*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Then I tried CNS "model_map.inp" to get the map for improving the model.
(a) generate.inp gave me output (generate.pdb) but I still miss the Hg
atoms in the output.
First, does the generate.pdb contain the Hg atoms?
If not, here are the common culprits:
- make sure the input file prior to the 'generate' step had the ion
atoms specified in a manner readable by CNS with proper column alignment
etc. (if help needed on this front, here's the lazy way out: look at
example PDB files).
- also make sure the following topology and parameter files are
specified in the generate_inp file as follows
{===================== ion topology and parameter files
====================}
{* ion topology file *}
{===>} ion_topology_infile="CNS_TOPPAR:ion.top";
{* ion parameter file *}
{===>} ion_parameter_infile="CNS_TOPPAR:ion.param";
(b) then I added Hg atoms manually in generate.pdb and ran
"minimize.inp". In the output (minimize.pdb) after minimize I am also
not getting Hg atoms.
Not sure if you meant earlier that generate.pdb was missing Hg atoms. In
that case, first fix above step. Not surprisingly, if generate.pdb is
missing Hg atoms, there is no way for minimize.inp to put back missing info.
(c) However, taking the minimize.pdb (with protein residues poly
ALA/Gly only) I am trying to run "model_map.inp". I would like to know
how I can get HL co-efficients from .SCA file (created by HKL2000) as
it requires as follows.
To my knowledge, CNS reads files in the .hkl format, not .sca. So I am
not sure how CNS read your .sca file, in the first place (unless my
understanding is getting rusty). Convert your_file.sca to your_file.hkl
before you proceed.
> to_cns your_file.sca your_file.hkl
Above should work if 'to_cns' is appropriately aliased.. Please look for
errors in your logfiles from the CNS jobs. The comments in the logfiles
often give clear indications as to the nature of the problem wrt files,
formats etc.
{* Hendrickson-Lattman coefficients A,B,C,D *}
{* required for the "mlhl" target and phase combined
or observed maps *}
{+ table: rows=1 "HL coefficients" cols=4 "A" "B" "C" "D" +}
{===>} obs_pa="pa";
{===>} obs_pb="pb";
{===>} obs_pc="pc";
{===>} obs_pd="pd";
Make sure pa, pb, pc, pd labels correspond to the labels in your input
.hkl file.
If I run "model_map.inp" without above parameters, then I get the map
but that does not cover the model and model chains (with helices and
strands) are also not going through the electron density.
If only the 'extent of the map' is the problem, you can re-pick the
output map extent by "map_mode" parameter selection in the input file.
HTH.
Raji
--
Raji Edayathumangalam
Postdoctoral Fellow
The Rockefeller University
Box 224. 1230 York Avenue
New York, NY 10021
