Re: [PyMOL] NME and ACE capping from script

[Thomas Holder]

Hi Simon,

My example works for me in PyMOL version 1.8.0 and later. Which version do you 
use?

Thomas

> On Nov 18, 2017, at 3:59 PM, Simon Kit Sang Chu  
> wrote:
> 
> Hi Thomas,
> 
> Thanks for your help! But the NME and ACE are added unattached and randomly 
> in the pdb. I simplified with a dipeptide AA instead. The file is attached 
> here.
> 
> Regards,
> Simon
> 
> 2017-11-18 17:04 GMT+08:00 Thomas Holder :
> Hi Simon,
> 
> I think this is the code you're looking for:
> 
> from pymol import cmd, editor
> cmd.set('retain_order', 0)
> cmd.fab('APAPAPAP')
> editor.attach_amino_acid("last name C", 'nme')
> editor.attach_amino_acid("first name N", 'ace')
> 
> Hope that helps.
> 
> Cheers,
>   Thomas
> 
> > On Nov 17, 2017, at 8:26 AM, Simon Kit Sang Chu  
> > wrote:
> >
> > Hi everyone,
> >
> > I am generating segments of peptide to be used in GROMACS. I might be using 
> > amber which does not allow automatic capping. Therefore, I hope to solve it 
> > with Pymol.
> >
> > Currently, I use a pml scipt to generate the pdb file automatically. The 
> > script is simple.
> >
> > for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
> > cmd.save("peptide.pdb")
> >
> > However, if I want to add NME and ACE caps, is there any residue code 
> > available? Like XAPAPAPAPY where X and Y are NME and ACE? The main point is 
> > to automize the process since I don't want to write NME / ACE manually 
> > everytime.
> >
> > I appreciate any suggestion and comment.
> >
> > Regards,
> > Simon
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] NME and ACE capping from script

[Simon Kit Sang Chu]

Hi Thomas,

Thanks for your help! But the NME and ACE are added unattached and randomly
in the pdb. I simplified with a dipeptide AA instead. The file is attached
here.

Regards,
Simon

2017-11-18 17:04 GMT+08:00 Thomas Holder :

> Hi Simon,
>
> I think this is the code you're looking for:
>
> from pymol import cmd, editor
> cmd.set('retain_order', 0)
> cmd.fab('APAPAPAP')
> editor.attach_amino_acid("last name C", 'nme')
> editor.attach_amino_acid("first name N", 'ace')
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> > On Nov 17, 2017, at 8:26 AM, Simon Kit Sang Chu 
> wrote:
> >
> > Hi everyone,
> >
> > I am generating segments of peptide to be used in GROMACS. I might be
> using amber which does not allow automatic capping. Therefore, I hope to
> solve it with Pymol.
> >
> > Currently, I use a pml scipt to generate the pdb file automatically. The
> script is simple.
> >
> > for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
> > cmd.save("peptide.pdb")
> >
> > However, if I want to add NME and ACE caps, is there any residue code
> available? Like XAPAPAPAPY where X and Y are NME and ACE? The main point is
> to automize the process since I don't want to write NME / ACE manually
> everytime.
> >
> > I appreciate any suggestion and comment.
> >
> > Regards,
> > Simon
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


peptide.pdb
Description: Protein Databank data
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Re: [PyMOL] NME and ACE capping from script

[Thomas Holder]

Hi Simon,

I think this is the code you're looking for:

from pymol import cmd, editor
cmd.set('retain_order', 0)
cmd.fab('APAPAPAP')
editor.attach_amino_acid("last name C", 'nme')
editor.attach_amino_acid("first name N", 'ace')

Hope that helps.

Cheers,
  Thomas

> On Nov 17, 2017, at 8:26 AM, Simon Kit Sang Chu  
> wrote:
> 
> Hi everyone,
> 
> I am generating segments of peptide to be used in GROMACS. I might be using 
> amber which does not allow automatic capping. Therefore, I hope to solve it 
> with Pymol.
> 
> Currently, I use a pml scipt to generate the pdb file automatically. The 
> script is simple. 
> 
> for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
> cmd.save("peptide.pdb")
> 
> However, if I want to add NME and ACE caps, is there any residue code 
> available? Like XAPAPAPAPY where X and Y are NME and ACE? The main point is 
> to automize the process since I don't want to write NME / ACE manually 
> everytime.
> 
> I appreciate any suggestion and comment.
> 
> Regards,
> Simon

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
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[PyMOL] NME and ACE capping from script

[Simon Kit Sang Chu]

Hi everyone,

I am generating segments of peptide to be used in GROMACS. I might be using
amber which does not allow automatic capping. Therefore, I hope to solve it
with Pymol.

Currently, I use a pml scipt to generate the pdb file automatically. The
script is simple.


for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
cmd.save("peptide.pdb")


However, if I want to add NME and ACE caps, is there any residue code
available? Like *X*APAPAPAP*Y* where X and Y are NME and ACE? The main
point is to automize the process since I don't want to write NME / ACE
manually everytime.

I appreciate any suggestion and comment.

Regards,
Simon
--
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