Re: [PyMOL] Creating of chmeric protein

2012-01-29 Thread James Starlight 
Hi Jordan!


Thank you for so detailed explanation


Indeed I've noticed that so simple operation is very routine in pymol :(

Now I'm looking for good easy-to-use modelling software wich is free
for accademical users. I'd like that this soft would have good
graphical interphace and flexibility like PyMol as well as good
editing functionality like amber XLEAP for instance.

By the way as I understood the MOE sotware is not free ( I've not
found any download lnks ). So I think use MoDELLER or MAESTRO software
for my purposes.

Thanks again,


James

2012/1/28, Jordan Willis :
> Is this a one time deal? Or a script you need to make for multiple proteins.
>
> You could probably transfer the volume by making TLG a new object. create
> TLG, protein_1 and resi (residue numbers of TLG).
>
> Then align TLG to the new protein X where you want it.
>
> align TLG, proteinX and resi (where you want TLG)
>
> Then you would have to remove the atoms of the old volume be selecting the
> residues and A -> remove atoms
>
> fuse (N-terminus of protein X atom, C terminus of TLG object)
> fuse (N -terminus of TLG, C terminus of protein X)
>
> That is so time consuming though, why don't you use a modeling program like
> everyone else suggested? for a nice graphical interface and bond
> satisfaction why not try and use MOE if you want a graphical interface.
> http://www.chemcomp.com/software.htm
>
> If this were me though, I would use Biopython.
>
> Jordan
>
>
>
>
> On Jan 28, 2012, at 11:41 PM, James Starlight wrote:
>
>> Dear PyMol Users!
>>
>>
>> I want to make simple chimeric mutant via PyMol by transferring
>> specified group from one protein to another.
>>
>>
>> E.g I have to proteins:
>>
>> 1 protein consist of triplet of TLG amino acids in the X place
>>
>> 2nd protein consist of specific group wich I w'd like to move in the X
>> place of first protein ( both of that groups have exactly the same
>> volume because specific group in second protein was made by
>> modification of the TLG triplet )
>>
>> How I could do that ransfection ?
>>
>> James
>>
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>
>

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Re: [PyMOL] Editing of the pdb structure

2012-01-29 Thread 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 
mailto: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 
mailto:spel...@users.sourceforge.net>>
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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[PyMOL] Open .pdb / .pml files in ubuntu/mint

2012-01-29 Thread Troels Emtekær Linnet 
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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Re: [PyMOL] Open .pdb / .pml files in ubuntu/mint

2012-01-29 Thread Jordan Willis 
Hmm,

Have you tried putting a .txt and .pdb file on your desktop. Right click either 
one and click Properties. There is an Open With tab. It should say "Open this 
file and other .txt files with" and then you can select gedit. Conversely do 
the same for .pdb files.

Jordan




On Jan 29, 2012, at 2:11 PM, Troels Emtekær Linnet wrote:

> 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
> 
> --
> Try before you buy = See our experts in action!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
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Re: [PyMOL] Open .pdb / .pml files in ubuntu/mint

2012-01-29 Thread Jordan Willis 
Oh duh,

You are saying the .pdb is read as a "plain text file"

You would then have to add a new mime type ".pdb" to the source XML file that 
gnome reads in /usr/share/mime/packages/freedesktop.org.xml


http://library.gnome.org/admin/system-admin-guide/stable/mimetypes-source-xml.html.en

Sorry for the earlier post.

jordan




On Jan 29, 2012, at 2:11 PM, Troels Emtekær Linnet wrote:

> 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
> 
> --
> Try before you buy = See our experts in action!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-dev2___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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