Hi all,
I might be missing something here, but in Coot, can you not just use File -> Fetch PDB & Map using EDS… to get both the model and the map? This definitely works for me for your example 1C75. Bernhard Bernhard C. Lechtenberg, PhD Postdoctoral Fellow Riedl Lab Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Road La Jolla, CA 92037, USA Phone: 858.646.3100 x 4216 Email: [email protected]<mailto:[email protected]> On May 27, 2014, at 2:51 PM, RiC <[email protected]<mailto:[email protected]>> 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]<mailto:[email protected]> Sent: Tue, 27 May 2014 18:47:28 -0300 To: [email protected]<mailto:[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 ____________________________________________________________ FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! ________________________________ [3D Earth Screensaver Preview]<http://www.inbox.com/earth> Free 3D Earth Screensaver Watch the Earth right on your desktop! Check it out at www.inbox.com/earth<http://www.inbox.com/earth> -- 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 ________________________________ [Protect your computer files with professional cloud backup. Get PCRx Backup and upload unlimited files automatically.]<http://backup.pcrx.com/mail>
