[PyMOL] showing sequence conservation on the surface

[camille]

Hello PyMol community!

is there any way to display sequence conservation on the surface of a 
protein?

i.e. to use the info I have in a sequence alignment.

do I have to do this by hand?

Thanks,
Camille

Re: [PyMOL] homologous alignments?

[camille]

Hello,
	 I am unable to read the archive at the moment so can anyone tell 
me the command that allows colouring of the edge of helices and strands 
(usually grey). I think this was posted recently but I don't have it in 
any of my saved scripts.


Many thanks,
Camille

Dr Camille Shammas
Medical Research Council Laboratory of Molecular Biology
Hills Road, Cambridge CB2 2QH, UK.
Tel: +44 (0)1223 402407
Mobile: 07812035842
E-mail: cami...@mrc-lmb.cam.ac.uk

[PyMOL] color by ss

[camille]

Hello Pymol community,
	I'm experiencing a problem when colouring a pdb by secondary 
structure. The colour bleeds from the ends of helices and sheets into 
loop.


for example, if I were to

color orange, a/49:52/
color purple, a/53:55/
color mred2, a/56:59/


where a/49:52/ is beta strand and a/53:55/ is loop and a/56:59/  is 
beta strand, I get bleed from the ends of the strand into the loop.



Is there any way around this to get the colors to only apply to the 
defined secondary structure elements (I read in an ss_pml with 
alter... yada yada yada) as in molscript?


I apologise if this question has been dealt with before (I have tried 
to find previous messages). I imagine that this would be important to 
many who would like to use pymol to make figures for publication.


Many thanks,

Camille

[PyMOL] surface charge?

[camille]

Hi Warren,
	I'm using PyMol to make the figures in a paper I am currently writing. 
I know that pymol can generate surfaces at the moment but not charge. 
Is there any way to colour a surface by charge in pymol using charges 
calculated in grasp? ...or can I import a grasp surface? I heard that 
this sort of thing was in the pipe-line, do you have a rough estimate 
of when it will be available?



Camille

p.s. I'm working on os x with npymol.

[PyMOL] RGB2CMYK

[camille]

Hi,
	can anyone direct me to a url with RGB colours (in the format below) 
and their CMYK equivalents? At the moment I'm messing around with the 
following kind of thing


set_color cyan2=[0.7, 1.0, 1.0]

	I need to use a cyan color in a figure but unfortunately this becomes 
very dark when the resulting ray traced image file is viewed in CMYK 
mode in illustrator. Greens, especially, seem to suffer in conversion. 
Help!


cheers,
Camille

MRC-LMB
Cambridge University
UK

[PyMOL] summary of CA trace

[camille]

Thanks for the helpful emails everyone.

What I did to get the figure I wanted (CA trace with every 10th ca 
highlighted) was as follows...


use your normal PDB file and do...

show ribbon
set ribbon_sampling, 0

..as suggested by Robert L. Campbell

...and then I just showed the sphere for specific CA atoms and reduced 
the radius with..


alter n, vdw=1

! where n is the name of the CA

Camille