Hi, with the help of "split #0" I created 10 segments of my protein and calculated the surface of each fragment. I can go to tools and measure volume and area but I'd prefer to write out the results as a file. Can Chimera do this ? I am asking because I intend to do more complex things than just 10 surfaces and it would be rather tedious if not impossible to do all this by hand. Thanks for any advice. Lothar
Hi Lothar, You can use a script with commands and then save the results from the Reply Log. More details... As soon as you calculate and show molecular surfaces, for example with the “surface” command, the analytical surface areas are reported in the Reply Log (open from Favorites menu). Similarly, if you use “measure area” and “measure volume” commands, the values will be in the Reply Log. The surface areas from “measure area” will be a little different than from the “surface” command, because the former just sums up the flat surface triangle areas rather than figuring out the analytical (curved) surface area like the latter. If you had used “split”, the surfaces would be in separate submodels but with the same main model number, e.g. #0.1, #0.2, etc., but you could just measure them en masse, e.g. command measure volume #0 They would still be listed separately in the Reply Log. Now, to loop through multiple structures, you may want to embed the Chimera commands in a Python script instead of just making a Chimera command script. How to do that is outlined here: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Saving the Reply Log contents to file: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-September/000924.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-July/005367.html> 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 Sep 28, 2016, at 9:09 AM, esserlo@helix.nih.gov wrote:
Hi,
with the help of "split #0" I created 10 segments of my protein and calculated the surface of each fragment. I can go to tools and measure volume and area but I'd prefer to write out the results as a file. Can Chimera do this ? I am asking because I intend to do more complex things than just 10 surfaces and it would be rather tedious if not impossible to do all this by hand.
Thanks for any advice.
Lothar
On Sep 28, 2016, at 9:28 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Saving the Reply Log contents to file: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-September/000924.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-September/000924.html>> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-July/005367.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-July/005367.html>>
Saving the Reply Log is actually a little simpler now than it was when those messages were written: from chimera.tkgui import saveReplyLog saveReplyLog(“file name”) Note that “file name” should be a full path to a file unless you know what folder the script is executing in. Also, you can use an initial “~” character to indicate your home folder, so e.g. “~/Desktop/reply_log.txt”. —Eric Eric Pettersen UCSF Computer Graphics Lab
Hi Elaine,
Hi Lothar, You can use a script with commands and then save the results from the Reply Log.
More details... As soon as you calculate and show molecular surfaces, for example with the âsurfaceâ command, the analytical surface areas are reported in the Reply Log (open from Favorites menu). Similarly, if you use âmeasure areaâ and âmeasure volumeâ commands, the values will be in the Reply Log. The surface areas from âmeasure areaâ will be a little different than from the âsurfaceâ command, because the former just sums up the flat surface triangle areas rather than figuring out the analytical (curved) surface area like the latter. If you had used âsplitâ, the surfaces would be in separate submodels but with the same main model number, e.g. #0.1, #0.2, etc., but you could just measure them en masse, e.g. command
measure volume #0
They would still be listed separately in the Reply Log.
This is very helpfu. I did not realize that there is a Reply Log as such.
Now, to loop through multiple structures, you may want to embed the Chimera commands in a Python script instead of just making a Chimera command script. How to do that is outlined here: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
Well, I am very fuzzy with Python - I am more tcl guy. But I think with simple command scripts I can do it followed copy and paste of the log file, I can in the end write a program to sort the log file for the entries and values I need. Thanks! Have a great day. Lothar
Saving the Reply Log contents to file: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-September/000924.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-July/005367.html>
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 Sep 28, 2016, at 9:09 AM, esserlo@helix.nih.gov wrote:
Hi,
with the help of "split #0" I created 10 segments of my protein and calculated the surface of each fragment. I can go to tools and measure volume and area but I'd prefer to write out the results as a file. Can Chimera do this ? I am asking because I intend to do more complex things than just 10 surfaces and it would be rather tedious if not impossible to do all this by hand.
Thanks for any advice.
Lothar
participants (3)
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Elaine Meng -
Eric Pettersen -
esserlo＠helix.nih.gov