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 Best, Fabian Best, Fabian 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/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701
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.: #1:~disp #1:rib etc. Also, you will need to change that entry field back to something that isn’t found in your script, e.g. “<FRAME>”. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 29, 2020, at 4:21 AM, Fabian Glaser <fglaser@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
Best,
Fabian
<Screenshot 2020-01-29 14.17.26.png>
Best,
Fabian
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/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701
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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 Thanks? On Jan 30, 2020 21:13, Eric Pettersen <pett@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.: #1:~disp #1:rib etc. Also, you will need to change that entry field back to something that isn’t found in your script, e.g. “<FRAME>”. —Eric Eric Pettersen UCSF Computer Graphics Lab On Jan 29, 2020, at 4:21 AM, Fabian Glaser <fglaser@technion.ac.il<mailto:fglaser@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 Best, Fabian <Screenshot 2020-01-29 14.17.26.png> Best, Fabian 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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Cfglaser%40technion.ac.il%7Cbd7960bb8fd54fef0e4608d7a5b88516%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637160084252741437&sdata=UYxzyRshkjlTfwVXEqUl7a46eQESa5%2FNGjcBvGMhLVQ%3D&reserved=0>
Hi Fabian, I guess the answer’s moot now, but you would have done that simply by not prepending “#1:” to the commands (and still ensuring the entry field doesn’t have text that is also found in your script). In that case the commands would be executed every frame. —Eric
On Jan 30, 2020, at 11:42 PM, Fabian Glaser <fglaser@technion.ac.il> wrote:
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
Thanks?
On Jan 30, 2020 21:13, Eric Pettersen <pett@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.:
#1:~disp #1:rib etc.
Also, you will need to change that entry field back to something that isn’t found in your script, e.g. “<FRAME>”.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 29, 2020, at 4:21 AM, Fabian Glaser <fglaser@technion.ac.il <mailto:fglaser@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
Best,
Fabian
<Screenshot 2020-01-29 14.17.26.png>
Best,
Fabian
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/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701
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participants (2)
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Eric Pettersen -
Fabian Glaser