[COOT] chain coloring
Hi Paul, hi all, besides for the principal task of building molecules, I like using coot for studying structures. I would however be very happy to give a given chain a determined color, rather than having colors attributed by the program. Is that possible? By the way, I don't know if that's a problem of mine only, but with the new version of coot (I'm currently using Bill Scott install of Coot 0.6.1 on MacOSX 10.6.2) when I try to change chain colors with the Edit-->Bond colors-->Molecule colors I only have one of the chain of a molecule that has the color changed, the others stay of the color they were. Keep up the excellent work, thanks a lot in advance, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094
Re: [COOT] chain coloring
Sebastiano Pasqualato wrote:
Hi Paul, hi all,
besides for the principal task of building molecules, I like using coot for
studying structures.
I would however be very happy to give a given chain a determined color, rather
than having colors attributed by the program.
Well, you (only) have
Edit -> Bond Colours -> { pull the slider }
that's all you have for now - and for at least the next year.
(those settings get saved to the state file, btw)
By the way, I don't know if that's a problem of mine only, but with the new version
of coot (I'm currently using Bill Scott install of Coot 0.6.1 on MacOSX 10.6.2) when
I try to change chain colors with the Edit-->Bond colors-->Molecule colors I
only have one of the chain of a molecule that has the color changed, the others stay
of the color they were.
If I understand you right, that should not be - and indeed does not
happen for me. (You are in "Bonds (Colour by Molecule)" mode, right?)
Paul
Re: [COOT] chain coloring
On Feb 16, 2010, at 1:22 PM, Paul Emsley wrote:
> Sebastiano Pasqualato wrote:
>> Hi Paul, hi all,
>> besides for the principal task of building molecules, I like using coot for
>> studying structures.
>> I would however be very happy to give a given chain a determined color,
>> rather than having colors attributed by the program.
>>
>>
>
> Well, you (only) have
> Edit -> Bond Colours -> { pull the slider }
>
> that's all you have for now - and for at least the next year.
yeah, that's what I feared :-(.
Ok I'll have to deal with it, but still think this is a main missing feature.
Won't' stop me from using coot, though!
>
> (those settings get saved to the state file, btw)
>
>> By the way, I don't know if that's a problem of mine only, but with the new
>> version of coot (I'm currently using Bill Scott install of Coot 0.6.1 on
>> MacOSX 10.6.2) when I try to change chain colors with the Edit-->Bond
>> colors-->Molecule colors I only have one of the chain of a molecule that has
>> the color changed, the others stay of the color they were.
>>
>
>
> If I understand you right, that should not be - and indeed does not happen
> for me. (You are in "Bonds (Colour by Molecule)" mode, right?)
No I'm not in Bonds (colour by molecule). In that case, all the chains of the
molecule have the same colour, and the colour do change when you pull the
slider.
What interests me is the "Bonds (Colour by Chain)" or "CAs + Ligands"
representation, in which different chains in the same molecule have different
colours.
In that case only one chain changes colour when I pull the slider, the others
don't htey used too, though).
Don't know if it's just me.
thanks Paul,
ciao
s
>
> Paul
--
Sebastiano Pasqualato, PhD
IFOM-IEO Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano
Italy
tel +39 02 9437 5094
Re: [COOT] chain coloring
On Tuesday 16 February 2010, Sebastiano Pasqualato wrote: > >> By the way, I don't know if that's a problem of mine only, but with the > >> new version of coot (I'm currently using Bill Scott install of Coot 0.6.1 > >> on MacOSX 10.6.2) when I try to change chain colors with the Edit-->Bond > >> colors-->Molecule colors I only have one of the chain of a molecule that > >> has the color changed, the others stay of the color they were. > >> > > > > > > If I understand you right, that should not be - and indeed does not happen > > for me. (You are in "Bonds (Colour by Molecule)" mode, right?) > > No I'm not in Bonds (colour by molecule). In that case, all the chains of the > molecule have the same colour, and the colour do change when you pull the > slider. > What interests me is the "Bonds (Colour by Chain)" or "CAs + Ligands" > representation, in which different chains in the same molecule have different > colours. > In that case only one chain changes colour when I pull the slider, the others > don't htey used too, though). > Don't know if it's just me. I see the same problem in 0.6.1 under linux. Ethan
Re: [COOT] chain coloring
Ethan Merritt wrote: On Tuesday 16 February 2010, Sebastiano Pasqualato wrote: By the way, I don't know if that's a problem of mine only, but with the new version of coot (I'm currently using Bill Scott install of Coot 0.6.1 on MacOSX 10.6.2) when I try to change chain colors with the Edit-->Bond colors-->Molecule colors I only have one of the chain of a molecule that has the color changed, the others stay of the color they were. If I understand you right, that should not be - and indeed does not happen for me. (You are in "Bonds (Colour by Molecule)" mode, right?) No I'm not in Bonds (colour by molecule). In that case, all the chains of the molecule have the same colour, and the colour do change when you pull the slider. What interests me is the "Bonds (Colour by Chain)" or "CAs + Ligands" representation, in which different chains in the same molecule have different colours. In that case only one chain changes colour when I pull the slider, the others don't htey used too, though). Don't know if it's just me. I see the same problem in 0.6.1 under linux. OK, I see what you mean. Uncheck the "Change colours for Carbons Only" checkbutton. Paul.
Re: [COOT] chain coloring
On Feb 16, 2010, at 5:21 PM, Paul Emsley wrote: > Ethan Merritt wrote: >> On Tuesday 16 February 2010, Sebastiano Pasqualato wrote: >> >> > By the way, I don't know if that's a problem of mine only, but with the > new version of coot (I'm currently using Bill Scott install of Coot 0.6.1 > on MacOSX 10.6.2) when I try to change chain colors with the Edit-->Bond > colors-->Molecule colors I only have one of the chain of a molecule that > has the color changed, the others stay of the color they were. > If I understand you right, that should not be - and indeed does not happen for me. (You are in "Bonds (Colour by Molecule)" mode, right?) >>> No I'm not in Bonds (colour by molecule). In that case, all the chains of >>> the molecule have the same colour, and the colour do change when you pull >>> the slider. >>> What interests me is the "Bonds (Colour by Chain)" or "CAs + Ligands" >>> representation, in which different chains in the same molecule have >>> different colours. >>> In that case only one chain changes colour when I pull the slider, the >>> others don't htey used too, though). >>> Don't know if it's just me. >>> >> >> I see the same problem in 0.6.1 under linux. >> >> >> > > OK, I see what you mean. Uncheck the "Change colours for Carbons Only" > checkbutton. > > > Paul. Bingo! That was it! Thanks a zillion, Paul! ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094
