Hi guys, ok so I really appreciate all the help.
I now have cif2mtz (setting up my bash file) and also have looked at PDB_REDO (which I had never heard of). Yes, for 1c75 (the example I used) when I searched on the EDS server it did NOT give a map but it did when I used COOT (again I never tried this since looking directly on the server did not give a map, assuming it did not exist). @Pete: I was wondering what you meant by "another MTZ file" So are you saying, I first download the 1c75-sf.cif then do cif2mtz then I use FFT to get the second MTZ file? (but this second MTZ file generation can be skipped if I open the 1st stage MTZ using COOT??) Have I understood your reply correctly? Thank you all once again for your help. Patrick > -----Original Message----- > From: [email protected] > Sent: Tue, 27 May 2014 16:50:41 -0500 > To: [email protected] > Subject: Re: Structure factors to CCP4 maps > > 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 >> >> ____________________________________________________________ >> 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> ____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth
