Re: [ccp4bb] mol rep help needed
Hi David, On Fri, Oct 01, 2010 at 11:40:13AM -0400, David Roberts wrote: My question - finally - how can I run automolrep with one dimer fixed, looking for the location of the other 2 monomers (so basically I want to fix a dimer as part of my solution, and then search for the other 2 molecules in the asu). I found the latest MOLREP binary from http://www.ysbl.york.ac.uk/~alexei/molrep.html#installation to work very well (thanks Alexei!). Something like: molrep_linux -f your.mtz \ -m monomer.pdb \ -mx fixed_dimer.pdb It doesn't get simpler than that I guess ;-) Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] mol rep help needed
Suggestions: Are you using the GUI - that gives you a molrep option to provide a fixed model.. Re Amore - yes you can do this - run first pass as autoamore which should find one monomer, the keep on redoing the TRAN fun providing the solution to 1st, 1st+2nd, etc as known solution - all done in GUI.. Some hints - if you have 4 monomers is there a non-crystallographic translation? MOLREP will report this.. If that NC translation has a coordinate as 0.5 then this will generate misleading absences along that axis and the SG may actaully be P 2 21 21 or P21 2 21 or P 21 21 2 depending on the axis.. And if you expect a dimer why not use that as your search model? Also try PHASER - it is often good but you may need to ask for less stingent packing checks than the default Eleanor David Roberts wrote: Hi all, I'm relatively new to using CCP4 (I've done most of my crystallography using x-plor, phases, etc...). But, I like ccp4, and so I'm using it in concert with amore (which I know is part of the ccp4i build now) for molecular replacement. I have a protein that I'm working on with data collected from Argonne. There are many forms, and I have several of these forms collected (metal bound, apo, mutants, etc...). I have a solution for a wild-type form, and am presently working on solving a mutant form. For molecular replacement, I used the wild type structure (obviously). It's a homodimer, so I tried using both the monomer and the dimer form of the protein (it's possible that the mutant is conformationally different from the wild type, so it's not a clear-cut problem). Furthermore, they both crystallize in the same space group (P212121), but unit cells are different (I don't have the exact numbers now, but the general idea is the wild type is 30/60/120, while the mutant is 60/70/120). As a result, the wild type has 2 monomers per asu while the mutant has 4 (I think). When I look at results from mol rep (ccp4i, auto-molrep routine), I get 4 molecules per asu with the monomer as a search. 2 of the molecules I think are right (map is good - they form a good dimer, etc...), while I think 2 are incorrect (the dimer overlaps, and it just doesn't look good). My question - finally - how can I run automolrep with one dimer fixed, looking for the location of the other 2 monomers (so basically I want to fix a dimer as part of my solution, and then search for the other 2 molecules in the asu). I know it's probably simple and possible, but it's not a world I am very familiar with (I seriously have just done MIR structures, they are easy for me, I have had very little work with mol rep). Could I do this with Amore as well (so fix 2 molecules and then look for an additional 2 using amore). Thanks for the help. Have a great week-end Dave
Re: [ccp4bb] mol rep help needed
HI Dave, Have you tried PHASER. I think you might get all the four molecules in auto mode. PHASER does a great job and it should be already installed along with your ccp4i. Ivan On Fri, Oct 1, 2010 at 8:40 AM, David Roberts drobe...@depauw.edu wrote: Hi all, I'm relatively new to using CCP4 (I've done most of my crystallography using x-plor, phases, etc...). But, I like ccp4, and so I'm using it in concert with amore (which I know is part of the ccp4i build now) for molecular replacement. I have a protein that I'm working on with data collected from Argonne. There are many forms, and I have several of these forms collected (metal bound, apo, mutants, etc...). I have a solution for a wild-type form, and am presently working on solving a mutant form. For molecular replacement, I used the wild type structure (obviously). It's a homodimer, so I tried using both the monomer and the dimer form of the protein (it's possible that the mutant is conformationally different from the wild type, so it's not a clear-cut problem). Furthermore, they both crystallize in the same space group (P212121), but unit cells are different (I don't have the exact numbers now, but the general idea is the wild type is 30/60/120, while the mutant is 60/70/120). As a result, the wild type has 2 monomers per asu while the mutant has 4 (I think). When I look at results from mol rep (ccp4i, auto-molrep routine), I get 4 molecules per asu with the monomer as a search. 2 of the molecules I think are right (map is good - they form a good dimer, etc...), while I think 2 are incorrect (the dimer overlaps, and it just doesn't look good). My question - finally - how can I run automolrep with one dimer fixed, looking for the location of the other 2 monomers (so basically I want to fix a dimer as part of my solution, and then search for the other 2 molecules in the asu). I know it's probably simple and possible, but it's not a world I am very familiar with (I seriously have just done MIR structures, they are easy for me, I have had very little work with mol rep). Could I do this with Amore as well (so fix 2 molecules and then look for an additional 2 using amore). Thanks for the help. Have a great week-end Dave
[ccp4bb] mol rep help needed
Hi all, I'm relatively new to using CCP4 (I've done most of my crystallography using x-plor, phases, etc...). But, I like ccp4, and so I'm using it in concert with amore (which I know is part of the ccp4i build now) for molecular replacement. I have a protein that I'm working on with data collected from Argonne. There are many forms, and I have several of these forms collected (metal bound, apo, mutants, etc...). I have a solution for a wild-type form, and am presently working on solving a mutant form. For molecular replacement, I used the wild type structure (obviously). It's a homodimer, so I tried using both the monomer and the dimer form of the protein (it's possible that the mutant is conformationally different from the wild type, so it's not a clear-cut problem). Furthermore, they both crystallize in the same space group (P212121), but unit cells are different (I don't have the exact numbers now, but the general idea is the wild type is 30/60/120, while the mutant is 60/70/120). As a result, the wild type has 2 monomers per asu while the mutant has 4 (I think). When I look at results from mol rep (ccp4i, auto-molrep routine), I get 4 molecules per asu with the monomer as a search. 2 of the molecules I think are right (map is good - they form a good dimer, etc...), while I think 2 are incorrect (the dimer overlaps, and it just doesn't look good). My question - finally - how can I run automolrep with one dimer fixed, looking for the location of the other 2 monomers (so basically I want to fix a dimer as part of my solution, and then search for the other 2 molecules in the asu). I know it's probably simple and possible, but it's not a world I am very familiar with (I seriously have just done MIR structures, they are easy for me, I have had very little work with mol rep). Could I do this with Amore as well (so fix 2 molecules and then look for an additional 2 using amore). Thanks for the help. Have a great week-end Dave
