Read PSF+DCD combo directly

[eackad@…]

Given the difficulty of creating a PDB for a large system in some cases (e.g. CHARMM-GUI uses ambiguous hex serial numbers), allow reading a PSF/DCD combo directly

[pett]

Tomorrow's daily build will support the command "open <PSF file> coords <coordinate file>".

Will get the Open dialog to support it in the next day or so.

[pett]

PSF files can now be opened by File→Open, and the coords keyword is optional (a browser will appear for the coordinates file).

[eackad@…]

This was really helpful! If I may suggest some improvements:
1) A way to choose first, last and skip (number of frames to skip) since
trajectory files can be large
2) A way to select only some of the elements to be loaded (protein only, no
water, no ions, etc to conserve mem)
3) A way to align w.r.t. a frame of a model

Thanks again!
Eddie


On Fri, May 21, 2021 at 2:07 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[pett]

In most cases we are using third-party code to read the coordinates file, so our ability to skip reading certain parts is frequently limited.


Some formats offer direct control over this, and for others we would have to at least temporarily read the whole thing and then cut down what gets used in a post-processing step.


Pretty awkward to both implement and to offer a user interface for.  Would be nice though.  The best bet for now is to pre-process the trajectory externally before using it in ChimeraX.


We do intend to offer this, along with a whole bunch of capabilities that Chimera had that are still missing from ChimeraX.

I will open separate enhancement-request tickets for these so that you will receive notifications when they get implemented.

--Eric