume_from_pdb, it should be in the same orientation 
as your volume. In the case it was not, which should not happen, you can 
find the appropriate rotation using xmipp_volume_align (use the --frm 
option for a fast alignment).

Kind regards, Carlos Oscar

El 25/07/2014 1:19, Toropova, Ekaterina escribió:
> Dear 3DEM community,
>
> I've been struggling all day with this problem and admit defeat, would 
> love some help.
>
> I'm trying to do an FSC comparison between my map and a crystal 
> structure, my stumbling block has been to keep the two maps aligned. 
> This is what I've tried.
>
> First approach:
> - I've docked the pdb file into my map in Chimera and saved it in the 
> coordinate system of the map.
> - I've then used the 'cp from pdb' command in spider to convert the 
> pdb to a spider volume. And here's where I've got a problem - this 
> introduces a rotation, such that when you open the volume in Chimera, 
> it no longer aligns with the EM map.
> - I thought I had got around this with a spider RT 3D rotation of 
> 270,180,0 (phi,theta, psi). As it turns out this got me most of the 
> way there - enough to fool me into proceeding with the FSC but on 
> getting lower values than I was expecting I went back to look at the 
> fit and saw that there was still a small rotation and possibly shift 
> that I have spent the last few hours trying to figure out with no avail.
>
> Second approach:
> I then decided to try to do this in Chimera using the molmap command 
> to convert the fitted pdb to density, save the map as an mrc file to 
> later convert to spider. This does work - the map stays in the same 
> place as an mrc but when I convert to spider the maps are no longer 
> aligned, there's some discrepancy in the volume center that I can't 
> figure out.
>
> So my questions are:
> 1) Does anyone know the rotations that need to be applied to a volume 
> generated from the 'cp from pdb' spider command to keep exactly the 
> same orientation as the original pdb when viewed in Chimera?
> 2) Can I do the FSC comparison with mrc files?
>
> Thanks very much in advance,
>
> Kat
>
> Katerina Toropova
> Charles H. Hood Postdoctoral Fellow (Leschziner lab)
> Dept. of Molecular and Cellular Biology
> Harvard University
> 305 NWB, 52 Oxford St.
> Cambridge, MA 02138
>
>
>
>
>
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> 3dem at ncmir.ucsd.edu
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-- 
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   coss at cnb.csic.es
Biocomputing unit                             http://biocomp.cnb.csic.es
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
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