[Chimera-users] hide a peptide in Chimera

C.J. biocjh at gmail.com
Fri Jul 29 05:16:35 PDT 2011

thank you.

2011/7/29 Elaine Meng <meng at cgl.ucsf.edu>:
> I forgot to mention that if the peptides are shown with ribbons and/or surfaces, those would be handled separately from the atoms and bonds.
> My previous reply described using "Actions... Atoms/Bonds... hide" or command "~display" for hiding the atoms and bonds.  Analagously you could use "Actions... Ribbon... hide" or command "~ribbon" for ribbons, and "Actions... Surface... hide" or command "~surface" for molecular surfaces.
> Another point is that the most convenient way to specify or select the individual peptides depend on how they are described in the PDB files.  They could be different chains, as mentioned in my previous message, or they could be different submodels, as is often the case for NMR structures in the PDB.  If they are different submodels, you could simply uncheck the S or Shown boxes in the Model Panel to hide them.  The Model Panel is in the Favorites menu.
> Elaine
> On Jul 28, 2011, at 8:36 AM, Elaine Meng wrote:
>> Hi C.J.,
>> There are many ways to hide specific atoms.  For example,
>> (A) use menu "Actions... Atoms/Bonds... hide" after selecting the atoms you want to hide.
>> There are several ways to select atoms, for example
>> (i) Ctrl-click on an atom or bond in the peptide, then up arrow key to expand to whole residue, then whole chain. The selection is shown with green highlighting.
>> (ii) use the "Select" menu, perhaps a particular chain
>> ... or ...
>> (B) use command "~display" with specification of the atoms you want to hide.  For example, to hide chain A:
>> ~disp :.a
>> Here is info on command-line atom specification:
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
>> You may want to take a look at the "getting started" tutorials:
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
>> <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.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 Jul 28, 2011, at 2:05 AM, C.J. wrote:
>>> Hi,all,
>>> I have a pdb file containing several peptides. And I want to hide some
>>> of them when visualizing the file in Chimera.
>>> Anyone would like to help me to that?
>>> I'm appreciated of any suggestions.
>>> --
>>> Regards!
>>> C.J.
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