Hi Arthur, Nobody is expected to magically know what “spec” “atom-spec” and “general-options” are…. each of those in the help pages is a link (that’s what the blue color and underline mean), and if you clicked the link, it would go to another section of the help that explains it.
“spec” is like Chimera atomspec, where you can give model number, chain, etc. In ChimeraX the chain symbol is “/“ so if you want chain BZ in model #1 your “spec” would be #1/BZ …so your command would be:
color #1/BZ red
You don’t even need the model number part, unless there were other models that also had a BZ chain that you didn’t want to color.
If you clicked the “spec” link you’d see the following, which includes both a general explanation and several examples: http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
Actually lots of things are easier in ChimeraX than in Chimera. For example, if I open 4wpo, it lists all the chains in the Log, and then this table:
In this case, each assembly is just one of the two copies of the ribosome. It is not clear from this table, but I can tell because if I go to the RCSB PDB page for 4wpo, http://www.rcsb.org/pdb/explore/explore.do?structureId=4wpo ... it shows that biological assembly 1 and biological assembly 2 both look like one copy. So if you click either number 1 or 2 (NOT both) and wait a few seconds, it will hide the original model and open a new model #2 that is just one copy. The command that was executed when you clicked the link is shown in the Log, for example:
sym #1 assembly 1
(note the “sym” is underlined which means it is also a link, and clicking it shows the “sym” command help)
Now your model is #2. It seems like all the “B” chains are in assembly 1 and all the “D” chains are in assembly 2, so depending on which number you clicked, your command would be
color #2/BZ red - or - color #2/DZ red
Or since you don’t care if it’s also affecting the invisible #1, it could just be
color /BZ red - or - color /DZ red
There is one trick with sym. If the biological assembly has to add more copies than what is in the original structure (like making a multimer from a monomer) instead of clicking the link in the assemblies table I recommand using the “sym” command directly with the “copies true” option, e.g.
sym #1 assembly 1 copies true
… without copies true it would just make the additional copies as graphical clones that you couldn’t color or show/hide separately. The reason the default doesn’t include copies true is that often with something like a viral capsid, you might get too many atoms for convenient interactive use. So if you’re making something huge like that, don’t use “copies true” but realize that the resulting copies can’t be managed independently, they always will loook the same as each other.
I think you will find everything much easier now that you realize that text with blue underlines are links that might show more information, or (in the Log) do something in ChimeraX.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 4, 2017, at 2:14 PM, Arthur Szabo agszabo@outlook.com wrote:
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 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 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 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 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 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 selAtoms ribbons help help:user select 4wpo #1, chain BZ Expected an objects specifier or a keyword help help:contact.html help help:contact.html color #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 [ polymer chain-spec ] 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 [ 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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