[Chimera-users] MD chimera bug

Fabian Glaser fglaser at technion.ac.il
Thu Jan 30 23:42:25 PST 2020

Hi thanks for your answer.

But i actually want to apply the command to all frames in order to see the neighbors through the simulation, to build also a movie. How should i do that?

In any case i solved it by using an external alias in the command line


On Jan 30, 2020 21:13, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
Hi Fabian,
By typing ‘1’ into the entry field of ’Substitute text [1] with frame number’, any ‘1’ in your script will be replaced by the frame number, so by frame 96 the text ’sel :1000 zr<5’ becomes ’sel :96000 zr<5’.  I’m guessing you want your command executed only on frame 1.  To do that, as it says just above the ’Script’ area, prepend the command with ‘#:’, e.g.:


Also, you will need to change that entry field back to something that isn’t found in your script, e.g. “<FRAME>”.


Eric Pettersen
UCSF Computer Graphics Lab

On Jan 29, 2020, at 4:21 AM, Fabian Glaser <fglaser at technion.ac.il<mailto:fglaser at technion.ac.il>> wrote:

Dear Chimera developers,

I think I have found abug in the  MD movies tool in Chimera, when trying to use the Per-Frame command Script: When selecting residues > :1000 (which have a residue number > 1000) it does not select the the residue, since it adds to the residue number the frame number, for example see the figure attached, with this logic, and trying to apply the script, if the I try to select residue :1000 the script gives a mistake and this is because it tries to select residue frame + residue number (in this case 96000) which of course does not exist. The same sequence works perfectly if the selection is done outside the script



<Screenshot 2020-01-29 14.17.26.png>



Fabian Glaser PhD

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
Tel +972 (0) 4 8293701

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