Hi Joseph,
AFAICS, your file doesn't conform to PDB specs, so I am not surprised
that Coot's parser (actually mmdb) doesn't work as you expect it to.
On the other hand, there are many checks for Ter atoms in Coot, but
perhaps I missed one. All bets are off until the PDB file is corrected.
Over to Paul! Where are you Paul Emsley??
I was in Spain. Back now still getting up to speed.
Regards,
Paul.
On 06/02/14 19:40, Joseph Noel wrote:
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
______________________________________________________________________________________
