Re: [PyMOL] H bonds

[Matthew Baumgartner]

Hi Amali,

For adding hydrogens, I have found that PyMOL does an OK job normally, 
but if you need more accurate placement of hydrogens, I can recommend 
using Reduce.


http://kinemage.biochem.duke.edu/software/reduce.php

HTH,
Matthew Baumgartner


On 11/11/2015 02:06 AM, Osvaldo Martin wrote:

Hi Amali,

Aspartic acid is also assumed to be charged (like Arg), but with 
opposite sign. Acids like Asp release hydrogens, bases like Arg accept 
hydrogens. That's why in one case there is one hydrogen more that what 
you are expecting and in the other case there is one hydrogen less. 
Nothing wrong with PyMOL, is just assuming the most plausible scenario 
(at pH 7) anyone can assume without any other information and without 
solving equations like the Poisson-Boltzmann equation. Almost every 
molecular modeling package out there is making the same assumptions.


Cheers,
Osvaldo.





On Wed, Nov 11, 2015 at 7:50 AM, Amali Guruge > wrote:


Dear Prof. Osvaldo,

Arg residue problem is solved. Thank you very much. Other thing is
for Aspartic acid the program doesn't add H to the OH
group. What is the reason behind this.

Thank you.

On Wed, Nov 11, 2015 at 11:17 AM, Osvaldo Martin
> wrote:

Hi Amali,

By the =NH group do you mean one of the nitrogens of the
guanidine group? If that's the case PyMOL is doing the right
thing. By default PyMOL assumes that (Arg, Lys, Glu, Asp) are
charged. In general that's a reasonable assumption (if
residues are exposed to the solvent or relative close to other
charges of the opposite sign), Is not a good assumption if you
have Arg too close to others Arg, Lys or other residue of
equal sign.

What is the other think you notice?

Cheers,
Osvaldo.
PD: please just call me Osvaldo.


On Wed, Nov 11, 2015 at 6:25 AM, Amali Guruge
> wrote:

Dear Prof. Osvaldo,

When I use the command h_add, the pymol program adds H to
the enzyme. But when it contains Arg group it added two
hydrogens to =NH group. How can I solve that problem? I
noticed another thing.

Thank you in advance.

On Mon, Nov 9, 2015 at 6:00 PM, Amali Guruge
> wrote:

Thank you very much for the reply.

On Sat, Nov 7, 2015 at 1:34 PM, Osvaldo Martin
>
wrote:

Hi Amali,

PyMOL has parameters like h_bond_max_angle that
are defined in terms of aceptor-donor-hydrogen,
hence if hydrogens are not present PyMOL has to
guess the position of hydrogens.

If you need to add hydrogens you can use PyMOL’s
h_add 
command, alternatively you can use openbabel
.

Cheers,

Osvaldo.

On Sat, Nov 7, 2015 at 2:33 AM, Amali Guruge
> wrote:

Dear All,

My question is related to find the polar
contacts between an enzyme and ligand. I want
to know  when we find polar contacts,

1) protein should contain H atoms or not?

2) ligand molecule should contain all H atoms
or not

Please can anyone help me.

Thank you in advance.


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Re: [PyMOL] H bonds

[Osvaldo Martin]

Hi Amali,

Aspartic acid is also assumed to be charged (like Arg), but with opposite
sign. Acids like Asp release hydrogens, bases like Arg accept hydrogens.
That's why in one case there is one hydrogen more that what you are
expecting and in the other case there is one hydrogen less. Nothing wrong
with PyMOL, is just assuming the most plausible scenario (at pH 7) anyone
can assume without any other information and without solving equations like
the Poisson-Boltzmann equation. Almost every molecular modeling package out
there is making the same assumptions.

Cheers,
Osvaldo.





On Wed, Nov 11, 2015 at 7:50 AM, Amali Guruge  wrote:

> Dear Prof. Osvaldo,
>
> Arg residue problem is solved. Thank you very much. Other thing is for
> Aspartic acid the program doesn't add H to the OH
> group. What is the reason behind this.
>
> Thank you.
>
> On Wed, Nov 11, 2015 at 11:17 AM, Osvaldo Martin 
> wrote:
>
>> Hi Amali,
>>
>> By the =NH group do you mean one of the nitrogens of the guanidine group?
>> If that's the case PyMOL is doing the right thing. By default PyMOL assumes
>> that (Arg, Lys, Glu, Asp) are charged. In general that's a reasonable
>> assumption (if residues are exposed to the solvent or relative close to
>> other charges of the opposite sign), Is not a good assumption if you have
>> Arg too close to others Arg, Lys or other residue of equal sign.
>>
>> What is the other think you notice?
>>
>> Cheers,
>> Osvaldo.
>> PD: please just call me Osvaldo.
>>
>>
>> On Wed, Nov 11, 2015 at 6:25 AM, Amali Guruge 
>> wrote:
>>
>>> Dear Prof. Osvaldo,
>>>
>>> When I use the command h_add, the pymol program adds H to the enzyme.
>>> But when it contains Arg group it added two hydrogens to =NH group. How can
>>> I solve that problem? I noticed another thing.
>>>
>>> Thank you in advance.
>>>
>>> On Mon, Nov 9, 2015 at 6:00 PM, Amali Guruge 
>>> wrote:
>>>
 Thank you very much for the reply.

 On Sat, Nov 7, 2015 at 1:34 PM, Osvaldo Martin 
 wrote:

> Hi Amali,
>
> PyMOL has parameters like h_bond_max_angle that are defined in terms
> of aceptor-donor-hydrogen, hence if hydrogens are not present PyMOL has to
> guess the position of hydrogens.
>
> If you need to add hydrogens you can use PyMOL’s h_add
>  command, alternatively you can
> use openbabel .
>
> Cheers,
>
> Osvaldo.
>
> On Sat, Nov 7, 2015 at 2:33 AM, Amali Guruge 
> wrote:
>
> Dear All,
>>
>> My question is related to find the polar contacts between an enzyme
>> and ligand. I want to know  when we find polar contacts,
>>
>> 1) protein should contain H atoms or not?
>>
>> 2) ligand molecule should contain all H atoms or not
>>
>> Please can anyone help me.
>>
>> Thank you in advance.
>>
>>
>> --
>>
>> ___
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives:
>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
> ​
>


>>>
>>
>
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Re: [PyMOL] H bonds

[Amali Guruge]

Dear Prof. Osvaldo,

Arg residue problem is solved. Thank you very much. Other thing is for
Aspartic acid the program doesn't add H to the OH
group. What is the reason behind this.

Thank you.

On Wed, Nov 11, 2015 at 11:17 AM, Osvaldo Martin 
wrote:

> Hi Amali,
>
> By the =NH group do you mean one of the nitrogens of the guanidine group?
> If that's the case PyMOL is doing the right thing. By default PyMOL assumes
> that (Arg, Lys, Glu, Asp) are charged. In general that's a reasonable
> assumption (if residues are exposed to the solvent or relative close to
> other charges of the opposite sign), Is not a good assumption if you have
> Arg too close to others Arg, Lys or other residue of equal sign.
>
> What is the other think you notice?
>
> Cheers,
> Osvaldo.
> PD: please just call me Osvaldo.
>
>
> On Wed, Nov 11, 2015 at 6:25 AM, Amali Guruge 
> wrote:
>
>> Dear Prof. Osvaldo,
>>
>> When I use the command h_add, the pymol program adds H to the enzyme. But
>> when it contains Arg group it added two hydrogens to =NH group. How can I
>> solve that problem? I noticed another thing.
>>
>> Thank you in advance.
>>
>> On Mon, Nov 9, 2015 at 6:00 PM, Amali Guruge 
>> wrote:
>>
>>> Thank you very much for the reply.
>>>
>>> On Sat, Nov 7, 2015 at 1:34 PM, Osvaldo Martin 
>>> wrote:
>>>
 Hi Amali,

 PyMOL has parameters like h_bond_max_angle that are defined in terms of
 aceptor-donor-hydrogen, hence if hydrogens are not present PyMOL has to
 guess the position of hydrogens.

 If you need to add hydrogens you can use PyMOL’s h_add
  command, alternatively you can
 use openbabel .

 Cheers,

 Osvaldo.

 On Sat, Nov 7, 2015 at 2:33 AM, Amali Guruge 
 wrote:

 Dear All,
>
> My question is related to find the polar contacts between an enzyme
> and ligand. I want to know  when we find polar contacts,
>
> 1) protein should contain H atoms or not?
>
> 2) ligand molecule should contain all H atoms or not
>
> Please can anyone help me.
>
> Thank you in advance.
>
>
> --
>
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
 ​

>>>
>>>
>>
>
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Re: [PyMOL] H bonds

[Osvaldo Martin]

Hi Amali,

PyMOL has parameters like h_bond_max_angle that are defined in terms of
aceptor-donor-hydrogen, hence if hydrogens are not present PyMOL has to
guess the position of hydrogens.

If you need to add hydrogens you can use PyMOL’s h_add
 command, alternatively you can use
openbabel .

Cheers,

Osvaldo.

On Sat, Nov 7, 2015 at 2:33 AM, Amali Guruge  wrote:

Dear All,
>
> My question is related to find the polar contacts between an enzyme and
> ligand. I want to know  when we find polar contacts,
>
> 1) protein should contain H atoms or not?
>
> 2) ligand molecule should contain all H atoms or not
>
> Please can anyone help me.
>
> Thank you in advance.
>
>
> --
>
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>
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[PyMOL] H bonds

[Amali Guruge]

Dear All,

My question is related to find the polar contacts between an enzyme and
ligand. I want to know  when we find polar contacts,

1) protein should contain H atoms or not?

2) ligand molecule should contain all H atoms or not

Please can anyone help me.

Thank you in advance.
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Re: [PyMOL] H-bonds representation

[James Starlight]

Dear all :)

I want to find Hbonds beetween different helices in the membrane receptor (
H bonds beetween sidechains only)

I know possible way to do it wihin selection if I defined different helixes
but is there any way to find almost all Hbonds between polar sidecains
groups ?

Could I use

 find- polar contact- sidechain only
for this purpose ?

James

2011/11/30 Jason Vertrees jason.vertr...@schrodinger.com

 James,

  It works quite well in case of not very compliated ligands ( e.g bonds
  beetween aa-tRNA and the  aa-tRNA syntase were correct ) but in the
  sugar-bound enzyme there were some mistakes in representation of the
 H-bonds
  netween water/ligand/active center ( some water also partisipate in the
  ligand binding but in case where water and some residues of the active
 sites
  were positioned iclosely the bonds were incorect ). So a I understood I
 can
  fix this mistakes only manually ?

 Please ask the pymol-users about this.


  By the way, on what assumptions helix elements of my proteins were
 colored
  after representation of the ligand binding with the cartoons ?

 It's colored rainbow from start to end.


  Finally how I could represent ionic contacts in the ion-binding proteins
 ?
  E.g now I'm studing calmodulin wich has Ef-hand Ca-binding motifs. I've
  tried to represent bonds beetwen some polar residues of the active site
 with
  the ligand but failed :(

 Please ask the pymol-users about this.

 I'm gearing up for the PyMOL v1.5.0 release, so I won't have time
 right now to personally answer your questions. Please keep relying on
 the pymol-users list--they're very knowledgeable about PyMOL.

 Cheers,

 -- Jason




  2011/11/29 Jason Vertrees jason.vertr...@schrodinger.com
 
  James,
 
   Is there any semi-avtomated way to find ligand binding pocket and do
 all
   such things ?
 
  For your given object, click A  preset  ligands sites  cartoon. Try
  other options under that menu.
 
  Cheers,
 
  -- Jason
 
 
   2011/11/28 Thomas Holder spel...@users.sourceforge.net
  
   Hi James,
  
   most trivial manner:
  
   as cartoon
   show sticks, resn LEU+ILE+VAL
   set cartoon_side_chain_helper
  
   and eventually something like this:
  
   show spheres, resn LEU+ILE+VAL and not name N+O+C
   set sphere_transparency, 0.5
  
  
   Cheers,
Thomas
  
   On 11/28/2011 02:58 PM, James Starlight wrote:
  
   Another question also linked with the non-covalent interaction.
  
   In particular I wounder to know how i Could represent all
 hydrophobic
   (
   Ley Ile Val etc) sidechains in my proteins in most trivial manner?
 I'd
   like to represent the hydrophobic core of the proteins made from
 those
   residues.
  
   Thanks,
  
   James
  
   --
   Thomas Holder
   MPI for Developmental Biology
   Spemannstr. 35
   D-72076 Tübingen
  
  
  
  
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  PyMOL Product Manager
  Schrodinger, LLC
 
  (e) jason.vertr...@schrodinger.com
  (o) +1 (603) 374-7120
 
 
 
 
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Re: [PyMOL] H-bonds representation

[James Starlight]

Thanks, Thomas, Jason

both of the methods are useable :)

By the way I've forced with the problem of the representation of the active
sites of different enzymes. I need to view all my protein as the cartoons
and the ligand as the shpere in the ligand binding pocket. Besides I need
to mark residues wich are contact with the ligand ( E.g I want to mark it
as the lines and with the individual colour ). Finally I want to represent
Hbonds between active site residues and the ligand.

I've done this manually but its very long if I want to study 20-30
different enzymes during evening :)
Also I've found such sollution wich could do all that i want
http://www.pymolwiki.org/index.php/PLoS#Case_2:_Ligand-binding_sites_.28.E2.89.A5_novice.2Fintermediate.29

 but this way also I need to rewrite script for specified enzyme ( e.g mark
the active site residues and the distances for Hbonds etc )

Is there any semi-avtomated way to find ligand binding pocket and do all
such things ?

James



2011/11/28 Thomas Holder spel...@users.sourceforge.net

 Hi James,

 most trivial manner:

 as cartoon
 show sticks, resn LEU+ILE+VAL
 set cartoon_side_chain_helper

 and eventually something like this:

 show spheres, resn LEU+ILE+VAL and not name N+O+C
 set sphere_transparency, 0.5


 Cheers,
  Thomas


 On 11/28/2011 02:58 PM, James Starlight wrote:

 Another question also linked with the non-covalent interaction.

 In particular I wounder to know how i Could represent all hydrophobic (
 Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd
 like to represent the hydrophobic core of the proteins made from those
 residues.

 Thanks,

 James


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

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Re: [PyMOL] H-bonds representation

[Jason Vertrees]

James,

 Is there any semi-avtomated way to find ligand binding pocket and do all
 such things ?

For your given object, click A  preset  ligands sites  cartoon. Try
other options under that menu.

Cheers,

-- Jason


 2011/11/28 Thomas Holder spel...@users.sourceforge.net

 Hi James,

 most trivial manner:

 as cartoon
 show sticks, resn LEU+ILE+VAL
 set cartoon_side_chain_helper

 and eventually something like this:

 show spheres, resn LEU+ILE+VAL and not name N+O+C
 set sphere_transparency, 0.5


 Cheers,
  Thomas

 On 11/28/2011 02:58 PM, James Starlight wrote:

 Another question also linked with the non-covalent interaction.

 In particular I wounder to know how i Could represent all hydrophobic (
 Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd
 like to represent the hydrophobic core of the proteins made from those
 residues.

 Thanks,

 James

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


 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
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PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] H-bonds representation

[James Starlight]

Thanks Jason.

It works quite well in case of not very compliated ligands ( e.g bonds
beetween aa-tRNA and the  aa-tRNA syntase were correct ) but in the
sugar-bound enzyme there were some mistakes in representation of the
H-bonds netween water/ligand/active center ( some water also partisipate in
the ligand binding but in case where water and some residues of the active
sites were positioned iclosely the bonds were incorect ). So a I understood
I can fix this mistakes only manually ?

By the way, on what assumptions helix elements of my proteins were colored
after representation of the ligand binding with the cartoons ?

Finally how I could represent ionic contacts in the ion-binding proteins ?
E.g now I'm studing calmodulin wich has Ef-hand Ca-binding motifs. I've
tried to represent bonds beetwen some polar residues of the active site
with the ligand but failed :(



Thanks again,


James

2011/11/29 Jason Vertrees jason.vertr...@schrodinger.com

 James,

  Is there any semi-avtomated way to find ligand binding pocket and do all
  such things ?

 For your given object, click A  preset  ligands sites  cartoon. Try
 other options under that menu.

 Cheers,

 -- Jason


  2011/11/28 Thomas Holder spel...@users.sourceforge.net
 
  Hi James,
 
  most trivial manner:
 
  as cartoon
  show sticks, resn LEU+ILE+VAL
  set cartoon_side_chain_helper
 
  and eventually something like this:
 
  show spheres, resn LEU+ILE+VAL and not name N+O+C
  set sphere_transparency, 0.5
 
 
  Cheers,
   Thomas
 
  On 11/28/2011 02:58 PM, James Starlight wrote:
 
  Another question also linked with the non-covalent interaction.
 
  In particular I wounder to know how i Could represent all hydrophobic (
  Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd
  like to represent the hydrophobic core of the proteins made from those
  residues.
 
  Thanks,
 
  James
 
  --
  Thomas Holder
  MPI for Developmental Biology
  Spemannstr. 35
  D-72076 Tübingen
 
 
 
 --
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  contains a definitive record of customers, application performance,
  security threats, fraudulent activity, and more. Splunk takes this
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 PyMOL Product Manager
 Schrodinger, LLC

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 (o) +1 (603) 374-7120

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Re: [PyMOL] H-bonds representation

[James Starlight]

Another question also linked with the non-covalent interaction.

In particular I wounder to know how i Could represent all hydrophobic ( Ley
Ile Val etc) sidechains in my proteins in most trivial manner? I'd like to
represent the hydrophobic core of the proteins made from those residues.


Thanks,

James

2011/11/27 Edward A. Berry ber...@upstate.edu

 Yes i think the strongest H-bonds are single acceptor and straight
 (angle at H = 180*). but these other bonds have significant
 strength also.
 Sorry, I'm a complete beginner at pymol. I have no idea how to
 do these things.

 ed


 James Starlight wrote:

 Thanks Edward

 but recently I've studied generation of the Hbond in the water crystalls
 ( ice ) where H
 could be as the donor of only one H-bond. It seems that I need to refresh
 my protein
 physics course again :)

 By the way as I understtod the mode=2 way shows not only H-bonds but also
 others
 electrostatic bonds ( e.g as the salt bridges)
 1- Is there any way to make clear difference betwen two distinguished
 electostatic contacts?

 2- Also I'm looking for the most trivial way to show S-S bonds ( between
 2 Cys resiudes)
 in the specified chain as well as between differen chains ( as in the
 inslulin for instance ).


 Thanks again,

 James

 2011/11/26 Edward A. Berry ber...@upstate.edu mailto:ber...@upstate.edu
 


While the single acceptor H-bond is most common, bifurcated (or
 three-centred) H-bods
are not uncommon in crystal structures, as described starting page 22
 of GA Jeffrey's
book:
http://www.amazon.com/__**Introduction-Hydrogen-Bonding-**
 __Physical-Chemistry/dp/__**0195095499/ref=sr_1_2?ie=UTF8**
 __qid=1322331503sr=8-2http://www.amazon.com/__Introduction-Hydrogen-Bonding-__Physical-Chemistry/dp/__0195095499/ref=sr_1_2?ie=UTF8__qid=1322331503sr=8-2

http://www.amazon.com/**Introduction-Hydrogen-Bonding-**
 Physical-Chemistry/dp/**0195095499/ref=sr_1_2?ie=UTF8**
 qid=1322331503sr=8-2http://www.amazon.com/Introduction-Hydrogen-Bonding-Physical-Chemistry/dp/0195095499/ref=sr_1_2?ie=UTF8qid=1322331503sr=8-2
 

James Starlight wrote:

Thomas, thank you for so detailed explanation.

This way works good but I'd like to ask you about possibe Hbonds
 in the protein chain.

As I remember for protein physics courses the H atom is always
 donor for only ONE
H-bond (
and O or N atoms could be akceptors for 1 or 2 Hbonds)

But In my case there are some cases where H atom ( white ) is
 donor for the 2
Hbonds.  By
the way I found the same on the picture in WIKI too.

How it could be explaned ?

James


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Re: [PyMOL] H-bonds representation

[Thomas Holder]

Hi James,

most trivial manner:

as cartoon
show sticks, resn LEU+ILE+VAL
set cartoon_side_chain_helper

and eventually something like this:

show spheres, resn LEU+ILE+VAL and not name N+O+C
set sphere_transparency, 0.5


Cheers,
   Thomas

On 11/28/2011 02:58 PM, James Starlight wrote:
 Another question also linked with the non-covalent interaction.

 In particular I wounder to know how i Could represent all hydrophobic (
 Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd
 like to represent the hydrophobic core of the proteins made from those
 residues.

 Thanks,

 James

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

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Re: [PyMOL] H-bonds representation

[Thomas Holder]

Hi James,

 As I've understood there are no posible ways to represent H-bonds in
 proteins in explicit manner. So I'm looking for possible way to do it
 via some plugin or another way.

PyMOL can find polar contacts and represent them as dashed lines. You 
don't need any extra plugin.

http://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts

It's the distance command with mode=2 that does the job.

http://pymolwiki.org/index.php/Distance

There are various dash_* settings that control the appearance of the 
dashed lines:

http://pymolwiki.org/index.php/Dash_Length
http://pymolwiki.org/index.php/Dash_color
(and many others...)

 In particular I need
 1) to visualize H-bonds in some structural motifs like coiled coil wich
 are dimers of alpha helices  ( so I'd like to see H-bonds beetwen
 separate alpha helices )

Try this (lets say helix 1 is resi 1-100 and helix 2 is resi 101-200):

# add hydrogens (if not already present)
h_add donors

# detect polar contacts
distance hb_coiled_coil, resi 1-100, resi 101-200, mode=2

 2) to visualize H-bonds in spicified SS structure ( e.g during formation
 of the alpha helices)- so I'd like to see H-bonds beetwen amide and
 Carboxy groups in specified amino acid sequence.

just like example 1, but with other selections:

distance hb_backbone, name O, name N, mode=2

 3) Finally I'd like to check H-bond in protein-ligand complex ( beetwenn
 specified ligand groups as well as some amino acid residues of the
 ligand binding pocket)

just like before, but with ligand as selection 1 and receptor as 
selection 2.

Hope that helps.

Cheers,
   Thomas

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

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Re: [PyMOL] H-bonds representation

[James Starlight]

Thomas, thank you for so detailed explanation.

This way works good but I'd like to ask you about possibe Hbonds in the
protein chain.

As I remember for protein physics courses the H atom is always donor for
only ONE H-bond ( and O or N atoms could be akceptors for 1 or 2 Hbonds)

But In my case there are some cases where H atom ( white ) is donor for the
2 Hbonds.  By the way I found the same on the picture in WIKI too.

How it could be explaned ?

James
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Re: [PyMOL] H-bonds representation

[Edward A. Berry]

While the single acceptor H-bond is most common, bifurcated (or three-centred) 
H-bods are 
not uncommon in crystal structures, as described starting page 22 of GA 
Jeffrey's book:
http://www.amazon.com/Introduction-Hydrogen-Bonding-Physical-Chemistry/dp/0195095499/ref=sr_1_2?ie=UTF8qid=1322331503sr=8-2

James Starlight wrote:
 Thomas, thank you for so detailed explanation.

 This way works good but I'd like to ask you about possibe Hbonds in the 
 protein chain.

 As I remember for protein physics courses the H atom is always donor for only 
 ONE H-bond (
 and O or N atoms could be akceptors for 1 or 2 Hbonds)

 But In my case there are some cases where H atom ( white ) is donor for the 2 
 Hbonds.  By
 the way I found the same on the picture in WIKI too.

 How it could be explaned ?

 James


 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-novd2d



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[PyMOL] H-bonds representation

[James Starlight]

Dear PyMol users!



As I've understood there are no posible ways to represent H-bonds in
proteins in explicit manner. So I'm looking for possible way to do it via
some plugin or another way.

In particular I need
1) to visualize H-bonds in some structural motifs like coiled coil wich are
dimers of alpha helices  ( so I'd like to see H-bonds beetwen separate
alpha helices )

2) to visualize H-bonds in spicified SS structure ( e.g during formation of
the alpha helices)- so I'd like to see H-bonds beetwen amide and Carboxy
groups in specified amino acid sequence.

3) Finally I'd like to check H-bond in protein-ligand complex ( beetwenn
specified ligand groups as well as some amino acid residues of the ligand
binding pocket)


Thanks,

James
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Re: [PyMOL] H-bonds and VDW

[Robert Immormino]

Kun,

When I'm interested in dimer interfaces, or protein ligand contacts I
usually use Molprobity to define the interface.

http://molprobity.biochem.duke.edu/

It is a bit of a process, but here's the rundown:

Load your .pdb into molprobity
Add hydrogens
Visualize interface contacts
Then select your two 'half-interfaces' and run probe

One of the output from this is a list that has:
residue from half 1 : residue from half 2 : contact type : details

I usually will take this list of residues and display them in pymol,
then add dashes for hydrogen bonds using the dist command

-bob

[PyMOL] H-bonds and VDW

[kun yang]

Hi,all

I want to show all the H-bonds and VDW between two
dimer interface. Would you please tell me how I use
pymol to do this?

Thank you very much.



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Re: [PyMOL] H-bonds

[Lieven Buts]

On Tuesday 06 January 2004 20:06, Sanishvili, Ruslan wrote:
 Is there a way to calculate and display H-bonds within a selected model
 without going through the distance wizard? Selecting the pairs of atoms
 manually via the distance wizard seems very inefficient and even
 dangerous (too subjective for H-bond assignment).

1) The dist command will draw distance lines between all atoms of two 
different selections that are within a a specified cutoff distance from each 
other. A very rough approach for identifying potential hydrogen bonds would 
be something like

dist (protein and elem n,o) , (ligand and elem n,o), 3.5

This will connect all nitrogen and oxygen atoms in objects protein and 
ligand that are within 3.5 A from each other.


2) A more thorough approach would be to use a program designed to identify 
hydrogen bonds using more complete criteria. The rTools for PyMOL (available 
at http://www.rubor.de/bioinf/pymol_rubor.html ) provide an interface to 
the HBExplore program at http://www.imb-jena.de/www_bioc/hbx/hbx.html.
See the rTools documentation for more details.


-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel

[PyMOL] H-bonds too thick

[Mario Sanchez]

I am drawing hydrogen bonds using command dist, but the rayied image
has a too thick line to these interactions. I was not able to find the
command to set the thickness of it, but I hope someone (DeLano?) will be
able to help me.

Thank you indeed.
-- 
Mario Sanches,  PhD Student
Protein Crystallography Group
São Paulo University, São Carlos Physics Institute
Phone:  +55 (16) 273 9868
sanc...@if.sc.usp.br

RE: [PyMOL] H-bonds too thick

[DeLano, Warren]

 From: Mario Sanchez [mailto:sanc...@if.sc.usp.br]

 I am drawing hydrogen bonds using command dist, but the rayied image
 has a too thick line to these interactions. I was not able to find the
 command to set the thickness of it, but I hope someone 
 (DeLano?) will be
 able to help me.

You can generally tweak fix hese kinds of issues using one of PyMOL's many 
settings -- most of them have verbose names.  Try Edit All under the settings 
menu for a complete list.  In this case:

set dash_radius=0.10
ray 

- Warren


--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.