[Chimera-users] Picking from list?

[Tom Goddard]

Hi Martin,

  A user interface panel that lists residues is a pretty easy tool for a student with some Python programming skills to add.  We have a ChimeraX app store called Toolshed that allows anyone to distribute just this kind of simple plugin that can be installed into ChimeraX using its Tools / More Tools... menu entry with a simple "Install" button click.

	https://cxtoolshed.rbvi.ucsf.edu <https://cxtoolshed.rbvi.ucsf.edu/>

We welcome contributions like that.

	Tom

Swiss PDBViewer control panel:


> On Apr 21, 2020, at 10:53 PM, Martin Mielke <m_mlk at yahoo.com> wrote:
> 
> Hi Elaine!
> 
> Thanks for your prompt reply and the explanations.
> 
> Still, I would like to ask/know: are there any plans to implement such a panel/feature in the near future? If not, would you guys be willing to add it to the development roadmap? :-) This is one of the main reasons to keep using SPDBV, and the main motivation to search for an alternative such as UCSF Chimera is that SPDBV fails at exporting selections correctly, the last column on the right is not added so it is near impossible to distinguish between a C-alpha and Ca, for example... hence the last column is important for some stuff I am coding :-)
> 
> Thanks once again in advance!
> 
> Best regards,
> 
> Martin
> 
> 
> On 2020-04-21 18:05, Elaine Meng wrote:
>> Hi Martin,
>> The Model Panel (open from Favorites menu) lists the models, but it does not list all the chains, residues, etc.  So I believe the short answer to your question is no.  Using the Select menu, you can select whole chains, or all residues of a given type (ALA etc.), functional groups, atoms of a specific element, etc.  If you want to choose ranges or individual residues from the sequence of a chain, you can do that in the Sequence window (open from Favorites menu).
>> 
>> This page explains what selection is for and lists some of the common ways:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
>> 
>> You can name the current selection using "Name Selection..." in the Select menu, after which that name will also be listed in the Select menu (under Named Selections) so you can easily get it back.
>> 
>> Usually once somebody becomes familiar with Chimera, they can just specify the targets directly in the command line without using selections, e.g.:
>> 
>> color red,r #0:24-58.A,35.B
>> 
>> model 0, residues 24-58 in chain A, 35 in chain B
>> 
>> See command-line atom specification:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> P.S. if you use the structureViz plugin to Cytoscape, I believe its interface to Chimera is more similar to what you showed in SPDBV.  However, access to other Chimera features is more limited, and it is intended mainly for those viewing protein-protein networks in Cytoscape.
>> 
>>> On Apr 21, 2020, at 4:54 AM, Martin Mielke <m_mlk at yahoo.com> wrote:
>>> 
>>> Dear all!
>>> I am new to Chimera so please accept my apologies in advance if this has been discussed previously.
>>> 
>>> I have read in the documentation
>>> https://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html that Chimera features the "pick on screen" function.
>>> 
>>> So far, so good.
>>> 
>>> Now, I was wondering if there is also an equivalent for the "Control Panel" featured in the Swiss PDB-Viewer. It can be seen here: https://spdbv.vital-it.ch/main_guide.html
>>> 
>>> It allows for a, maybe, more granular cheery-picking from a list. Selections can later be exported as PDB.
>>> Thanks in advance!
>>> 
>>> Best regards,
>>> Martin
>>> 
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