[Chimera-users] Aligning a protein into a membrane
chiendarret at yahoo.com
Thu Nov 22 09:22:48 PST 2007
--- Elaine Meng <meng at cgl.ucsf.edu> wrote:
> On Nov 22, 2007, at 3:08 AM, Francesco Pietra wrote:
> > 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.
> Hi Francesco,
> The example command above means: select atoms that are (1) in model 0
> AND (2) that are in residues with any atom within 1.5 angstroms of
> model 1. Perhaps your POPC molecules are in model 0 and your water
> molecules are not.
As I wrote, the plugin furnishes the membrane with the lipid molecules hydrated
at the polar head. The pdb (all atoms ATOM) is a series of POPC residues
alternated with series of WAT residues (as I renamed them, because they call
them TIP3). I even exchanged the names, calling POP the water residues and WAT
the lipid residues: still the water in the area freed from the lipid. This is
why I asked what is "select" addressing.
>Hopefully your protein is model 1.
Absolutely it is.
> You could try
> ":wat" instead of "#0" but I recommend spending a little time to
> understand command-line atom specification, which will allow to you
> generalize to your different situations. There are some examples on
> the second page of the PDF "quick reference"
> and this is the User's Guide page (see especially the parts about zones
> and combinations):
I'll try also all that. I am replying just to assure you that - although naive
and primitive - before asking for help I am reflecting.
> > All atoms, for both POPC molecules and water molecules, are called
> > ATOM. This
> > was done by the plugin. (if this matters).
> > Thanks
> > francesco
> I am not sure what you mean by "plugin" (VMD plugin?)
Yes, VMD, the only one I am aware of.
> but I believe
> they are supposed to be HETATM in the file written out by Chimera.
Yes, they are renamed HETATM by Chimera.
> Maybe they are only HETATM when combined with the protein in a single
> file. Either way, it may still be necessary for you to edit the file
> depending on what AMBER needs, sorry.
Having to use more than one "house" in this case, I am becoming more patient
than usual. Luckily, it is easy to write Python scripts for modifying the
files. I came to Python just for that and it was an extraordinary encounter.
> 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
Be a better pen pal.
Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/
More information about the Chimera-users