[Chimera-users] Centroid/axis question

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 8 09:48:18 PDT 2019

Hi Luca,
I forgot to mention that for centroids, it’s basically the same as for axes, except you would search for CentroidManager in the session file.  

An additional tricky thing is that the centroids or axes are not in the same order in the session file as they appear in the Axes/Planes/Centroids dialog, and if you have ones with the same names, they are hard to tell apart.  I did some more experiments and it looks like the number before the name is the numerical part of the ID.  For example, I had two axes with the same name “2gbp H9” but their IDs were a9 and a19.  Although I do not see “a9” and “a19” in the session file, I do see the two axes with the same name, and one of them has 9 before the name and the other has 19 before the name.

Thus the integer before the object name may be better than the name for uniquely identifying the object (axis or centroid) in the session file.

> On Oct 8, 2019, at 9:28 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Luca,
> Unfortunately there is no friendly way to do it, but you could try saving the session and then editing the python in the session file (very carefully).
> According to Eric, you would open the session file in a text editor and search for AxisManager, which will be followed by lots of comma-separated values in parentheses.  For each axis there are two numbers, then axis name, then a zero, and then the radius value, and then more numbers for other stuff like color and length.  I guess you can look for the axis name and then the zero, and then edit the next value for each axis.  I tried this and it works, but it is somewhat difficult because there are so many values all on one line in the file. 
> Sorry it is not a friendly approach.  Depending on how you made the axes, it might be easier to script making them again than to manually edit the session.  I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Oct 8, 2019, at 5:25 AM, Luca Pellegrini <lp212 at cam.ac.uk> wrote:
>> Hello,
>> I have generated a bunch of axes and centroids for my protein complex structure. Now I would like to change their appearance by changing their radius, to make them the size I want for a picture. Is there a way to do this for an existing axis/centroid, or do I need to create them again? I have got quite a lot of them…
>> Thanks,
>> Luca

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