[Chimera-users] Visualisation of membrane proteins

[Elaine Meng]

Hi James,
Personally I would not recommend changing it from the OPM-predicted location.  The GPCR is not itself symmetrical, and if you change the relationship between the protein and the membrane, you can no longer say that you are using the OPM prediction, which is based on the physicochemical properties of the atoms. See:
<http://opm.phar.umich.edu/about.php?subject=methods>

In other words, you could be making it prettier but more likely to be inaccurate.

However, if you are sure you want to change it, I think you’d have to split and move things manually.  At first I thought there might be another way using Axes/Planes/Centroids and the “align” command, but it didn’t work because it moves everything  (it wouldn’t move protein and membrane separately even if they were separate models).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/align.html>

I hope this helps,
Elaine

> On Feb 15, 2017, at 7:00 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> Thanks so much Elaine for very usefull tips!
> 
> One question - is it possible to align resulted structure (e.g againts
> its principal axes) with the membrane plane to be sure that it is
> represented symmetrically? E.g as you can see on the enclosed picture
> that the membrane plane looks not absolutely symmetrical in all
> directions and it's tricky to fix it manually.
> 
> James
> 
> 2017-02-14 21:31 GMT+04:00 Elaine Meng <meng at cgl.ucsf.edu>:
>> Hi James,
>> (1) The easiest way to allow moving the ligand separately from the receptor is to put them in two different models. You could use the “split” command.  For example, if the structure is model #0 and your ligand is residue XYZ, command:
>> 
>> split #0 atoms :xyz
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
>> 
>> You would still need to delete any other stuff you didn’t want, like water molecules.  Or, you could open the same structure twice and in one copy, delete everything except your ligand, and in the second copy, delete everything except the receptor.  Then when you have two separate models, it is simple to move them separately.  Show Model Panel (from Favorites menu) and use the “A” checkboxes to deactivate (freeze) one while you move the other one with the mouse.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
>> 
>> You can also do fancy things like save different positions of the ligand and then show it moving from one position to another (see commands savepos, reset, and fly).
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>
>> 
>> (2) there is no tool specifically to create some membrane representation.  However, I like to use the OPM database (Orientations of Proteins in Membranes)
>> <http://opm.phar.umich.edu/>
>> ...which has downloadable PDB files of membrane proteins with additional fake atoms showing the estimated plane of the membrane.  If you open one of these you can see all the fake atoms, and you can show them as balls or, as I have done in this image, use the Chimera Axes/Planes/Centroids tool to show planes (discs) calculated from the fake atoms.
>> <http://www.rbvi.ucsf.edu/chimera/features.html#axesplanes>
>> 
>> Your specific receptor may not be in this database, or even if it is, the coordinates may be moved.  However, if you get the OPM structure for that protein or just a related protein, you can use matchmaker to superimpose the two, and then hide the protein part of the OPM file, showing just the membrane representation.
>> 
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Feb 14, 2017, at 6:03 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>> 
>>> Dear Chimera users!
>>> 
>>> I am on the preparation of interactive molecular visualisation,
>>> focusing on ligand-binding representation in GPCRs system.
>>> Working with the X-ray structures of the receptor bound with the
>>> ligand, I wonder to ask some suggestions:
>>> 
>>> 1 - I need to move ligand from ligand binding pocket burried within
>>> receptor (as on default in the X-ray structure) towards the selected
>>> position outside of it - e.g in case where I would like to depict
>>> "vestibule" for the ligand enterance. As I understood for the
>>> realisation  I should to select ligand within the current model and
>>> than to copy it to new model (layer) which then should be moved
>>> against the structure, shouldn't it?
>>> 
>>> 2- Is it possible using some Chimera tool to indicate "approximate"
>>> membrane plane assuming that GPCRs structure is shown in latteral
>>> perspective?
>>> 
>>> Thanks so much for the help!
>>> James
>>> 
>> 
> <test777a.png>