Re: [PyMOL] Slice

2018-08-17 Thread Divya Kaur Matta 
Dear Thomas,

It’s phimap.cube file. ( .cube is an extension). These cube files are from 
Delphi. ( Poisson Boltzmann solver).

Thank you ,

Best Regards
Divya

Get Outlook for iOS

From: Thomas Holder 
Sent: Friday, August 17, 2018 4:51 AM
To: Divya Kaur Matta
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Slice

Hi Divya,

I can confirm that slices don't work properly with some map formats (those 
which define a transformation matrix).

What's the file format (file extension) of your map?

Cheers,
Thomas

> On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta  
> wrote:
>
> Dear all,
>
>
> I would like to use the "Isomesh" and "Slice" command for the protein I am 
> working on to get the electrostatic potential map of that protein. For that , 
> it requires map. I have got Delphi map for that. When I use the commands 
> below, I got the mesh that aligns with the atoms of the pdb, however for 
> slice, it is not aligned with the atoms. I would like to have a slice plane 
> for my protein.
>
>
> For isomesh,
>
> isomesh map_n20, phimap, -20.0 ; color red, map_n20
>
> isomesh map_p20, phimap, 20.0 ; color blue, map_p20
>
> For slice,
>
> I did actions, show slice(default)
>
> Please find attached images for the slice I got.
>
>
> Thank you!
>
> Best Regards,
>
> Divya K. Matta
> Ph.D. Student in Chemistry

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Slice

2018-08-17 Thread Divya Kaur Matta 
Dear Thomas ,

Thank you so much for your suggestion. I will try this.

I appreciate your help.

Best Regards
Divya

Get Outlook for iOS

From: Thomas Holder 
Sent: Friday, August 17, 2018 11:05 AM
To: Divya Kaur Matta
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Slice

Hi Divya,

Try to output a .phi file with delphi, that format should work fine with slices.

In your delphi .param file:
out(phi,file=phimap.phi,format=0)

Cheers,
Thomas

> On Aug 17, 2018, at 4:28 PM, Divya Kaur Matta  
> wrote:
>
> Dear Thomas,
>
> It’s phimap.cube file. ( .cube is an extension). These cube files are from 
> Delphi. ( Poisson Boltzmann solver).
>
> Thank you ,
>
> Best Regards
> Divya
>
> Get Outlook for iOS
> From: Thomas Holder 
> Sent: Friday, August 17, 2018 4:51 AM
> To: Divya Kaur Matta
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Slice
>
> Hi Divya,
>
> I can confirm that slices don't work properly with some map formats (those 
> which define a transformation matrix).
>
> What's the file format (file extension) of your map?
>
> Cheers,
> Thomas
>
> > On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta  
> > wrote:
> >
> > Dear all,
> >
> >
> > I would like to use the "Isomesh" and "Slice" command for the protein I am 
> > working on to get the electrostatic potential map of that protein. For that 
> > , it requires map. I have got Delphi map for that. When I use the commands 
> > below, I got the mesh that aligns with the atoms of the pdb, however for 
> > slice, it is not aligned with the atoms. I would like to have a slice plane 
> > for my protein.
> >
> >
> > For isomesh,
> >
> > isomesh map_n20, phimap, -20.0 ; color red, map_n20
> >
> > isomesh map_p20, phimap, 20.0 ; color blue, map_p20
> >
> > For slice,
> >
> > I did actions, show slice(default)
> >
> > Please find attached images for the slice I got.
> >
> >
> > Thank you!
> >
> > Best Regards,
> >
> > Divya K. Matta
> > Ph.D. Student in Chemistry

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Slice

2018-08-17 Thread Thomas Holder 
Hi Divya,

Try to output a .phi file with delphi, that format should work fine with slices.

In your delphi .param file:
out(phi,file=phimap.phi,format=0)

Cheers,
  Thomas

> On Aug 17, 2018, at 4:28 PM, Divya Kaur Matta  
> wrote:
> 
> Dear Thomas,
> 
> It’s phimap.cube file. ( .cube is an extension). These cube files are from 
> Delphi. ( Poisson Boltzmann solver). 
> 
> Thank you ,
> 
> Best Regards
> Divya
> 
> Get Outlook for iOS
> From: Thomas Holder 
> Sent: Friday, August 17, 2018 4:51 AM
> To: Divya Kaur Matta
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Slice
>  
> Hi Divya,
> 
> I can confirm that slices don't work properly with some map formats (those 
> which define a transformation matrix).
> 
> What's the file format (file extension) of your map?
> 
> Cheers,
> Thomas
> 
> > On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta  
> > wrote:
> > 
> > Dear all,
> > 
> > 
> > I would like to use the "Isomesh" and "Slice" command for the protein I am 
> > working on to get the electrostatic potential map of that protein. For that 
> > , it requires map. I have got Delphi map for that. When I use the commands 
> > below, I got the mesh that aligns with the atoms of the pdb, however for 
> > slice, it is not aligned with the atoms. I would like to have a slice plane 
> > for my protein.
> > 
> > 
> > For isomesh, 
> > 
> > isomesh map_n20, phimap, -20.0 ; color red, map_n20
> > 
> > isomesh map_p20, phimap, 20.0 ; color blue, map_p20
> > 
> > For slice,
> > 
> > I did actions, show slice(default) 
> > 
> > Please find attached images for the slice I got.
> > 
> > 
> > Thank you!
> > 
> > Best Regards,
> > 
> > Divya K. Matta
> > Ph.D. Student in Chemistry

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Serine phosphorylation

2018-08-17 Thread Thomas Holder 
Hi Wei,

Phosphorylating a serine with the builder works fine for me.

1) click "Builder" button -> opens panel and should automatically switch to 
"3-Button Editing" mouse mode
2) click on the serine's OG atom -> should create "pk1" selection
3) click "P=O3" button on the Builder panel

To change the orientation of the phosphate group, make sure you're in "3-Button 
Editing" mouse mode, then
1) double click the CB-OG bond with the *right* mouse button -> shows dihedral 
indicator
2) CTRL-drag any of the phosphate group atoms with the left mouse button

Cheers,
  Thomas

> On Jul 31, 2018, at 6:42 PM, Wei Song  wrote:
> 
> Hi all, 
> 
> I have a peptide structure and would like to phosphorylate one of the serine 
> residues to test its binding capacity to a ligand. I tried the Build function 
> with a PyMol 2.0, but only a phosphorous can be added to the serine. Does 
> anyone have experiences of creating a phosphorylated residue with PyMol or 
> other tools? 
> Any suggestions would be appreciated. 
> 
> Thanks,
> Wei 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Slice

2018-08-17 Thread Thomas Holder 
Hi Divya,

I can confirm that slices don't work properly with some map formats (those 
which define a transformation matrix).

What's the file format (file extension) of your map?

Cheers,
  Thomas

> On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta  
> wrote:
> 
> Dear all,
> 
> 
> I would like to use the "Isomesh" and "Slice" command for the protein I am 
> working on to get the electrostatic potential map of that protein. For that , 
> it requires map. I have got Delphi map for that. When I use the commands 
> below, I got the mesh that aligns with the atoms of the pdb, however for 
> slice, it is not aligned with the atoms. I would like to have a slice plane 
> for my protein.
> 
> 
> For isomesh, 
> 
> isomesh map_n20, phimap, -20.0 ; color red, map_n20
> 
> isomesh map_p20, phimap, 20.0 ; color blue, map_p20
> 
> For slice,
> 
> I did actions, show slice(default) 
> 
> Please find attached images for the slice I got.
> 
> 
> Thank you!
> 
> Best Regards,
> 
> Divya K. Matta
> Ph.D. Student in Chemistry

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net