Here is what I found out. If I do not insert a Ter card between the last HETAM in a particular chain and the next chain, then all is fine. If I insert a Ter card, it seems that COOT is somehow looking for an additional alternative conformation. Only applies to the cations I am using (Lu3+, Li1+, Hg1+). Seems that other HETATMS that are part of monomers (i.e. GOL) work fine. ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA
Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected] Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________ On Feb 6, 2014, at 4:21 AM, Eleanor Dodson <[email protected]> wrote: > Over to Paul! Where are you Paul Emsley?? > > > On 5 February 2014 18:14, Joseph Noel <[email protected]> wrote: >> Dear Eleanor, >> >> No its not the B-factors as this was an artificially high set of values but >> the more realistic ones - in the mid 50s - also did not work for the final >> atom. It is something with the final (or only, only defined as its own chain >> ID) heavy atom in the PDB file. If I include the heavy atoms as part of the >> same chain ID as the protein, A, they all refine in real space except for >> the last one again. Something special about the last item. The alt loc >> doesn't matter either. If I pick Measures, Residue Info for the offending >> heavy atom, in addition to the normal line at the bottom of the window, >> >> "B/5 LU/LU ...." >> >> I get the additional line for editing, >> >> " B/5 LU/..." >> >> with the latter line having the occupancy, b-factor and Alt-conf boxes empty. >> >> Joe >> ______________________________________________________________________________________ >> Joseph P. Noel, Ph.D. >> Arthur and Julie Woodrow Chair >> Investigator, Howard Hughes Medical Institute >> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics >> The Salk Institute for Biological Studies >> 10010 North Torrey Pines Road >> La Jolla, CA 92037 USA >> >> Phone: (858) 453-4100 extension 1442 >> Cell: (858) 349-4700 >> Fax: (858) 597-0855 >> E-mail: [email protected] >> >> Publications & Citations: >> http://scholar.google.com/citations?user=xiL1lscAAAAJ >> >> Homepage Salk: http://www.salk.edu/faculty/noel.html >> Homepage HHMI: http://hhmi.org/research/investigators/noel.html >> ______________________________________________________________________________________ >> >> On Feb 5, 2014, at 2:58 AM, Eleanor Dodson <[email protected]> wrote: >> >>> Is the format OK or does coot dislike partial occpancy or such high B >>> factors.. >>> >>> Maybe there is no density for an atom with such a B factor? >>> Eleanor >>> >>> On 4 February 2014 20:11, Joseph Noel <[email protected]> wrote: >>>> I'm sure I am doing something wrong but I have a set of coordinates for a >>>> structure containing five Lu3+ ions created by Phenix autosol. When read >>>> into COOT (and afterwards upon modification), I can seem to real space >>>> refine the last Lu3+ in the list. The first four work fine but the last one >>>> returns an error message - "No restraints found! ...." >>>> >>>> Here is the extracted Lu3+ positions from the PDB. I'm sure I am missing >>>> something but my brain is froze (or more likely withering slowly away with >>>> age and occassional blasts of EtOH and x-ray photons). >>>> >>>> TER >>>> HETATM10242 LU L LU B 1 84.960 20.150 49.139 0.99 35.49 >>>> Lu3+ >>>> HETATM10243 LU L LU B 2 80.752 24.659 51.587 0.99104.78 >>>> Lu3+ >>>> HETATM10244 LU L LU B 3 61.052 53.144 23.645 0.99184.97 >>>> Lu3+ >>>> HETATM10245 LU L LU B 4 73.304 6.676 29.987 0.99254.64 >>>> Lu3+ >>>> HETATM10246 LU L LU B 5 81.973 25.555 53.290 0.99237.32 >>>> Lu3+ >>>> TER >>>> >>>> ______________________________________________________________________________________ >>>> Joseph P. Noel, Ph.D. >>>> Arthur and Julie Woodrow Chair >>>> Investigator, Howard Hughes Medical Institute >>>> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics >>>> The Salk Institute for Biological Studies >>>> 10010 North Torrey Pines Road >>>> La Jolla, CA 92037 USA >>>> >>>> Phone: (858) 453-4100 extension 1442 >>>> Cell: (858) 349-4700 >>>> Fax: (858) 597-0855 >>>> E-mail: [email protected] >>>> >>>> Publications & Citations: >>>> http://scholar.google.com/citations?user=xiL1lscAAAAJ >>>> >>>> Homepage Salk: http://www.salk.edu/faculty/noel.html >>>> Homepage HHMI: http://hhmi.org/research/investigators/noel.html >>>> ______________________________________________________________________________________ >>>> >>> >> >
