Re: [PyMOL] Set values for dihedral angles

2012-01-27 Thread James Starlight
Also I've tried to test set_dihedral command but failed

:)

E.g I want to change PHI value ( the angle beetween H-N and C-alpha-C-beta
in the residue)

I've type

set_dihedral resi 40 and name H, resi 40 and name N, resi 40 and  name
CA, resi 40 and name CB, -30

and obtain error

Selection 1 doesn't contain a single atom/vertex.

I suppose this error might be due to incorect definition of H atom in the
first selection. By the way how I could define PHI in case if my structure
lack for hydrogens at all ?

James

2012/1/27 James Starlight jmsstarli...@gmail.com

 Dear Thomas, Jed!

 Firstly, thanks for the advise in further days I'll try Modeller software!

 But also I've tried to use above advises in PyMol and in general I was
 satisfy with the results.

 I have just only several questions


 1- What exactly is the Sculpping ? As I've understood its something like
 real-time minimisation of the edited structure. Is what cases this might be
 better than rigid rotation\edition of the selected bonds/ angles by
 mouse-mode editing ? :)

 2- I'm looking for the possible way to set the values for psi and phi
 dihedral-angles.

 As I understood the commands like torsion or set dihedrals need in the
 definition of the edited angles. Is there more trivial way to set values
 for the pre-defined backbone dihedrals like

 set phi value, sele, 120

 ?
 :)

 Something like this I can do via DynoPlot plugin where I can move point on
 the graph wich correspond to the pair of psi-phy angles but I need in more
 accuracy way to define the exactly values of this dihedrals.


 Thanks again,


 James


 2012/1/26 Jed Goldstone jedg...@gmail.com

 James-

 I think you need to seriously consider using software that's actually
 designed to compute and refine protein models, such as Modeller. There
 are forcefield and structural constraints that PyMol is just not
 designed to do, and your results may not have the scientific validity
 you require.

 Jed

 Thomas Holder wrote:
  Hi James,
 
  the modeling capabilities of PyMOL are rather limited, there are
  probably more powerful tools for such tasks.
 
  Without guaranty that the result will be reasonable, try this:
 
  # lock all but the STG tripeptide
  protect not pepseq STG
 
  # activate sculpting
  sculpt_activate all
  set sculpting
 
  # switch to edit mode
  edit_mode
 
  Now drag atoms with the mouse or pick bonds and use commands like
 torsion.
 
  Hope that helps.
 
  Cheers,
 Thomas
 
  James Starlight wrote, On 01/26/12 13:45:
  Dear PyMol users!
 
  I'm looking for the possible way to change some backbone didedral
 values
  in my peptide and dont perturbe the secondary structure of the rest of
  the peptide.
 
  E.g I have alpha-helix with sequence   x-S-T-G-xI want to
  make turn motif in the STG tripeptide only by  changing dihedral of
 this
  amino acids. When I've tried make it by means of DYNOPLOT plugin the
  rest of the alpha helix was distorded.
 
  Is there any possible ways to make this conversion ?
 
  James
 


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Re: [PyMOL] Set values for dihedral angles

2012-01-27 Thread Thomas Holder

1- What exactly is the Sculpping ? As I've understood its something like
real-time minimisation of the edited structure. Is what cases this might
be better than rigid rotation\edition of the selected bonds/ angles by
mouse-mode editing ? :)


It's a geometry optimizer. It has bond/angle/torsion/vdw terms as far as 
I can judge from the various sculpt_* settings and the Build  
Sculpting menu.


http://www.pymolwiki.org/index.php/Molecular_Sculpting

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09358.html


2- I'm looking for the possible way to set the values for psi and phi
dihedral-angles.

As I understood the commands like torsion or set dihedrals need in the
definition of the edited angles. Is there more trivial way to set values
for the pre-defined backbone dihedrals like

set phi value, sele, 120


see attachment. It's the function from DynoPlot, modified to work with 
selections.


Note that you can quickly query phi/psi angles with phi_psi command.

Cheers,
  Thomas

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen


set_phipsi.py
Description: application/chimera
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Re: [PyMOL] Set values for dihedral angles

2012-01-26 Thread Thomas Holder
Hi James,

the modeling capabilities of PyMOL are rather limited, there are 
probably more powerful tools for such tasks.

Without guaranty that the result will be reasonable, try this:

# lock all but the STG tripeptide
protect not pepseq STG

# activate sculpting
sculpt_activate all
set sculpting

# switch to edit mode
edit_mode

Now drag atoms with the mouse or pick bonds and use commands like torsion.

Hope that helps.

Cheers,
   Thomas

James Starlight wrote, On 01/26/12 13:45:
 Dear PyMol users!
 
 I'm looking for the possible way to change some backbone didedral values 
 in my peptide and dont perturbe the secondary structure of the rest of 
 the peptide.
 
 E.g I have alpha-helix with sequence   x-S-T-G-xI want to 
 make turn motif in the STG tripeptide only by  changing dihedral of this 
 amino acids. When I've tried make it by means of DYNOPLOT plugin the 
 rest of the alpha helix was distorded.
 
 Is there any possible ways to make this conversion ?
 
 James

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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Re: [PyMOL] Set values for dihedral angles

2012-01-26 Thread Jed Goldstone
James-

I think you need to seriously consider using software that's actually 
designed to compute and refine protein models, such as Modeller. There 
are forcefield and structural constraints that PyMol is just not 
designed to do, and your results may not have the scientific validity 
you require.

Jed

Thomas Holder wrote:
 Hi James,
 
 the modeling capabilities of PyMOL are rather limited, there are 
 probably more powerful tools for such tasks.
 
 Without guaranty that the result will be reasonable, try this:
 
 # lock all but the STG tripeptide
 protect not pepseq STG
 
 # activate sculpting
 sculpt_activate all
 set sculpting
 
 # switch to edit mode
 edit_mode
 
 Now drag atoms with the mouse or pick bonds and use commands like torsion.
 
 Hope that helps.
 
 Cheers,
Thomas
 
 James Starlight wrote, On 01/26/12 13:45:
 Dear PyMol users!

 I'm looking for the possible way to change some backbone didedral values 
 in my peptide and dont perturbe the secondary structure of the rest of 
 the peptide.

 E.g I have alpha-helix with sequence   x-S-T-G-xI want to 
 make turn motif in the STG tripeptide only by  changing dihedral of this 
 amino acids. When I've tried make it by means of DYNOPLOT plugin the 
 rest of the alpha helix was distorded.

 Is there any possible ways to make this conversion ?

 James
 

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Re: [PyMOL] Set values for dihedral angles

2012-01-26 Thread James Starlight
Dear Thomas, Jed!

Firstly, thanks for the advise in further days I'll try Modeller software!

But also I've tried to use above advises in PyMol and in general I was
satisfy with the results.

I have just only several questions


1- What exactly is the Sculpping ? As I've understood its something like
real-time minimisation of the edited structure. Is what cases this might be
better than rigid rotation\edition of the selected bonds/ angles by
mouse-mode editing ? :)

2- I'm looking for the possible way to set the values for psi and phi
dihedral-angles.

As I understood the commands like torsion or set dihedrals need in the
definition of the edited angles. Is there more trivial way to set values
for the pre-defined backbone dihedrals like

set phi value, sele, 120

?
:)

Something like this I can do via DynoPlot plugin where I can move point on
the graph wich correspond to the pair of psi-phy angles but I need in more
accuracy way to define the exactly values of this dihedrals.


Thanks again,


James

2012/1/26 Jed Goldstone jedg...@gmail.com

 James-

 I think you need to seriously consider using software that's actually
 designed to compute and refine protein models, such as Modeller. There
 are forcefield and structural constraints that PyMol is just not
 designed to do, and your results may not have the scientific validity
 you require.

 Jed

 Thomas Holder wrote:
  Hi James,
 
  the modeling capabilities of PyMOL are rather limited, there are
  probably more powerful tools for such tasks.
 
  Without guaranty that the result will be reasonable, try this:
 
  # lock all but the STG tripeptide
  protect not pepseq STG
 
  # activate sculpting
  sculpt_activate all
  set sculpting
 
  # switch to edit mode
  edit_mode
 
  Now drag atoms with the mouse or pick bonds and use commands like
 torsion.
 
  Hope that helps.
 
  Cheers,
 Thomas
 
  James Starlight wrote, On 01/26/12 13:45:
  Dear PyMol users!
 
  I'm looking for the possible way to change some backbone didedral values
  in my peptide and dont perturbe the secondary structure of the rest of
  the peptide.
 
  E.g I have alpha-helix with sequence   x-S-T-G-xI want to
  make turn motif in the STG tripeptide only by  changing dihedral of this
  amino acids. When I've tried make it by means of DYNOPLOT plugin the
  rest of the alpha helix was distorded.
 
  Is there any possible ways to make this conversion ?
 
  James
 


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