[Chimera-users] move a structure into another one
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
> 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:
> about writing a PDB file:
> 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.
> 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
> 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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