Hello there, I'm currently having trouble with the morphing code in chimera and I don't know how to use Python to make the morph.py. Is there any way you can help me with this? Thank you, Minh
Hello MInh, It’s not really intended for use with Python. Is there a reason you can’t use the Chimera Morph Conformations tool or the “morph” command? <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/morph.html> You might also consider trying ChimeraX instead, since the “morph” command is easier to use and has more options than in Chimera. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2018, at 5:16 PM, Minh Le <mhl2468@rit.edu> wrote:
Hello there, I'm currently having trouble with the morphing code in chimera and I don't know how to use Python to make the morph.py. Is there any way you can help me with this? Thank you, Minh
Hi, I have tried using the "morph" command line as follow: morph start #0 frames 60 morph interpolate #1 frames 60 morph movie nogui true coordset #2 41,1 wait 30 coordset #2 1, wait 30 coordset #2 41,1 wait 30 coordset #2 1, wait 30 coordset #2 41,1 wait 30 coordset #2 1, wait 30 but the error box said that I have already define the default? Regards, Minh On Fri, Oct 12, 2018 at 12:21 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello MInh, It’s not really intended for use with Python. Is there a reason you can’t use the Chimera Morph Conformations tool or the “morph” command? <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/morph.html>
You might also consider trying ChimeraX instead, since the “morph” command is easier to use and has more options than in Chimera. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2018, at 5:16 PM, Minh Le <mhl2468@rit.edu> wrote:
Hello there, I'm currently having trouble with the morphing code in chimera and I don't know how to use Python to make the morph.py. Is there any way you can help me with this? Thank you, Minh
Hi MInh, Your commands are fine the first time you use them after starting Chimera to create the morph. The “default already defined” warning is just when you use the morph commands again before quitting from Chimera. It is saying you already set up and created the morph and there is no need to do it again. You could just use the first 3 commands one time (morph start, morph interpolate, morph movie) after starting Chimera and opening your input structures #0 and #1. Then save session. Then restore session and just use the coordset commands to play the morph. There is no need to try to create the morph trajectory #2 multiple times once it has already been created. 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 12, 2018, at 10:22 AM, Minh Le <mhl2468@rit.edu> wrote:
Hi,
I have tried using the "morph" command line as follow:
morph start #0 frames 60 morph interpolate #1 frames 60 morph movie nogui true
coordset #2 41,1 wait 30 coordset #2 1, wait 30 coordset #2 41,1 wait 30 coordset #2 1, wait 30 coordset #2 41,1 wait 30 coordset #2 1, wait 30
but the error box said that I have already define the default?
Regards, Minh On Fri, Oct 12, 2018 at 12:21 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello MInh, It’s not really intended for use with Python. Is there a reason you can’t use the Chimera Morph Conformations tool or the “morph” command? <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/morph.html>
You might also consider trying ChimeraX instead, since the “morph” command is easier to use and has more options than in Chimera. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2018, at 5:16 PM, Minh Le <mhl2468@rit.edu> wrote:
Hello there, I'm currently having trouble with the morphing code in chimera and I don't know how to use Python to make the morph.py. Is there any way you can help me with this? Thank you, Minh
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Elaine Meng -
Minh Le