Re: [PyMOL] Editing of the pdb structure

[Thomas Evangelidis]

Is it a small organic molecule or a modified amino acid within the context
of a protein?


2012/1/29 Tim Schulte 

>  Dear James,
> I agree with Joao, for fast and dirty minimisation you might try the
> program Chimera or VegaZZ. If you just wanna have an energy-minimized small
> molecule the Prodrg server is the way to go.
> Cheers,
> Tim
>  --
> *Von:* João Rodrigues [anar...@gmail.com]
> *Gesendet:* Freitag, 27. Januar 2012 09:56
> *Bis:* James Starlight
> *Cc:* pymol-users@lists.sourceforge.net
> *Betreff:* Re: [PyMOL] Editing of the pdb structure
>
>  Dear James,
>
>  As someone has told you already, Pymol is a visualization tool, not a
> modelling suite. I guess you would be better off using something like
> AMBERTOOLS or MODELLER, depending on what you want to model, or any other
> "real" simulation/modelling package otherwise your results are very weak...
>
>  My opinion only.
>
> João [...] Rodrigues
> http://nmr.chem.uu.nl/~joao
>
>
>
> No dia 27 de Janeiro de 2012 09:50, James Starlight <
> jmsstarli...@gmail.com> escreveu:
>
>> Arne, Thomas
>>
>> Thanks alot. Bond works finw
>>
>>
>> I'd like just to ask what about geometry optimisation of the new structure
>>
>> E.g I want create 5memb imidazole ring where the 2 adj atoms are apart
>> from 1.5 A from each other.
>>
>> When I've create new bond by bond command new ring look like 6memb ( like
>> benzol) because of long distance between adj atoms.
>>
>> How I could optimise geometry of the new mollecule? Have pymol some
>> built-in functions like conformational search be means of monte carlo or
>> energy minimisation ?
>>
>>
>> James
>>
>>
>> 2012/1/27 Thomas Holder 
>>
>>>  On 01/27/2012 09:11 AM, James Starlight wrote:
>>>
 Dear PyMol users!

 I need to create NEW covalent bond between two adjacent atoms. How this
 could be done in PyMOl?

>>>
>>>  you could have guessed it: 
>>> http://pymolwiki.org/index.**php/Bond
>>> :-)
>>>
>>> The atoms must both be within the same object.
>>>
>>>
>>> Cheers,
>>>  Thomas
>>>
>>> --
>>> Thomas Holder
>>> MPI for Developmental Biology
>>> Spemannstr. 35
>>> D-72076 Tübingen
>>>
>>
>>
>>
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>
>
>
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-- 

==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [PyMOL] Open .pdb / .pml files in ubuntu/mint

[Ramiro Téllez Sanz]

I had exactly the same problem but under Gentoo Linux 64bits using KDE 
4.7.4.


In my case, I solved it by re-installing the package for 
chemical-mime-data (sci-chemistry/chemical-mime-data), which was missing 
since the removal of some Gnome chemical packages with all their 
dependencies I didn't use anymore . I had to add it back manually.


Hope this helps.

Ramiro Téllez Sanz


Hi guys.

Ehh. I have a newly installed Mint 12 box with gnome 3.

I have that annoying thing, that when I click a text .pdb files, it 
opens with gedit.

Then I can right click and select .pdb files to open with pymol.
But when I then click a .txt file, it opens it with pymol.

Grrr...
I know its something with mimetypes, and I got it to work on my mint 11.
But now I am a little lost, and can't find it on the web...

So, anyone did this?

Best
Troels



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[PyMOL] Missing residues in PDB

[gontchar andrey]

Hi.
We have a pdb-file of a small sequence of aminoacids. In this file there are 
atom names, atom coordinates, connects etc. except residue names records. Sure 
we can try to write them manually, but I'd like to know if there is some tool 
to do this automatically?

--

Andrey

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Re: [PyMOL] Missing residues in PDB

[Thomas Holder]

Hi Andrey,

I have a script that updates the sequence based on residue numbering 
(resi). See attachment.


Usage: set_sequence sequence [, selection [, start ]]

Example:

# import script
run setseq.py

# create a poly-ala peptide
fab A, myobj

# set new sequence
set_sequence CDEFGHIKL, myobj

# update sequence viewer
rebuild

Cheers,
  Thomas

On 01/30/2012 01:38 PM, gontchar andrey wrote:

Hi.
We have a pdb-file of a small sequence of aminoacids. In this file there are 
atom names, atom coordinates, connects etc. except residue names records. Sure 
we can try to write them manually, but I'd like to know if there is some tool 
to do this automatically?

--

Andrey


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


setseq.py
Description: application/chimera
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Re: [PyMOL] Missing residues in PDB

[gontchar andrey]

Thanks a lot! 
A very useful script, but not exactly that I need...
In my pdb file residues are not numbered. I think that I have to determine 
amino acids only by atom sequence and connetcions... This problem is a little 
more complicated than assigning names to numbered residues, I think... 
Do you think, is it possible?

On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote:
> Hi Andrey,
> 
> I have a script that updates the sequence based on residue numbering
> (resi). See attachment.
> 
> Usage: set_sequence sequence [, selection [, start ]]
> 
> Example:
> 
> # import script
> run setseq.py
> 
> # create a poly-ala peptide
> fab A, myobj
> 
> # set new sequence
> set_sequence CDEFGHIKL, myobj
> 
> # update sequence viewer
> rebuild
> 
> Cheers,
>   Thomas
> 
> On 01/30/2012 01:38 PM, gontchar andrey wrote:
> >Hi.
> >We have a pdb-file of a small sequence of aminoacids. In this file there are 
> >atom names, atom coordinates, connects etc. except residue names records. 
> >Sure we can try to write them manually, but I'd like to know if there is 
> >some tool to do this automatically?
> >
> >--
> >
> >Andrey
> 
> -- 
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen



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Re: [PyMOL] Missing residues in PDB

[Thomas Holder]

On 01/30/2012 02:24 PM, gontchar andrey wrote:

Thanks a lot!
A very useful script, but not exactly that I need...
In my pdb file residues are not numbered. I think that I have to determine 
amino acids only by atom sequence and connetcions... This problem is a little 
more complicated than assigning names to numbered residues, I think...
Do you think, is it possible?


this is indeed more complicated. A simple heuristic would be to assume 
that the first atom in a residue is always "N". I added a 
"set_numbering" function to the script, maybe this works for you?


Example:

set_numbering myobj
set_sequence CDEFGHIKL, myobj

Cheers,
  Thomas


On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote:

Hi Andrey,

I have a script that updates the sequence based on residue numbering
(resi). See attachment.

Usage: set_sequence sequence [, selection [, start ]]

Example:

# import script
run setseq.py

# create a poly-ala peptide
fab A, myobj

# set new sequence
set_sequence CDEFGHIKL, myobj

# update sequence viewer
rebuild

Cheers,
   Thomas

On 01/30/2012 01:38 PM, gontchar andrey wrote:

Hi.
We have a pdb-file of a small sequence of aminoacids. In this file there are 
atom names, atom coordinates, connects etc. except residue names records. Sure 
we can try to write them manually, but I'd like to know if there is some tool 
to do this automatically?

--

Andrey


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


setseq.py
Description: application/chimera
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Re: [PyMOL] Missing residues in PDB

[gontchar andrey]

Thanks! I'll try it!
On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote:
> Hi Andrey,
> 
> I have a script that updates the sequence based on residue numbering
> (resi). See attachment.
> 
> Usage: set_sequence sequence [, selection [, start ]]
> 
> Example:
> 
> # import script
> run setseq.py
> 
> # create a poly-ala peptide
> fab A, myobj
> 
> # set new sequence
> set_sequence CDEFGHIKL, myobj
> 
> # update sequence viewer
> rebuild
> 
> Cheers,
>   Thomas
> 
> On 01/30/2012 01:38 PM, gontchar andrey wrote:
> >Hi.
> >We have a pdb-file of a small sequence of aminoacids. In this file there are 
> >atom names, atom coordinates, connects etc. except residue names records. 
> >Sure we can try to write them manually, but I'd like to know if there is 
> >some tool to do this automatically?
> >
> >--
> >
> >Andrey
> 
> -- 
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen



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[PyMOL] list of polar contacts

[Abhinav Verma]

Hi,

 I am trying to get the list of hbonds formed using
Apply-find-polarcontacts.

 I searched and found some scripts, but they never give me the same result
as the one by default pymol.

 Any ideas how I can get the hbonds as a list.

Thanks,

Abhinav
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[PyMOL] To build protein structure model?

[Hong ZHAN]

Hi everyone, 

I am a new guy in this area.. And I just want to know how to build a structure 
model of my protein from homologues crystal structure and protein seq.???

Thx

Hong
Sincerely, 
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Re: [PyMOL] To build protein structure model?

[João Rodrigues]

Try MODELLER.
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Re: [PyMOL] To build protein structure model?

[Nat Echols]

On Mon, Jan 30, 2012 at 6:05 AM, Hong ZHAN  wrote:
> I am a new guy in this area.. And I just want to know how to build a 
> structure model of my protein from homologues crystal structure and protein 
> seq.???

You probably want to try using a homology modeling server for this
rather than PyMOL:

http://robetta.bakerlab.org/
https://modbase.compbio.ucsf.edu/scgi/modweb.cgi
http://swissmodel.expasy.org/

However, the "Mutagenesis Wizard" in PyMOL may be suitable for simple
editing if the only differences between your sequence and the crystal
structure is point mutations.

-Nat

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Re: [PyMOL] list of polar contacts

[Thomas Evangelidis]

Probably because they set diffently the acceptor-donor cutoff and the
acceptor-hydrogen-donor angle. Use list_hbonds.py from:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

and set the cutoff and angle to the values you wish.

Thomas



On 30 January 2012 16:34, Abhinav Verma  wrote:

> Hi,
>
>  I am trying to get the list of hbonds formed using
> Apply-find-polarcontacts.
>
>  I searched and found some scripts, but they never give me the same result
> as the one by default pymol.
>
>  Any ideas how I can get the hbonds as a list.
>
> Thanks,
>
> Abhinav
>
>
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-- 

==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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[PyMOL] atom structure

[nami sugiyama]

Hi,

We would like to visualize the protein structure at the atoms level,  
by visualizing atoms as "balls" and the bonds between them as  
"sticks". Is there a way??

Nami


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Re: [PyMOL] atom structure

[João Rodrigues]

Hi,

You can set something like this:

set sphere_scale, 0.2
set stick_radius, 0.15
show spheres
show sticks


I usually use lines for the bonds though.

Best,

João
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Re: [PyMOL] list of polar contacts

[Thomas Evangelidis]

I think you can reproduce the results from "apply->find->polar contacts"
option with the PyMOL built-in "distance" command. E.g.

distance hbonds, all, all, 3.2, mode=2

The problem is that you cannot set the A-H-D angle which is important for
the definition of the H-bond.


On 30 January 2012 18:45, Abhinav Verma  wrote:

> Thanks Thomas,
>
>  I have been here and my problem is that I could not reproduce the results
> of default pymol behaviour. I just need to either reproduce 100% the pymol
> default behaviour or to just get a list of what is painted in the window.
> It should be possible I guess.
>
>  Do you have more ideas?
>
>
>
>
> On Mon, Jan 30, 2012 at 5:38 PM, Thomas Evangelidis wrote:
>
>> Probably because they set diffently the acceptor-donor cutoff and the
>> acceptor-hydrogen-donor angle. Use list_hbonds.py from:
>>
>> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
>>
>> and set the cutoff and angle to the values you wish.
>>
>> Thomas
>>
>>
>>
>> On 30 January 2012 16:34, Abhinav Verma  wrote:
>>
>>> Hi,
>>>
>>>  I am trying to get the list of hbonds formed using
>>> Apply-find-polarcontacts.
>>>
>>>  I searched and found some scripts, but they never give me the same
>>> result as the one by default pymol.
>>>
>>>  Any ideas how I can get the hbonds as a list.
>>>
>>> Thanks,
>>>
>>> Abhinav
>>>
>>>
>>> --
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>>>
>>
>>
>>
>> --
>>
>> ==
>>
>> Thomas Evangelidis
>>
>> PhD student
>>
>> Biomedical Research Foundation, Academy of Athens
>>
>> 4 Soranou Ephessiou , 115 27 Athens, Greece
>>
>> email: tev...@bioacademy.gr
>>
>>   teva...@gmail.com
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
>>
>>
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>>
>
>


-- 

==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [PyMOL] atom structure

[Katherine Sippel]

Hi Nami,

You want http://www.pymolwiki.org/index.php/Ball_and_Stick

Katherine

On Mon, Jan 30, 2012 at 10:46 AM, nami sugiyama
wrote:

> Hi,
>
> We would like to visualize the protein structure at the atoms level,
> by visualizing atoms as "balls" and the bonds between them as
> "sticks". Is there a way??
>
> Nami
>
>
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Re: [PyMOL] Editing of the pdb structure

[Thomas Evangelidis]

I think you got your answers from the AMBER and GROMACS mailing list :)

Just a comment about PRODRG server, it is not the best choice for geometry
optimization and charge calculation.

Lemkul, J.A., Allen, W.J., and Bevan, D.R. (2010) Practical Considerations
for Building GROMOS-Compatible Small Molecule Topologies. *J. Chem. Inf.
Model.* *50* (12): 2221-2235.

To our experience in the group it tends to define the "charge groups"
inaccurately and produce optimized geometries that have out of plane
hydrogens. There is a new online service for creating GROMOS compatible
topologies for organic compounds:

http://compbio.biosci.uq.edu.au/atb/

It uses a knowledge-based approach and higher level QM calculations for
geometry optimization and charge derivation. Yet the GROMOS ffs are united
atom thus you lose in resolution.

If I had to chose an all-atom ff I would go for the AMBER99SB-ILDN for the
protein and GAFF for the organic compound (your chromophore). Unless you
have problems with the size of the organic molecule, you could optimize its
geometry and calculate RESP charges using the R.E.D. server:

http://q4md-forcefieldtools.org/REDS/

Also check out the option "Use RED IV for automatically generating amino
acid fragments " since your chromophore is covalently bonded to the protein
(I never used it so I am not sure if this will do your job).


Thomas



On 30 January 2012 14:16, James Starlight  wrote:

> Thomas,
>
> It's a big protein with the some non-standart functional group like GFP
>
> So the servers like PRORG are not good for that because of big size of the
> protein and subsiquent integration of both fragments.
>
> James
>
>
> 2012/1/30 Thomas Evangelidis 
>
>> Is it a small organic molecule or a modified amino acid within the
>> context of a protein?
>>
>>
>>
>> 2012/1/29 Tim Schulte 
>>
>>>  Dear James,
>>> I agree with Joao, for fast and dirty minimisation you might try the
>>> program Chimera or VegaZZ. If you just wanna have an energy-minimized small
>>> molecule the Prodrg server is the way to go.
>>> Cheers,
>>> Tim
>>>  --
>>> *Von:* João Rodrigues [anar...@gmail.com]
>>> *Gesendet:* Freitag, 27. Januar 2012 09:56
>>> *Bis:* James Starlight
>>> *Cc:* pymol-users@lists.sourceforge.net
>>> *Betreff:* Re: [PyMOL] Editing of the pdb structure
>>>
>>>  Dear James,
>>>
>>>  As someone has told you already, Pymol is a visualization tool, not a
>>> modelling suite. I guess you would be better off using something like
>>> AMBERTOOLS or MODELLER, depending on what you want to model, or any other
>>> "real" simulation/modelling package otherwise your results are very weak...
>>>
>>>  My opinion only.
>>>
>>> João [...] Rodrigues
>>> http://nmr.chem.uu.nl/~joao
>>>
>>>
>>>
>>> No dia 27 de Janeiro de 2012 09:50, James Starlight <
>>> jmsstarli...@gmail.com> escreveu:
>>>
 Arne, Thomas

 Thanks alot. Bond works finw


 I'd like just to ask what about geometry optimisation of the new
 structure

 E.g I want create 5memb imidazole ring where the 2 adj atoms are apart
 from 1.5 A from each other.

 When I've create new bond by bond command new ring look like 6memb (
 like benzol) because of long distance between adj atoms.

 How I could optimise geometry of the new mollecule? Have pymol some
 built-in functions like conformational search be means of monte carlo or
 energy minimisation ?


 James


 2012/1/27 Thomas Holder 

>  On 01/27/2012 09:11 AM, James Starlight wrote:
>
>> Dear PyMol users!
>>
>> I need to create NEW covalent bond between two adjacent atoms. How
>> this
>> could be done in PyMOl?
>>
>
>  you could have guessed it: 
> http://pymolwiki.org/index.**php/Bond
> :-)
>
> The atoms must both be within the same object.
>
>
> Cheers,
>  Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>



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