Miguel wrote:
Jan wrote:
I think the all color schemes should be available down and up the
hierarchy if applicable to atom and derived rendering, e.g.
cartoon on
select tyr237:A
color cartoon amino # this is OK
cpk 100
color cpk amino # not OK
This should be: color atoms amino
color cpk yellow # even this is not OK !
This should be: color atoms yellow
you are right, sorry I forget to check RasMol against my imperfect
remembrance, in RasMol, too, coloring the cpk rendering requires a color
atoms command and coloring the wireframe rendering was done by color bonds
wireframe 50
color wireframe amino # compatibility! not OK
'ScriptException:invalid argument'
I do not understand what you are saying by 'compatibility' ... this does
not exist in RasMol/Chime ... so it does not exist in Jmol
There are two problems with this command
1. 'color wireframe {color}' does not exist in RasMol/Chime. Therefore it
does not exist in Jmol. The command is 'color bonds {color}'
2. see below ...
color bonds amino # not OK
bonds either have no color or they have one color.
If they have no color, then each half of the bond independently inherits
the color of the atom that is connected.
If there is one color then it is applied to the entire bond.
If you say 'color bonds amino' then I assume that you are saying that you
want to color each half of the bond, independently, according to the amino
group of the connected atom. This means that bonds between amino groups
would have to be split in two different colors. But you want to color the
atoms something else.
There is no mechanism to support this.
Adding this mechanism would require supporting two different colors in all
bonds.
This would be more work/complexity/overhead, and I don't see what the
benefit would be. Can you give me an example?
I completely agree with your argumentation
select tyr237:A.CA
label %n%r
color label amino # not OK
This one might make sense and would probably not be too difficult to
implement.
And this was the start of my excursion. I want to color parts of the
cartoon amino and label this parts in the same color (while for some
residues there should be a ball and stick representation in an atom
color scheme, too). I failed with the color label amino command and then
tried to use none and inherit the cpk (!) color, which is in fact the
atom color.
# only this works
color atom amino # OK
color cpk none
color bonds none
color label none
# and inherit the amino color to cpk, bonds, cartoon, label
a difference between atom and cpk is definitively not RasMol compatible.
I believe that you are mistaken. The commands:
color cpk {color}
color wireframe {color}
do not exist in RasMol.
I don't think that we should introduce 'cpk' as an alias for 'atoms' and
'wireframe' as an alias for 'bonds' ... although if you think that is a
good idea then we should discuss it separately. It affects more things
than just colors.
it would make writing scripts more intuitive, but incompatible. I think
it was my fault, being so intuitive after just a short time not using
Ras/Jmol daily.
The command:
color bonds amino
does not exist in RasMol. Adding it to Jmol would require (slightly) more
complex data structures and more complex code. I see no reason to add this
unless you have a very good example of how it would be used.
in most cases only wireframe rendering in conjunction with amino
coloring (and not cpk with atom coloring, too) was used and this could
be done by color atoms amino; color bonds none;
We can consider adding
color labels amino
This has been my main aim. I would very much support this.
With kind regards, Jan
Miguel
-------------------------------------------------------
This SF.Net email is sponsored by: InterSystems CACHE
FREE OODBMS DOWNLOAD - A multidimensional database that combines
robust object and relational technologies, making it a perfect match
for Java, C++,COM, XML, ODBC and JDBC. www.intersystems.com/match8
_______________________________________________
Jmol-developers mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
