Hi Patrick,
For the majority of deposited structures, you need an additional step
between 3 and 4. Format conversion can be done using CCP4 program
cif2mtz.
However, most deposited structures (including 1C75) don't include phase
information, which is required for electron density calculation. Phases
can be calculated from the model using a variety of programs (this is
"step 3.5"). This will give you another mtz file containing the
amplitudes and phases, which can be used to calculate electron density.
MTZ files store reciprocal space data, some of which can be used to
calculate real space data (aka a map) - but a MTZ file doesn't store a
map (although this seems to be a common misunderstanding).
You'd use fft (also part of ccp4) to calculate a real-space map from a
phased mtz file - but if you're goal is to visualize it in coot,
auto-open mtz within coot usually works just as well.
Hope this helps,
Pete
RiC wrote:
I am NOT trying to open the CCP4 file on a text editor !
I am trying to do the following on CCP4/COOT:
1) Download a PDB (example 1c75.pdb) from the PDB database
2) Download the corresponding structure factors (example 1c75-sf.cif.txt)
3) Now from the above sf-cif file How can I get a MTZ file using CCP4
4) Then display the map (either in CCP4 format or MTZ format) in COOT
I want to know how to do step 3 above.
Sorry, I was not more clearer earlier.
Patrick
-----Original Message-----
*From:* [email protected]
*Sent:* Tue, 27 May 2014 17:31:47 -0400
*To:* [email protected], [email protected]
*Subject:* RE: Structure factors to CCP4 maps
I am terribly sorry, but ccp4 maps are understandable to nobody. They are
binary files, for starters. Even if you develop an uncanny ability to read
these you will still be left with random looking sea of numbers.
If you trying to generate a model map, you can use sfall. Given that you
are posting on coot bb, the easiest way to visualize such map is to use Fc
column from, say, zero step refmac run.
Be more specific. Look at pdb_redo, it may be what you are looking for.
Sent on a Sprint Samsung Galaxy S® III
-------- Original message --------
From: RiC
Date:05/27/2014 4:42 PM (GMT-05:00)
To: [email protected]
Subject: Structure factors to CCP4 maps
HI,
Does anyone have a step by step guide to go from a structure factor file
from the PDB to a CCP4 map (understandable to a biologist) like the one I
can download on the electron density server?
I am confused and my attempts at using CCP4 keeps coming up with "failed"
Thanks
Patrick
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