[ccp4bb] lithium incorporation in refmac
Dear all i have downloaded lithium coordinates for the density i guess is for lithium but i think while refinement in refmac is not taking lithium into the consideration. i want to know how to obtain cif file for lithium and incorporate it into the refmac for refinement.. thanx in advance l -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] lithium incorporation in refmac
Hi You don't need a CIF file for elements or their ions, only for compounds. Li and Li+1 are already in the list of scattering factors ($CLIBD/atomsf.lib) as indeed are all the elements with their common ions. Are you sure you have the atom name in the right columns on the HETATM record (e.g. Li in 13-14 and LI1+ in 77-80)? Cheers -- Ian On 8 June 2012 19:35, Faisal Tarique faisaltari...@gmail.com wrote: Dear all i have downloaded lithium coordinates for the density i guess is for lithium but i think while refinement in refmac is not taking lithium into the consideration. i want to know how to obtain cif file for lithium and incorporate it into the refmac for refinement.. thanx in advance l -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] lithium incorporation in refmac
On Friday, June 08, 2012 11:35:25 am Faisal Tarique wrote: Dear all i have downloaded lithium coordinates for the density i guess is for lithium but i think while refinement in refmac is not taking lithium into the consideration. If you see density, it might not be lithium :-) i want to know how to obtain cif file for lithium and incorporate it into the refmac for refinement.. LI is in the standard monomer dictionary. You don't have to do anything special. But given that it has no scattering power to speak of, you may have to add explicit restraints to hold it in place during refinement. LI appears in 41 PDB entries. You might want to inspect the density in some of them to get a feel for how it looks. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] lithium incorporation in refmac
thanx a lot... On Sat, Jun 9, 2012 at 12:23 AM, Ian Tickle ianj...@gmail.com wrote: Hi You don't need a CIF file for elements or their ions, only for compounds. Li and Li+1 are already in the list of scattering factors ($CLIBD/atomsf.lib) as indeed are all the elements with their common ions. Are you sure you have the atom name in the right columns on the HETATM record (e.g. Li in 13-14 and LI1+ in 77-80)? Cheers -- Ian On 8 June 2012 19:35, Faisal Tarique faisaltari...@gmail.com wrote: Dear all i have downloaded lithium coordinates for the density i guess is for lithium but i think while refinement in refmac is not taking lithium into the consideration. i want to know how to obtain cif file for lithium and incorporate it into the refmac for refinement.. thanx in advance l -- Regards Faisal School of Life Sciences JNU -- Regards Faisal School of Life Sciences JNU
