[COOT] ramachandran fit error

2009-11-18 Thread Andreas Förster 

Hey all,

I have a structure with three chains in the asymmetric unit.  When I 
select Refine/Improve Ramachandran Plot from Extensions/All Molecule, 
coot does its thing until it reaches the end of the second chain, then 
stops with the errors pasted below.  It says something about alternate 
conformations, but they have all been removed.  When I execute 
(stepped-refine-protein-for-rama 2), coot seems to do the same thing, 
but finishes the entire protein.  (It even checks every water molecule...)


Any ideas why the coot extension should fail while the scheme function 
executes happily?  Oh, I should say I'm using coot 0.6-pre-1 rev. 2189 
on RHEL 5.4beta).


Thanks


Andreas


Little window with error message:

In /csb/soft/Linux/src/coot0.6pre/share/guile/gtk-2.0/gtk.scm:
 147:  0* [apply #procedure #f () ()]
In unknown file:
   ?:  1  [#procedure #f ()]
In /csb/soft/Linux/src/coot0.6pre/share/coot/scheme/fitting.scm:
...
 216:  2  (let* ((imol-map #)) (func (car *multi-refine-spec-list*) 
imol-map) ...)

 217:  3* [fit-protein-rama-fit-function (4 B -1 #f) 1]
 176:  4  (let ((imol #) (chain-id #) (res-no #) ...) (let (# #) (map # 
#) ...))

 180:  5  (let (# #) (map # #) ...)
 182:  6* [map #procedure #f (alt-conf) ...
 191:  7*  [residue-alt-confs 4 B -1 #f]
In /csb/soft/Linux/src/coot0.6pre/share/coot/scheme/coot-utils.scm:
1497:  8   [reverse ...
1498:  9*   [f ...
1498: 10*[residue-info 4 B -1 #f]
/csb/soft/Linux/src/coot0.6pre/share/coot/scheme/coot-utils.scm:1498:21: 
In procedure SWIG_Guile_scm2newstr in expression (residue-info imol 
chain-id ...):
/csb/soft/Linux/src/coot0.6pre/share/coot/scheme/coot-utils.scm:1498:21: 
Wrong type argument in position 1: #f



In shell where coot was started:

INFO:: replace_coords: 15 atoms updated.
INFO:: graphics_info_t::clear_up_moving_atoms...
DEBUG:: in safe_python_command_with_return() pValue is 0x897e86c
clearing intermediate object...
 ERROR! ---
   moving_atoms_asc_type not known: 0
 ERROR! ---
INFO:: graphics_inf



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [COOT] ramachandran fit error

2009-11-18 Thread Paul Emsley 

Andreas Förster wrote:


I have a structure with three chains in the asymmetric unit.  When I 
select Refine/Improve Ramachandran Plot from Extensions/All Molecule, 
coot does its thing until it reaches the end of the second chain, then 
stops with the errors pasted below.  ...


Any ideas why the coot extension should fail while the scheme function 
executes happily?  Oh, I should say I'm using coot 0.6-pre-1 rev. 2189 
  


Ancient Coot :)

OK, I'll take this to mean please make it trivially easy for me to 
update my Coot


Paul.

[COOT] Non-standard residue

2009-11-18 Thread S. Shunmugasundararaj 
Dear Cooters,

Is it possible to mutate a residue to a non-standard residue in coot? 

Thanks
Raj

Re: [COOT] Non-standard residue

2009-11-18 Thread Paul Emsley 

S. Shunmugasundararaj wrote:


Is it possible to mutate a residue to a non-standard residue in coot?





Yes. Section 5.6.13 of the Coot User Manual.  You could have found it by 
searching for mutating to a non-standard residue


Extensions - Modelling - Replace Residue...

Paul.