[Chimera-users] Models or chain

Elaine Meng meng at cgl.ucsf.edu
Sun Aug 31 10:53:26 PDT 2008

Hi Hernando,
As mentioned you can't do it in Chimera.  You would need to find some  
other program or server that does it (unfortunately I don't know of  
any ...  other chimera-users, opinions?)  or just write a script.   
Depending on how robust to different types of input it must be, the  
script could be fairly simple.

I attach a little fortran program 'multichain.f' I just whipped up.   
If you are on some unix-type computer with a fortran compiler, you  
could just compile it with something like

f77 multichain.f -o multichain

then just enter multichain or whatever you called the executable at  
the command line, and it would prompt you for input and output file  

This program worked fine on the one NMR ensemble I tested it on, but  
I did not test it comprehensively.  It is pretty simple and does not  
change any atom or residue numbers, and does not add SEQRES, so if  
you need that stuff you would need to use something else.  I only  
provided for up to 26 chains because I couldn't remember what IDs  
aresupposed be used after that, but it could easily be modified to  
accommodate more chains.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 31, 2008, at 6:54 AM, hsosa at aecom.yu.edu wrote:

> Hi Elaine,
> The problem  I have is actually not whith chimera. itself.  I can  
> display all the models etc nicely within it.  However, I want to  
> make now a PDB file of a multi-protein complex in a format that can  
> be deposited in the PDB database. Then I run into problems if the  
> models are separated by Model ENDMDL lines or have chains with the  
> same letter identifier. I was hoping to be able to generate a   
> multi-protein  PDB file from  my chimera fitting without having to  
> manually edit a lot of lines in the multimodel PDB file. Any  
> suggestions on how to best do this would be appreciated.
> Thanks
> Hernando
> Elaine Meng wrote:
>> Hi Hernando,
>> Sorry, Chimera does not have an option for changing chain IDs.
>> However, in Chimera I find it more convenient to work with  
>> structures read as multiple models as opposed to multiple chains  
>> in a single model:

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