Can e2pdb2mrc create a map file with the same coordinate as PDB file?

[Kui Xu]

Dear Users and Developers,

I use e2pdb2mrc to create a map file from PDB file, but how can I know the position of a C atom from PDB file in mrc file? Thank you!

Best Regards,

Kui 

[Kui Xu]

eg. the range of x in PDB(5ftm.pdb) is 16.725 ~ 169.84.  169.84-16.725 = 153.19

but the mrc file create by e2pdb2mrc, MRC.nx = 158

 158 is not equal to 153.19.

so I don't know how ATOM in PDB correspond to the density value in mrc file.

在 2016年7月12日星期二 UTC+8下午4:45:32，Kui Xu写道：

[Steven Ludtke]

Hi Kui. Normally you would also specify the box size yourself. The PDB will be centered in the box. If you wish to understand the location of a specific atom in the density map, the easiest thing to do is to simply load the map and model into Chimera, and use "fit in map". You can then visually see where any atom is in the density map visually.

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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

[Kui Xu]

Dear Steven,

Yeah, I can use Chimera to do that, but what I want to do is get to density value of an atom in command line without any manually operations.

Thank you!

在 2016年7月12日星期二 UTC+8下午7:19:32，Steve Ludtke写道：

[Kui Xu]

Dear Steven,

Can I get the density value of an atom in map in command line without any manually operations? Or can eman2 create a map that the same box with the PDB? Or not, can eman2 tell me the shift of X,Y,Z in map according to PDB?

I really need your help, Thank you!

Best Regards,

Kui

[Steve Ludtke]

What you are describing is one of the tests used to judge the quality of an alignment of a PDB to a density map. Clearly you have to do an alignment to relate the two coordinate systems before you can do this. The program e2fhstat.py I believe includes this as a metric. You can contact Matthew Baker <mba...@bcm.edu> for more info on this. 

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Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Mike Strauss]

Hi Kui,

perhaps you can try sxpdb2em.py.   I have found it useful in the past.

mike

[Paul Penczek]

I am afraid there is some confusion here.  PDB coordinates are in an arbitrary coordinate system as

for crystallographers it does not matter. EM system is

fixed such that the origin is at a center of the box

and typically center of gravity of the structure coincided with the center of the box. 

PDB coordinates are easily manipulated, so

the PDB structure can be 'shifted' and/or 'rotated' 

by operating on coordinates. 

All that is easily accomplished using sxpdb2em.py

and other commands in Sparx that modify PDB coordinates.

However, it requires reading the documentation and

putting some effort in understanding the geometry

and conventions used. 

Regards,

Pawel