Re: [COOT] pymol does not cartoon-ize my helices : coot helical restraints

[Chavas Leo]

Dear Hari --

Not being an expert, I can't answer for you... but it might be a good  
idea to post at:

pymol-us...@lists.sourceforge.net

Good luck.

-- Leo --

On 6 Feb 2009, at 17:50, hari jayaram wrote:

I have a low-ish resolution (3.5 ) map for a membrane protein. I  
have been using helical restraints heavily in pymol to do the model  
building (versions 0.4.2 to 0.5.1 to 0.6 pre release ) . The  
structure is very homologous to something else and these are really  
long membrane spanning helices. So a large part of the structure   
should be helical and thats my justification for using the  
restraints in coot.


I have mostly refined in refmac ( newest 5.3 ) and some in phenix.  
Both of these pick the refining  restraints automagically.


My problem is that my helices look perfect in coot , with the  
torsions and h-bonding looking pretty good .All the traffic lights  
( with and without torsional and ramchandran and helical  
restraints) are green. But pymol simply refuses to cartoonize my  
helices as helix.


I know I can force the pymol cartoon algorithm to treat those  
regions as helix but am concerned that something is not correct in  
the way I built my model.


Any clues on forcing my helices to conform to what pymols idea of a  
helix is. The pymol version is also 1.0r2 and does cartoonize  
everything else  as expected.


Hari Jayaram





Chavas Leonard, Ph.D. @ home
Research Associate
Marie Curie Actions Fellow

Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
Oxford Road
Manchester Lancashire
M13 9PT

Tel: +44(0)161-275-1586
e-mail: leonard.cha...@manchester.ac.uk
http://personalpages.manchester.ac.uk/staff/leonard.chavas/

Re: [COOT] pymol does not cartoon-ize my helices : coot helical restraints

[Paul Emsley]

hari jayaram wrote:
I have a low-ish resolution (3.5 ) map for a membrane protein. I have 
been using helical restraints heavily in pymol to do the model building 
(versions 0.4.2 to 0.5.1 to 0.6 pre release ) . The structure is very 
homologous to something else and these are really long membrane spanning 
helices. So a large part of the structure  should be helical and thats 
my justification for using the restraints in coot.


I have mostly refined in refmac ( newest 5.3 ) and some in phenix. Both 
of these pick the refining  restraints automagically.


My problem is that my helices look perfect in coot , with the torsions 
and h-bonding looking pretty good .All the traffic lights ( with and 
without torsional and ramchandran and helical restraints) are green. But 
pymol simply refuses to cartoonize my helices as helix.


I know I can force the pymol cartoon algorithm to treat those regions as 
helix but am concerned that something is not correct in the way I built 
my model.


Any clues on forcing my helices to conform to what pymols idea of a 
helix is. The pymol version is also 1.0r2 and does cartoonize everything 
else  as expected.


Are the residues in helical secondary structure? (the DSSP algorithm is 
built in to Coot - perhaps Pymol uses something else to define ss?)


You can look at the sequence view (coloured by secondary structure) or 
view as CA with Secondary Structure to see if Coot (at least) thinks 
your residues are alpha helices.


Paul.