Re: [ccp4bb] strange MR problem
csymmatch pdbin-ref my_favorite.pdb pdbin the-other.pdb -origin-hand This should move the-other.pdb to overlay my-favorite.pdb It WONT relabel the Chain IDs though.. Eleanor On 12/13/2011 04:26 AM, intekhab alam wrote: Hi All I have a 3.0A dataset of a protein-protein complex. I used one of the protein structure solved previously as a template and used phaser in CCP4 as well as in phenix. I used the sca file in phenix which gave a solution with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the converted .mtz file which gave 6 molecules in ASU but with a different packing. In both the cases map fits well in the model and there is some extra density that may correspond to second protein partner of the complex molecule. when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes. what kind of approach should i take so as to resolve this ambiguity. Regards
Re: [ccp4bb] strange MR problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear , Can you clearify what you mean by the sentence "when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes"? I do not understand what you need the mtz file for in order the check for clashes. At 3A you may have serious model bias and one or both of the solutions may not be correct. The best would be to try and fit the second protein (by MR, or if only the sequence is known, try e.g. buccaneer). If your R/Rfree eventually drop below, say, 40%, you are probably on the right track. Tim On 12/13/2011 05:26 AM, intekhab alam wrote: > Hi All > > I have a 3.0A dataset of a protein-protein complex. I used one of the > protein structure solved previously as a template and used phaser in CCP4 > as well as in phenix. I used the sca file in phenix which gave a solution > with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used > the converted .mtz file which gave 6 molecules in ASU but with a different > packing. In both the cases map fits well in the model and there is some > extra density that may correspond to second protein partner of the complex > molecule. when i tried to use the MR solution generated in phenix with the > mtz file from ccp4 the model shows a lot of clashes. > > what kind of approach should i take so as to resolve this ambiguity. > > Regards - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5x2YUxlJ7aRr7hoRAsp3AKC7ljNgMNuLHASo8TTQ3157GMzsowCeN/sq yJMgPbBDS/+j8obfudpxFFo= =SAle -END PGP SIGNATURE-
[ccp4bb] strange MR problem
Hi All I have a 3.0A dataset of a protein-protein complex. I used one of the protein structure solved previously as a template and used phaser in CCP4 as well as in phenix. I used the sca file in phenix which gave a solution with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the converted .mtz file which gave 6 molecules in ASU but with a different packing. In both the cases map fits well in the model and there is some extra density that may correspond to second protein partner of the complex molecule. when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes. what kind of approach should i take so as to resolve this ambiguity. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
