[Chimera-users] trying to use per-frame pdb 'CONECT' information in movie maker

[Eric Pettersen]

Hi Kersey,
	I assume you mean the MD Movie tool.  AFAIK, PDB format doesn’t support differing connectivity for different members of a multi-MODEL PDB file.  I’m not sure which model Chimera uses the CONECT records from, but it’s either the first or last, and that is then applied to all the models.  The result in MD Movie is one model, with one set of atoms and bonds, with the atoms repositioned every frame.
	If your CONECT records are merely indicating reasonable chemical bonding, there is a hidden feature of MD Movie to force it to recompute the bonds based on reasonable bonding distances every frame.  If you run the attached script after starting MD Movie (simply by opening it with File->Open), it will turn on the recomputation mode.  The recomputation won’t start until you start playing the trajectory, so the initial frame may look wrong until you start playing.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



> On May 4, 2018, at 9:45 AM, Black, Kersey <KBlack at kecksci.claremont.edu> wrote:
> 
> Hi,
> 
> Just recently back to using Chimera after a long time, so a bit rusty on this.
> I am reading in a trajectory of a small hydrocarbon for a single pdb file, and with each fram I include the geometry and the connectivity I want with ‘CONECT’ lines.  But, when I use the Movie Maker tool to read it in, it seems to using one or more frames (perhaps the last one? to detect connectivity to auto detect connectivity and then applying it to all geometries, and this is putting bonds in places where I do not want them.  
> Does movie maker honor CONECT information for each step?
> Is there a way to have it do so?   Or is connectivity set once for the entire trajectory?
> 
> Thanks much for any help on this,
> Kersey
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180504/2811ce8b/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: dynamBonds.py
Type: text/x-python-script
Size: 288 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180504/2811ce8b/attachment.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180504/2811ce8b/attachment-0001.html>