Hi Ben -
Try this:
editor.attach_fragment("pk1", "methane", 1, 0)
Here's how I tracked this down, not having known about this function before
your email. cmd._alt() and likewise cmd._ctrl() are functions (you can see for
yourself in the source code in pymol/modules/pymol/cmd.py), and they are
basically wrappers (via internal.py and back through cmd.py again) for
functions in keyboard.py called keyboard.get_alt() and keyboard.get_ctrl(),
which each return a dictionary list of commands to run for each shortcut key.
For example:
def get_alt(self_cmd=cmd):
return {
'1' : [ editor.attach_fragment , ("pk1","formamide",5,0), {}],
'2' : [ editor.attach_fragment , ("pk1","formamide",4,0), {}],
'3' : [ editor.attach_fragment , ("pk1","sulfone",3,1), {}],
'4' : [ editor.attach_fragment , ("pk1","cyclobutane",4,0), {}],
'5' : [ editor.attach_fragment , ("pk1","cyclopentane",5,0), {}],
'6' : [ editor.attach_fragment , ("pk1","cyclohexane",7,0), {}],
'7' : [ editor.attach_fragment , ("pk1","cycloheptane",8,0), {}],
'8' : [ editor.attach_fragment , ("pk1","cyclopentadiene",5,0), {}],
'9' : [ editor.attach_fragment , ("pk1","benzene",6,0), {}],
'0' : [ editor.attach_fragment , ("pk1","formaldehyde",2,0), {}],
'a' : [ editor.attach_amino_acid, ("pk1","ala"), {}],
'b' : [ editor.attach_amino_acid, ("pk1","ace"), {}],
'c' : [ editor.attach_amino_acid, ("pk1","cys"), {}],
'd' : [ editor.attach_amino_acid, ("pk1","asp"), {}],
'e' : [ editor.attach_amino_acid, ("pk1","glu"), {}],
'f' : [ editor.attach_amino_acid, ("pk1","phe"), {}],
...etc
}
So to add a methyl group, just model it after the cyclobutane example, and just
run the editor.attach_fragment command (which you can explore in
pymol/modules/pymol/editor.py) for methane. A little more info from the
editor.attach_fragment() docstring:
def attach_fragment(selection,fragment,hydrogen,anchor,_self=cmd):
'''
ARGUMENTS
selection = str: must be "pk1"
fragment = str: fragment name to load from fragment library
hydrogen = int: hydrogen atom ID in fragment to fuse
anchor = int: none-hydrogen atom ID in fragment to fuse
'''
You can also define custom
fragments<http://www.pymolwiki.org/index.php?title=Modeling_and_Editing_Structures#Adding_and_using_your_own_fragments>.
Also, in case you didn't know about it, an easier way to create your peptide
might be the `fab` function (so long as you don't need to continue editing it
afterward):
fab GTHYRD, my_peptide
Hope that helps!
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On May 20, 2015, at 8:43 AM, Benjamin Bobay
<[email protected]<mailto:[email protected]>> wrote:
H
i All,
I was wondering if someone could point me to the correct notation for something.
When making a peptide from the command line one could type:
for aa in "GTHYRD":cmd._alt(string.lower(aa))
Let's say that I want to add a methane. The key code is CTRL+SHIFT+M
I was wondering how to alter the "cmd.
_
alt" to be CTRL-SHIFT.
I've tried
"cmd._ctrl+_shift"
"cmd._ctrl and _shift"
"cmd.(_ctrl and _shift)"
"cmd._ctrl._shift"
Nothing has worked. I searched the list serve but came up empty on how to
combine two keys to the "cmd'.
Any help would be greatly appreciated!
Thanks
Ben
--
____________________________________________
Research Assistant Professor
North Carolina State University
Department of Molecular and Structural Biochemistry
128 Polk Hall
Campus Box 7622
Raleigh, NC 27695
Phone: (919)-513-0698
Fax: (919)-515-2047
http://biochem.ncsu.edu/
http://biochem.ncsu.edu/faculty/bobay/bobaypage.php
http://biochem.ncsu.edu/faculty/bobay/index.php
http://biochem.ncsu.edu/NMR
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