[chimerax-users] Alternate locations

[Jeschke Gunnar]

Hi Eric,

> I could add you to the recipient list for that ticket if you'd like

Yes, please do so.

Thanks and kind regards

Gunnar

---

Der Schlaf der Vernunft gebiert Ungeheuer - Francisco Goya

Prof. Dr. Gunnar Jeschke
ETH Zurich
Department of Chemistry and Applied Biosciences
Vladimir-Prelog-Weg 2
CH-8093 Zurich Switzerland

www.epr.ethz.ch

________________________________________
From: Eric Pettersen [pett at cgl.ucsf.edu]
Sent: Monday, July 27, 2020 7:50 PM
To: Jeschke  Gunnar
Cc: ChimeraX Users Help
Subject: Re: [chimerax-users] Alternate locations

Hi Gunnar,
It looks like MMMx will be pretty useful!  We also intend to implement a REST interface that is more machine friendly, in that you don't have to parse free text to extract return values.  We have a ticket open for that here: #1534 (Machine-friendly REST interface)<https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1534>.  I could add you to the recipient list for that ticket if you'd like.

--Eric

On Jul 24, 2020, at 10:25 AM, Jeschke Gunnar <gunnar.jeschke at phys.chem.ethz.ch<mailto:gunnar.jeschke at phys.chem.ethz.ch>> wrote:

Hi Eric,

thanks a lot for the fast answer. In fact, the solution is very logic. I could or even should have guessed it.

For me this completely suffices, as my application communicates with ChimeraX via REST by commands and by parsing the response (I know that the response format is not explicitly specified, but I can live with that).

My own application is only at design stage, but it also derives from an earlier project (MMM, a Matlab package that had its own slow visualization and is used by a much smaller community).

I want to adopt ChimeraX as visualization engine and also for retrieving or saving information beyond only coordinates from/to PDB and mmCIF. I might use functionality beyond that, certainly the DSSP implementation.

Just in case that you are curious, my current (and continuously updated) design document is at GitHub (some abuse of GitHub, as I store the HTML rather than the .rst source):

https://github.com/gjeschke/MMMx

Thanks again for your nice work and incredible response time

Gunnar

---

Der Schlaf der Vernunft gebiert Ungeheuer - Francisco Goya

Prof. Dr. Gunnar Jeschke
ETH Zurich
Department of Chemistry and Applied Biosciences
Vladimir-Prelog-Weg 2
CH-8093 Zurich Switzerland

www.epr.ethz.ch

________________________________________
From: Eric Pettersen [pett at cgl.ucsf.edu]
Sent: Friday, July 24, 2020 5:21 PM
To: Jeschke  Gunnar
Cc: chimerax-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] Alternate locations

Hi Gunnar,
       Glad you like the program!  Our experience with the design of Chimera and Midas before it allowed us to identify what we felt was good and what we felt could be improved, and ChimeraX has benefited from that in many ways.
       The handling of alternate locations was one of the things that changed between Chimera and ChimeraX.  In Chimera, each alternate location was treated as a completely separate atom, and therefore they were all displayed at once, but the flip side of that is that it made some kinds of chemical computations much uglier in that it was much more work to figure out how many bonds a specific atom had if its neighbor atoms had alternate locations.  In ChimeraX, there is only one atom, which can have several alternate locations.  You switch between them by setting the atom's alternate location identifier, which will not only switch that atom's location, but all related nearby alternate locations so that the set of alternate locations are consistent.
       We haven't developed a user interface to alternate locations yet, so the only way to set the alternate location (outside of Python code) is with the "setattr" command.  So to set your example atom's alternate location to 'B' the command would be:

       setattr /A:8 at NE2 a alt_loc B

(FYI, assuming the structure has no lower-case chains, both the chain ID and atom name could be typed in lower case)

       You don't describe what you will be using the alternate locations for, but if you did that might help shape the design of the user interface that we eventually develop for alternate locations.

--Eric

       Eric Pettersen
       UCSF Computer Graphics Lab


On Jul 23, 2020, at 11:07 PM, Jeschke Gunnar <gunnar.jeschke at phys.chem.ethz.ch> wrote:

Hi ChimeraX team,

very nice program and remote control scheme! Clear thinking, cool implementation.

My question/suggestion is about alternate atom locations. ChimeraX knows about them.

I load 1lcd

info atoms /A:8 at NE2 attribute alt_locs

correctly responds:

atom id /A:8 at NE2 alt_locs A,B

When I show /A:8 at NE2 or I show /A:8 as sticks, only location A is displayed. When I retrieve atom coordinates, only location A is returned.

Could you implement full handling of alternate locations (or am I doing something wrong here? I really tried a lot to find location B).

Kind regards

Gunnar

---

Der Schlaf der Vernunft gebiert Ungeheuer - Francisco Goya

Prof. Dr. Gunnar Jeschke
ETH Zurich
Department of Chemistry and Applied Biosciences
Vladimir-Prelog-Weg 2
CH-8093 Zurich Switzerland

www.epr.ethz.ch

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