pymol-users

[PyMOL] Add fragment

[Benjamin B. <bg...@nc...>]

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
____________________________________________

Re: [PyMOL] Add fragment

[Sampson, J. <Jar...@ny...>]

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 <bg...@nc...<mailto:bg...@nc...>> 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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Re: [PyMOL] Add fragment

[Benjamin B. <bg...@nc...>]

Jared -

Many thanks for the quick reply. I think you and I found the same thing at
the same time.

I noticed in the keyboard.py file that there was a "get_ctsh" section.
Which I assumed (and it is) equivalent to "Ctrl-Shift".

Also under the "get_ctsh" section there was no definition for
"Ctrl-Shift-M":
        'm' : [ editor.attach_amino_acid, ("pk1","methane"), {}],

So I added it and it works.

Now you can type on the command line.

for aa in "M": cmd._ctsh(string.lower(aa))

and get a methane molecule.

Thanks for the help and guidance.

Ben



On Wed, May 20, 2015 at 12:49 PM, Sampson, Jared <Jar...@ny...>
wrote:

>  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 <bg...@nc...> 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
> ____________________________________________
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
>
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y_______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>


-- 
____________________________________________
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
____________________________________________

[PyMOL] Bug report: cmd.fab() with existing object name produces unexpected results and downstream segfault

[Sampson, J. <Jar...@ny...>]

In the process of investigating Ben Bobay's question<https://sourceforge.net/p/pymol/mailman/message/34128680/> about keyboard shortcuts for adding a methyl group, I may have found a bug, or at least unexpected behavior, in cmd.fab().

When first creating a peptide, it works fine:

    fab AAAA, pep

However, if I call it again with a different (or the same) sequence,

    fab DDDD, pep

The new residues are overlaid right on top of the initial ones, and interspersed in the sequence order (overlapping sticks, Screenshot1<https://www.dropbox.com/s/e6hmr0vb8jlfq6q/Screenshot%202015-05-20%2013.00.36.png?dl=0>).  This breaks cartoon representation, as Ala1 and Ala2 are no longer contiguous in the sequence (`as cartoon` leaves nothing drawn, Screenshot2<https://www.dropbox.com/s/p85bsftrgi54pq3/Screenshot%202015-05-20%2013.00.49.png?dl=0>).

Also, something happens when switching representations (e.g. from cartoon to sticks) that segfaults with certain sequences.  I can semi-reproducibly produce a segfault (perhaps 2/3 of the time) with the following commands in Open Source PyMOL (1.7.4.0), PyMOLX11Hybrid (1.7.6.0), and MacPyMOL (1.7.6.0).

    reinitialize
    fab AAAA, pep
    fab ADAA, pep
    as cartoon
    as sticks
    # sometimes it takes an extra line or two
    #fab AADA, pep
    #as sticks

I believe this happens specifically when some residues are the same and some are different: I haven't been able to produce a segfault using "DDDD" as the second sequence, but adding the third sequence (second to last line) reintroduces the segfault.

I would expect calling `fab` with an existing object name to perform one of the following actions (from most to least preferable):

1. Append the residues to the C-terminus of the existing object with sensible geometry, similar to `editor.attach_fragment()`.
2. Add a new state to the object with the new sequence, as with `cmd.load(state=0)`.
3. Overwrite the existing object (probably not a good idea).

It may also be helpful to have additional arguments to fab, such as append=1 or state=0, depending on which of the above options might be implemented.

I'm adding this as a bug report on SourceForge as well.

Cheers,
Jared