[chimerax-users] Not a software whiz!!!!!!!!!

[Arthur Szabo]

Have downloaded ChimeraX as I would like to include a ribosome structure or part of it in my work.

ChimeraX is, I am aware, largely a command based operational process.

I feel like a real dummy because I do not understand how to achieve the imagery that I would like

I  have been able  to open PDB 4WPO can rotate it and similar things, and there seem to be two molecules in the unit cell. I stumbled on a list of all the proteins, rRNAs and some other components in the structure such as EFG, an elongation factor.

Can't figure out how to delete one of the model units from the image, as I was able to do with Chimera. I find it virtually impossible to understand the logic of the commands. Of course the command structure is similar to that in Chimera, but I only used  that infrequently. I used the menu driven tools etc almost exclusively. I could achieve what I wanted with them and the learning curve was quite tolerable.  Then when I got stuck I received excellent advice from Chimera staff on how to use the commands when needed.


For example

color  spec<atomspec.html>   colorname   general-options
What is the designation or meaning of spec ? How would I select the EGF protein from the ribosome to color it. 4wpo #1, chain DZ: 50S ribosomal protein L9,Elongation factor G.  4WPO is the pdb number, #1, I believe to one of the two units in the model. Chain DZ refers to the protein. I  tried several permutations of this information and only received error messages.

color<help:user/commands/color.html> 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword
color<help:user/commands/color.html> red 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G
Expected one of 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
color<help:user/commands/color.html> ribbons red 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword
color<help:user/commands/color.html> ribbons red 4wpo #1, chain BZ
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword


Colorname I think I understand, and I think that I have found a log of the different colors.

Have no idea of what general-options might refer to.

Here is more of my log.

show<help:user/commands/show.html> selAtoms ribbons
help<help:user/commands/help.html> help:user
select<help:user/commands/select.html> 4wpo #1, chain BZ
Expected an objects specifier or a keyword
help<help:user/commands/help.html> help:contact.html
help<help:user/commands/help.html> help:contact.html
color<help:user/commands/color.html> #1 BZ red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword

Similarly I can't understand  what the terms in

select  spec<atomspec.html>  [ polymer  chain-spec<atomspec.html> ]
might mean.
The learning curve will be very much steeper than that for Chimera.
Please allow me to make a suggestion. It would be useful to have a list with the definition of the terms used in the commands with clear examples. One example is spec another would be ref-spec or  general-options
I couldn't find one if it was there.

These are only a few examples. Such terms are not defined anywhere. The persons most familiar with them are the persons who have written the programs, and those who have used the programs extensively.
Some things like ( cartoon | ribbon )  atom-spec<atomspec.html>  [ smooth  factor | default ] [ suppressBackboneDisplay  true | false ] appear to be well explained but again atom-spec is not defined nor an example given at least  none that I could find.

Kindly consider my comments as questions and friendly suggestions.

I downloaded Pymol the other day, and couldn't get to first base. Would have to take a course on how to use it. I removed it from my computer. I don't have the time to learn even the basics about Pymol, and there are no clear explanations anywhere. I assume students  learn from their colleagues who have spent considerable time learning the nuances of the program.

I have a similar view  of Photoshop - huge learning curve.

Maybe an interactive course on YouTube video might be useful for ChimeraX

Regards
And thanks.

AGS



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