[Chimera-users] Alteration of C-terminal AA-sequence within an X-ray model data set with Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 14 11:05:44 PDT 2011

Whoops, I just realized that "Fit in Map" also has an option to fit only the selected atoms.  Thus it is not necessary to do any deleting or combining as described for (B), which makes it much simpler.  

Sorry about that!  However, the problems (1) and (2) mentioned below still apply.

On Apr 14, 2011, at 11:01 AM, Elaine Meng wrote:

> Dear Heinrich,
> I can think of a couple possibilities.  First you would open the structure and the density map.  Opening the density map will automatically start Volume Viewer, in which you can adjust the display type (surface, mesh, etc.) and contour level by moving the slider on the histogram.  
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf>
> Then...
> (A) you could select those 30 residues, then use "Movement Mouse Mode" (under Tools... Movement) "move selection" option to manually reposition them.   However, that would not automatically fit the residues to density, it would just let you rotate and translate them as a rigid body yourself with the mouse, which can be difficult if you are trying to dock into density.  The selecting could be done in several ways, such as by command (e.g. "select #0:356-end.a" to select model 0 chain A residues 356 to the end) or interactively in the Sequence tool (under Favorites in the menu).  After the movement you could save the modified structure with "File... Save PDB" in the Chimera menu or the "write" command, and you would probably want to save "relative to" the map model.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
> (B) you could make those 30 residues a separate model and then automatically fit them as a rigid whole into the density using "Fit in Map" (under Tools... Volume Data).   You would delete the rest of the structure, for example with command "delete ~#0:356-end.a"  to delete all atoms EXCEPT model 0 residues 356-end in chain A.  Next, using the mouse, manually move it to an approximate position relative to the map.  You can freeze the map and move only the structure by un-checking the "Active" box for the map model below the Command Line or in the Model Panel (both tools are under Favorites in the menu).  Then use Fit in Map, which will perform a local optimization.  You may want to run it a few times to see if the result improves.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html>
> Saving a whole model is less convenient than in (A).  You would need to open another copy of the structure, delete the opposite part (e.g. command "delete #0:356-end.a") and probably also fit that one into the density.  You could either save both as PDB relative to the map model and then manually combine them into one PDB file, or in Chimera merge the models (see command "combine" or the "copy/combine" function in the Model Panel), possibly add the bond if you need it (see command "bond" or the Build Structure tool) and then save the PDB of the combined model relative to the map model.
> Even if method (B) is not too long for you, I can think of two problems:
> (1) It is not flexible fitting.  Each part is treated as a rigid body, and you have to decide yourself how to split a structure into parts.
> (2) The parts do not "see" each other, there is nothing to stop them from bumping into each other or even going to the same place in the density map.   In the Chimera daily builds, we have recently added a tool that addresses this problem:  MultiFit (under Tools... Volume Data) will perform simultaneous fitting of multiple rigid structures.  However, it currently assumes overall Cn (cyclic) symmetry, so it cannot be applied to your problem.   We hope to have it working for structures without cyclic symmetry soon, but that is not yet available.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multifit/multifit.html>
> 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 Apr 14, 2011, at 2:01 AM, Heinrich Lünsdorf wrote:
>> Dear Elaine,
>> here I'm again to ask for your constructive help on another item. My question: Is it possible with Chimera functions and commands to pick up and activate an AA-sequence, i.e. the last 30 C-terminal AAs, and to 'move'  or 'bend' them in parts or as a whole but without changing or moving the rest of the X-ray model to get the C-terminal AA-tail fit along with an overlaid EM-density model?? Can such alterations be stored for the original X-ray model?
>> Thank you cordially for your help in advance.
>> Sincerely yours,
>> Heinrich
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