[Chimera-users] Aligning a protein into a membrane

Francesco Pietra chiendarret at yahoo.com
Thu Nov 22 03:08:53 PST 2007

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

> On Nov 21, 2007, at 1:14 PM, Francesco Pietra wrote:
> > Elaine:
> > Most sorry that you had to repeat. I succeeded now, with still a  
> > problem. I.e,
> > the membrane lipid (POPC) is hydrated at the head (this is how it  
> > can be built
> > with the plugin). Those molecules of water are still in the space  
> > cleaned from
> > lipid molecules, i.e. they superimpose the protein.
> >
> > I am not sure if such water should be removed before solvating the  
> > system,
> > adding ions and MD. If it should be removed, is is another command?
> You would just use the same approach as for the lipid molecules -  
> find some way of selecting the residues you don't want (using a  
> distance cutoff from the protein atoms) and then delete them.  Try  
> different selecting commands similar to what I sent before and see if  
> they select what you want.  It is not possible to give the exact  
> command without knowing all the details of your system.

I tried a lot of different combinations, without picking the right one, in
order to remove water from only the zone from where POPC molecules are removed.
I changed selections in Taskbar .. Select ... Zone, as if they were reflected
to  the command-line command or not. In all cases, it was only the command
command-line command

select #0 & #1 z<1.5

that worked. Of course, select solvent .. delete did not work, all WAT residues
were removed. That is, I don't understand is how "select" of command "select #0
& #1 z<1.5" operates, i.e. why it only recognizes POP residues and not WAT
residues in the membrane pdb. I tried to remove TER records, and even renaming
WAT: in any case, only POPC were removed.

> >
> > Before posting, I have now checked the saved file for the membrane.  
> > Probably
> > there is a more serious problem: all "TER" records inserted between  
> > the POPC
> > residues and between the WAT residues have been removed on saving  
> > (using "Save
> > relative to model"). That will create problems to Amber, unless  
> > lack of TER
> > records is accounted for by the CONECT records added (in the  
> > membrane pdb file
> > from the plugin I had to add all mentioned TER records to have the  
> > file
> > accepted by Amber)
> It is technically correct to remove the TERs between HETATM residues,  
> since HETATM residues in PDB format are not connected to each other  
> unless there are CONECT records that say they are connected.

All atoms, for both POPC molecules and water molecules, are called ATOM. This
was done by the plugin. (if this matters).


> However, AMBER may need the technically incorrect format (sounds like  
> it does), and you may just have to put the TER lines in yourself or  
> write a script to do that.
> Best
> Elaine

Get easy, one-click access to your favorites. 
Make Yahoo! your homepage.

More information about the Chimera-users mailing list