converting .pdb files to .mrc files

[SANJU SINGH]

Hello,

I am a student from India working on protein structures. I need to convert a set of .pdb files (1000 at a time) to there corresponding density representation in .mrc files. Can anyone tell how i can do this conversion?
 Any inputs are of great value to me.

Thank you

[Steven Ludtke]

The program e2pdb2mrc.py will do simple pdb to density conversion (the output doesn't have to be MRC format, this is just a historical naming convention).  If you want to do many files at a time, shell scripting is the easiest way. For example, if you are using the bash shell:

> ls

1AGT.pdb 1BXN.pdb 1CGX.pdb

> for i in *.pdb

do

e2pdb2mrc.py --apix 2 --res 8

done

--
--
----------------------------------------------------------------------------------------------
You received this message because you are subscribed to the Google
Groups "EMAN2" group.
To post to this group, send email to em...@googlegroups.com
To unsubscribe from this group, send email to eman2+un...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/eman2

---
You received this message because you are subscribed to the Google Groups "EMAN2" group.
To unsubscribe from this group and stop receiving emails from it, send an email to eman2+un...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

----------------------------------------------------------------------------

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

[Paul Penczek]

I do not know much about shell scripting, 
but shouldn't e2pdb have i as a parameter?
Regards,

Pawel

[Steven Ludtke]

What can I say, it's early in the morning  :^)

> for i in *.pdb
do

e2pdb2mrc.py  $i  ${i%.pdb}.hdf  --apix 2  --res 8
done