Re: [COOT] Structure factors to CCP4 maps

Tue, 27 May 2014 14:51:34 -0700

 HI Alejandro

This is going to sound like a really dumb question but I found cif2mtz 
in my /Applications/ccp4-6.4.0/bin/cif2mtz 

in my MacOSX machine.

How do I run this ? I have a CCP4 GUI interface but I cannot find the corresponding command in that (cif2mtz).

I tried running it on my normal terminal but that did not work.

Thank you,
Patrick


-----Original Message-----
From: [email protected]
Sent: Tue, 27 May 2014 18:47:28 -0300
To: [email protected]
Subject: Re: Structure factors to CCP4 maps

cif2mtz hklin 1c75-sf.cif hklout 1c75-sf.mtz

no extra keywords should be needed (but you may want to look at http://www.ccp4.ac.uk/html/cif2mtz.html for more info on these)

...tend to believe it's better to change the name of your file avoiding the .txt extension (probably included at the time of downloading)

hth

alejandro


On 5/27/14, 18:36, 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)
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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-- 
Alejandro Buschiazzo, PhD 
Research Scientist 
Unit of Protein Crystallography 
Institut Pasteur de Montevideo 
Mataojo 2020 
Montevideo 11400 
URUGUAY 
Phone: +598 25220910 int. 120 
Fax:   +598 25224185 
http://www.pasteur.edu.uy/pxf
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