Regarding e2pdb2mrc.py: Box size too small

[Arun Prasad]

Dear All,

I am trying to calculate the simulated map from a pdb model for the purpose of calculating FSC between the map and model.

I took the following example

Map details

ID: EMD-2325

Resolution: 8.9 Å

Apix: 2.08 Å

Box size: 180x180x180

PDB Model fitted: 3zpz.pdb

I created the simulated map from 3zpz.pdv using the following EMAN2 program

e2pdb2mrc.py --apix=2.08 --res=8.9 --box=180 3zpz.pdb 3zpz_simulated.mrc

I received a message in the log saying "Boz size too small. Will use 201 instead"

This has an effect on my FSC map/model calculation as EMAN2 requires the box size of the experimental and simulated map to be the same. I wonder why e2pdb2mrc.py is expanding the box size? Is there a way force the box size of the simulated to a specified value?

Thank you in advance.

Best wishes,

Arun Prasad

[Steve Ludtke]

Most likely related to the location of the PDB coordinates in virtual space. Try adding --center. Unless you pre-aligned the PDB to the map, you will probably also have to rotationally align the output MRC file to the map you're comparing with. 

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Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

[Arun Prasad]

Dear Steve,

Thank you for your message. I have tried adding --center. I still have the same issue.

I too think that it has to do with the location of the PDB coordinate in virtual space. When I open the map (EMD-2325.mrc) and the model (3zpz.pdb) in e2display the model appears larger than the map dimension and that explains the issue. But however, when I open them in chimera, they are perfectly aligned as expected because it the aligned fit deposited in EMDB.

 Could you please suggest a work around to address this issue in EMAN2? Thank you.

Best wishes,

Arun Prasad

[Steve Ludtke]

Hi Arun. I just tried this myself, and you are absolutely correct. It appears that a few months ago someone added a "feature" to e2pdb2mrc to insure that the box sizes were large enough, but didn't do their math correctly. I have pushed a fix to this, which will be in 2.2 when we finally push the button, but for the moment, the stopgap solution is to run:

e2proc3d.py 3zpz_simulated.mrc 3zpz_simulated.mrc --clip 180,180,180

which will chop the volume down to the correct size. This bug only kicks in when A/pix values are larger than ~1.2 A/pix, so it won't influence a lot of modern structures done at <1 A/pix, but it will bite you on this one.

Very sorry for the annoyance and wasted time!

[Arun Prasad]

Dear Steve,

No worries. Thank you very much for suggesting a workaround! It is very helpful fix to carry on until the new release comes out.  It is good to know about the bug and its association with A/pix value.

I much appreciate your support and advice on this forum!

Best wishes,

Arun Prasad