[Chimera-users] move a structure into another one

Francesco Pietra chiendarret at yahoo.com
Sun Nov 18 10:16:36 PST 2007

--- Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Francesco,
> Chimera does not have any option to create a lipid bilayer.

That I can make for POPC with VMD

  If you 
> have a bilayer structure already, open as a different model, you can 
> move the protein and bilayer individually by activating/deactivating 
> them for motion.   Then you would have to delete lipid molecules that 
> overlap the protein manually before saving to a file.

Manually graphically? Neither the POPC molecules nor the water molecules
embedded in have a number, only detectable on file through their xyz values. I
understand that there is no trick to delete around the protein, by say 1A

>  In other words, 
> there is no automatic embedding of a structure in a membrane or a 
> solvent box.
> about activating/deactivating for motion:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef
> about writing a PDB file:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb
> Note even if you save to a single file, the models will still be 
> treated as separate models.  You would still have to manually edit the 
> file to get everything into one model, avoiding use of duplicate atom 
> numbers, etc.

Combining can be easily done with xleap in Amber. Already tried successfully,
getting top/crd for the whole as a single unit. As that of the bilayer is a
step after docking to run MD with Amber, that is OK.


> Best
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> On Nov 18, 2007, at 8:26 AM, Francesco Pietra wrote:
> > I have installed chimera-1.2470 on Debian Linux i386. Thank you.
> > I want to insert a protein into a lipid membrane in a precise 
> > opientation, then
> > save the protein pdb in this configuration.
> > I used VMD in the last few days to this redard. I wonder whether I can 
> > stick to
> > Chimera for this purpose too. I tried by selecting "protein", though 
> > it was
> > difficult to proceed.
> > Thanks
> > francesco pietra

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