Re: [COOT] pymol does not cartoon-ize my "helices" : coot helical restraints
The last time I looked (which was some time ago!) PyMol would cartoonize if EITHER (a) the secondary structure was defined in the PDB file; OR (b) the Action Menu item "assign sec. struc." was selected. I don't know when this behavior changed, but the latest build from fink seems to display cartoon renderings independently of the presence or absence of HELIX and SHEET records. You might also check the order of the atom records in the peptide bonds in case an unexpected ordering is confusing PyMol. Lynn Ten Eyck On 7 Feb 2009, at 05:24, Paul Emsley wrote: 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.
Re: [COOT] pymol does not cartoon-ize my "helices" : coot helical restraints
On 13:24 Sat 07 Feb , Paul Emsley wrote:
> hari jayaram wrote:
> Are the residues in helical secondary structure? (the DSSP algorithm is
> built in to Coot - perhaps Pymol uses something else to define ss?)
PyMol indeed has its own algorithm. Here is a brief paste from it:
./layer3/Selector.c:
int SelectorAssignSS(PyMOLGlobals *G,int target,int present,int state_value,int
preserve,int quiet)
{
/* PyMOL's secondary structure assignment algorithm:
General principal -- if it looks like a duck, then it's a duck:
I. Helices
- must have reasonably helical geometry within the helical span
- near-ideal geometry guarantees helix assignment
- a continuous ladder stre i+3, i+4, or i+5 hydrogen bonding
with permissible geometry can reinforce marginal cases
- a minimum helix is three residues with i+3 H-bond
II. Sheets
- Hydrogen bonding ladders are the primary guide
- Out-of-the envelope
- 1-residue gaps in sheets are filled unless there
is a turn.
*/
--
Thanks,
Donnie
Donnie Berkholz
Developer, Gentoo Linux
Blog: http://dberkholz.wordpress.com
pgp4dWcaJnf79.pgp
Description: PGP signature
Re: [COOT] pymol does not cartoon-ize my "helices" : coot helical restraints
DSSP did indeed think they were helices. Also thanks for the sec str coloring tip-didnt realize coot had that feature. For the model coot also colors the helices pink as would be expected. So it must be that pymol cartoons still dont implement "DSSP" ..which I thought was the case Hari On Sat, Feb 7, 2009 at 8:24 AM, Paul Emsley wrote: > 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. >
Re: [COOT] pymol does not cartoon-ize my "helices" : coot helical restraints
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.
Re: [COOT] pymol does not cartoon-ize my "helices" : coot helical restraints
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/
[COOT] pymol does not cartoon-ize my "helices" : coot helical restraints
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
