It's probably a PATH problem (your Mac is not looking at that bin
directory where your applications are, to find for executables)
you might want to add a line in your .bash_profile file (in your home
directory; if you do not have it, you can create it with that name),
such as this :
export PATH=$PATH:/Applications/ccp4-6.4.0/bin/
save the file.
Now when you open your terminal, you should be able to type cif2mtz at
your prompt, and get the program to run for you.
Having said that, Pete Mayer is absolutely right. Now, Coot can do that
3.5 step, if you choose not the aitomatic open of mtz's, but rather the
other option where you can choose coefficients (and choose the observed
amplitudes; coot will use the model to get calculated phases, and you
will see the [Fobs;PHIcalc] map, pretty much the best you can do without
re-refinement (I guess)
best
alejandro
On 5/27/14, 18:51, RiC wrote:
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] <mailto:[email protected]>
*Sent:* Tue, 27 May 2014 17:31:47 -0400
*To:* [email protected]
<mailto:[email protected]>, [email protected]
<mailto:[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] <mailto:[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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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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--
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
