[Chimera-users] drawing shapes

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 25 11:10:14 PDT 2015

Hi Bala,
After websearch and looking at


… maybe you could get the pseudoatoms (fake atoms) from opening a HOLE output .sph file as a PDB file?   You said you opened the channel as #0, but I couldn’t tell if that meant some output from HOLE or just the PDB structure of the original molecule. Also, “didn’t work” is not a helpful description. However, I wouldn’t recommend making a tube anyway, since the tube only has one radius, whereas HOLE will allow the radius to vary throughout a channel.  Further, as mentioned in the manual, the “center” option does not apply to “shape tube” (because the coordinates are already specified by the pre-existing atoms). 


> On Jun 25, 2015, at 10:23 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Bala,
> The “shape tube” command draws a wavy tube that connects a series of already existing atoms one after the other.  This doesn’t sound like what you wanted. Your specification of #0 would mean all pre-existing atoms in #0.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#tube>
> Here are the ways I can think of to get capsule shapes in Chimera:
> (1) For each capsule, two sphere objects with one cylinder object connecting them.  These could be created with the “shape sphere” and “shape cylinder” commands or the simple BILD format input.  In my opinion, it is difficult to specify cylinder orientation with the “shape” command.  However, BILD has the disadvantage of making a VRML model (whereas shape makes a surface model) that does not allow color changes after creation or work well with transparency.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>
> (2) For each capsule, two atoms with one bond connecting them (fake atoms/bonds or equivalently, markers/links).  These could be created with PDB format input with appropriate CONECT information, but you’d still have to set the display radii of the atoms and bond for each capsule, e.g. with “setattr” commands.  Thus it would probably be easier to create them with “marker file” format, since it includes marker and link radii.  This is a fairly simple XML-based format, just plain text (filename *.cmm), described in the Volume Tracer manpage:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> I don’t understand the HOLE output coordinates specification, thus don’t know how to convert it to atoms/bonds input or cylinders/spheres-creating instructions for Chimera.  I can see that cap-len is the bond or cylinder length and cap-rad is the atom/bond or sphere/cylinder radius, but I’m not sure about the other stuff. Will let you know if I come up with anything, but the information above may enable you make progress on your own.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jun 25, 2015, at 6:28 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:
>> Friends,
>> I have used HOLE program (http://www.sciencedirect.com/science/article/pii/S026378559700009X) to find the pore radius of a channel as a function of z-axis. As output, the program gives the location of capsules (that were filled inside the channel), capsule length and radius etc, as a function of z-axis.
>> Capsule graph option*****
>> Data:
>> cenxyz.cvec     eff.rad        area     CAP.LEN     cap.rad angle.X-axi cen.line.di integ.s/(ar point sourc
>>  -14.00000     2.23465    15.68804     1.72142     1.39301    73.21487     0.00000     0.03187  (sampled)
>>  -14.50000     2.40709    18.20262     1.96609     1.46141    58.41143    -0.54015     0.05934  (sampled)
>>  -15.00000     2.51292    19.83844     1.37866     1.78410    73.19154    -1.11224     0.08454  (sampled)
>>  -15.50000     2.69525    22.82171     1.34834     1.97026    87.40431    -1.71545     0.10645  (sampled)
>> I was wondering if i can use the shape command to draw the capsules in Chimera. I thought to create 'tube' with 'shape' command but i was not lucky. For instance, the following command didnt work (i opened channel as model #0)
>> shape tube #0 radius 2.23 bandLength 1.72 center  0, 0, -14.00 
>> Pls help to know some way to do this.
>> Thanks,
>> Bala

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