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/
Re: [COOT] where did add alt conf go?
Dear Paul -- On 26 Jul 2008, at 14:57, Paul Emsley wrote: I recently discovered that on a laptop with 100dpi fonts and a 800- pixel height resolution (not uncommon), then the tool-bar is so long that the GNOME panel obscures the status bar. Not good. I suppose that the Right Thing is to make it runtime configurable. Just a quick thought (I'm sure you're only considering this, but well...): what about adding an option just like your Tips window? What I have in mind is to add a pop-up window when you click on the Model/Fit/Refine button that will ask you which option you'd like to have in your refinement bar. You might put the all list of functions, with pre-selected buttons for the most common ones. The user will then have the possibility to choose what (s)he want according to the most used functions /or the size of the screen. Sorry for the post if you already implemented it or already planed to do it. Just a thought. Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate 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: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
