[chimerax-users] Re: Visualisation of distances

Both of your commands are wrong. 2dlabel does not apply to some existing model, it just makes a new label. You should look at the examples. For example: 2dlabel text test size 50 ... makes a big label in the middle of the screen that says "test" Your "label" command uses 200 which would be 200 Angstroms high, probably much too large. But it is also wrong because it has #2.1 in it, which is not an atom-spec, since it was already a label model (not atoms). If your labels are already there, you don't need to put a model number, just use label height 5 As the help says, it will change the labels that are already there. There is no option with "label" to only change one of the labels. However, with "2dlabels" you can make each new label a different size. Elaine

On Mar 21, 2024, at 8:55 AM, Enrico Martinez wrote:

Hello Elaine and thank you for these tips !

Indeed, I have already tried it but it still does not work.

So, as I've explained before I could draw several distances using the Distance command. It produced two new objects #2 with distances and #2.1 with labels (which are the measured distances written in a very small size). The both objects are visible in the ChimeraX gui.

Then i tried both commands that produced nothing ..

2dlab #2.1 text "test" size 50 label #2.1 height 200 text "test"

Anyway, how to modify the legend of a specific distance? (there is #2 for all of them ..)

Yours sincerely,

Enrico

Il giorno gio 21 mar 2024 alle ore 16:08 Elaine Meng ha scritto: You would use the "label" option "height" (not "size") to make the labels bigger. Since our website is down at the moment, instead view your own copy of the manual by using command "help label" to see the explanations of these two options.

For legends, titles, etc. in paper figures or a movie, it is probably better to use 2D labels instead of the 3D labels that move with the structure. Use command "help 2dlabels" to see the manual page for the "2dlabels" command, which includes examples of how to use it.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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On Mar 21, 2024, at 2:50 AM, Enrico Martinez wrote:

Thank you very much Elaine !

Actually this command works very well, and I just have a question about the labelling of the distances (I have not found it in the manual !!)

for example I could draw to distances using distance :1@CA :19@CA color orangered dashes 10 radius 0.2 decimalPlaces 1 distance :2@CA :116@CA color darkgreen dashes 7 radius 0.2 decimalPlaces 1

visually it looks very well and it automatically labels for all distances as the object #2.1, which I suppose corresponds to the measured length. I tried to increase the size of these labels e.g. using label #2.1 size 20 but it didn't work

Would it be possible additionally to add some label-legend manually to each distance during its creation e.g. "TheNtoCdistance" etc ?

Many thanks in advance !

Enrico

Il giorno lun 18 mar 2024 alle ore 19:08 Elaine Meng ha scritto: The whole website was down. It is back up now, try again. Yes, you would use the "distance" command.

command: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/distance.html

Distances tool: https://www.cgl.ucsf.edu/chimerax/docs/user/tools/distances.html

If you use the Distances tool it will show the commands that it uses in the Log. Most GUI actions are shown as commands in the Log so that you can see examples of the commands even if you don't look at the help pages. However, you should look at the help pages because they are written so that we don't have to repeat the same information all the time in email.

Elaine

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On Mar 18, 2024, at 1:25 AM, Enrico Martinez via ChimeraX-users wrote:

Sorry it seems that I composed my message incorrectly !

Actually I was able to draw distances manually using chimera-x GUI buy just need to understand whether it would be possible to script adding the chain of the commands directly to my visualisation script.

P.S. at the present moment the help page https://www.cgl.ucsf.edu/chimerax/docs/user/tools/distances.html

does not work at all !

Yours with thanks

Enrico

Il giorno dom 17 mar 2024 alle ore 23:40 Greg Couch ha scritto: I'd say "https://letmegooglethat.com/?q=chimerax+distance" but the resulting links don't work for me. But using google.com directly does. The top two links are ChimeraX's distance command and the Distances tool. So https://www.cgl.ucsf.edu/chimerax/docs/user/commands/distance.html and https://www.cgl.ucsf.edu/chimerax/docs/user/tools/distances.html. Using the Distances tool might be the easiest way to start. If you click on Create, it tells you to select two atoms. So do that and then click on Create. You will see the corresponding distance command, that you could type in, shown in the Log. The documentation gives several other ways to show distances. I recommend learning to read the documentation :-). An aside, you can toggle whether the links in the Log take you to the documentation for the command or repeat the command, by right-mouse clicking on the Log and selecting Executable Command LInks.

HTH,

Greg

On 3/17/2024 2:57 PM, Enrico Martinez via ChimeraX-users wrote:

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Dear ChimeraX users !

I need to draw several distance vectors on the 3D structure. Could you provide me with an example of the commands that could automatically draw the distances between two selected atoms with some basic labels on it ?

Many thanks in advance

Enrico