Hello, I want to move a mrc near another mrc from terminal controlled, the problem is that I don't know how ChimeraX defines the center point of movement when loading a mrc file. So I wanted to know if you can explain to me that ChimeraX defines the X, Y, Z coordinates in which it will load the center of the cube? Best regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98
Hi Luis, MRC files define an origin in the binary file header. Sometimes that origin is the center of the box, sometimes the lower left corner, sometimes in different position. ChimeraX uses the center defined within the MRC file. If you open the file in ChimeraX then you can see the origin used with menu Tools / Volume Data / Map Coordinates. The "Origin index" indicates the grid index where x,y,z = 0,0,0 (Angstrom units usually). In the example below it lists the index as 0 (which is shorthand for 0,0,0 since it is the index in 3 dimensions), meaning for this MRC file the origin was the lower left corner of the file. The origin index could be changed with a ChimeraX command, e.g. "volume #1 originIndex 191.5,191.5,191.5" to move x,y,z = 0,0,0 to the center of the box where this map has 384 by 384 by 384 grid points. All ChimeraX commands like moving a model with the move command use physical coordinates (Angstroms), not grid indices. Tom
On Aug 20, 2020, at 10:41 AM, Luis José Castillo Valverde <luis.castillo.valverde.98@gmail.com> wrote:
Hello,
I want to move a mrc near another mrc from terminal controlled, the problem is that I don't know how ChimeraX defines the center point of movement when loading a mrc file. So I wanted to know if you can explain to me that ChimeraX defines the X, Y, Z coordinates in which it will load the center of the cube?
Best regards,
Luis --
Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hello, when a I save several models in a single mmcif file and I need to open it for a different purpose in ChimeraX it appears as a group with several submodels. Does anyone know how to convert this group in a single structure with no submodels? Otherwise, how can I save them to have a single model?. I used to use copy/combine in Chimera but I cannot find anything similar in ChimeraX. Thank you very much in advance: MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez@cnb.csic.es
Hi Marta, ChimeraX does not yet have this feature, sorry. Currently it is listed in the missing features section of the ChimeraX download page, and it is on the "to do" list, but I'm told is not likely to happen very soon given the many things on the list. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 24, 2020, at 11:02 AM, Marta Martinez <mmmtnez@cnb.csic.es> wrote:
Hello, when a I save several models in a single mmcif file and I need to open it for a different purpose in ChimeraX it appears as a group with several submodels. Does anyone know how to convert this group in a single structure with no submodels? Otherwise, how can I save them to have a single model?. I used to use copy/combine in Chimera but I cannot find anything similar in ChimeraX.
Thank you very much in advance: MARTA -- Marta Martinez Gonzalez
There is a basic merge-models implementation in the latest ISOLDE release (still for ChimeraX 1.0 - a bit swamped right now but I'll hopefully be able to get updated builds out soon). Once ISOLDE's started, you'll see a new entry ("ISOLDE") in the top menu bar. The menu entry ISOLDE/Model Building/Merge Models will merge all currently-selected atomic models (that is, all models that have at least one atom selected), renaming chains as necessary to avoid conflicts. Note that rather than merging into a new model, the first model in the list will be extended to include the atoms from the others. To the ChimeraX team: you're welcome to the code behind this, if you find it useful! -- Tristan ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Elaine Meng <meng@cgl.ucsf.edu> Sent: 24 September 2020 19:27 To: Marta Martinez <mmmtnez@cnb.csic.es> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Transform a group in a single structure Hi Marta, ChimeraX does not yet have this feature, sorry. Currently it is listed in the missing features section of the ChimeraX download page, and it is on the "to do" list, but I'm told is not likely to happen very soon given the many things on the list. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 24, 2020, at 11:02 AM, Marta Martinez <mmmtnez@cnb.csic.es> wrote:
Hello, when a I save several models in a single mmcif file and I need to open it for a different purpose in ChimeraX it appears as a group with several submodels. Does anyone know how to convert this group in a single structure with no submodels? Otherwise, how can I save them to have a single model?. I used to use copy/combine in Chimera but I cannot find anything similar in ChimeraX.
Thank you very much in advance: MARTA -- Marta Martinez Gonzalez
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participants (5)
-
Elaine Meng -
Luis José Castillo Valverde -
Marta Martinez -
Tom Goddard -
Tristan Croll