how to link two pdb files to create one new protein structure

[msu math]

Hi, I have the pdb files of two proteins, and would like to link one
protein's C-terminal to the other protein's N-terminal, as a way to
generate a new protein.

So does anyone know any software that can do this kind of work? my
goal is to get the coordinates of this new protein.

Thanks!

[Alex Eletski]

Try DS Visualizer from Accelrys - it is freeware.

Alex.

--
Alexander Eletsky, Ph.D.

University at Buffalo
Department of Chemistry
807 NSM Complex
Buffalo, NY 14260-3000

Phone +1 716 6454304
Fax +1 716 6456963

[Pius Padayatti]

if you have vi or jot editor you just cut and paste one PDB at the end of the other PDB and

save as a new file.

Hope this is what you are looking for

PSP

[Jiang Yusheng]

I don't think this works. If you simply put coordinates together, the structures from two files will stay far away... I tried Modeller, but this software cannot control the rotation.

--
Yusheng Jason Jiang
Department of Chemistry
Georgia State University
Atlanta, 30302 GA

[Dong Luo]

Both VMD and SPDBViewer can help you put two molecules close to each other.
In VMD, translation is straight forward but for rotation, you have to use script commands ($molSel moveby transMatrix). And VMD can easily reset the resid and chain name.
SPDBViewer give the ability to do both translate and rotate using mouse.
After saving out the new coordinates, just put them together and it should be fine. But I guess you may need set the same chain name for them beforehand.

Dong

---

From: Jiang Yusheng <yushe...@gmail.com>
To: Pius Padayatti <ps...@case.edu>
Cc: msu math <mao...@gmail.com>; PredictProtein <predict...@googlegroups.com>
Sent: Tuesday, October 6, 2009 5:07:25 PM
Subject: [PredictProtein] Re: how to link two pdb files to create one new protein structure

[Partha Sarathi Mitra]

Hi
 
Can any one tell me the very  simple program to show the possible altered protein structure due to  non synonymous SNP of a gene.

Partha S Mitra, Ph.D.

Research Associate 

Molecular Genetics Laboratory, Room # 408, EE Just Hall

Department of Biology, Howard University

415 College Street, NW; Washington DC 20059

TEL # (202) 806-4176; FAX # (202) 806-5832

email: partha...@gmail.com; p_m...@howard.edu

 

 

[shashank rana]

Dear friend
I think SPDV viewer software use in that process.
All the best.
Bye

[Renato Froidevaux]

Hi everybody,

I would research sequence homology between a short aminoacid sequence
(5 AA) and a protein (130 AA). How can I do a screening of this
protein with my sequence to research potential homologuous sequences.

Thank you very much !

best regards

Renato Froidevaux, HDR
Laboratoire de Procédés Biologiques, Génie Enzymatique et Microbien
(ProBioGEM)-
UPRES EA 1026
IUT"A"-Polytech'Lille-USTL
Boulevard Paul Langevin - Cité Scientifique
59 655 Villeneuve d'Ascq Cedex
Tel: +33 (0)3 20 41 75 66
Fax: +33 (0)3 28 76 73 56



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