In most cases, cif file you can download from the PDB doesn't contain map coefficients.
You need to specify which map you're trying to visualize. If it's model map (fo? fc?), you can calculate that using sfall. If you are trying to check the electron density (2fo-fc), you need to add bulk solvent correction at the very least. You can use refmac to do that (zero cycles if you don't want the model to move) or better yet get it from pdb_redo. There is coot plugin there and maps are precalculated. Coot reads output mtz files from all major refinement programs. No need to calculate the ccp4 map. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: RiC <[email protected]> </div><div>Date:05/27/2014 5:36 PM (GMT-05:00) </div><div>To: Ed Pozharski <[email protected]>, [email protected] </div><div>Subject: RE: Structure factors to CCP4 maps </div><div> </div>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 ____________________________________________________________ FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! Free 3D Earth Screensaver Watch the Earth right on your desktop! Check it out at www.inbox.com/earth
