'open' syntax problem

[santiago.jus.are@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
I am not able to identify why the argument coord does not recognize the true

command:
open C:\Users\Santiago\Escritorio\gromacs\protein_md_corrected.xtc coord true structureModel #1 

error:
'coord' has no suffix

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/Santiago/Escritorio/gromacs/protein_md_5ns.pdb

Summary of feedback from opening
C:/Users/Santiago/Escritorio/gromacs/protein_md_5ns.pdb  
---  
warning | Ignored bad PDB record found on line 302669  
END  
  
Chain information for protein_md_5ns.pdb #1  
---  
Chain | Description  
| No description available  
  

> open C:\Users\Santiago\Escritorio\gromacs\protein_md_corrected.xtc coord
> true structureModel #1

'coord' has no suffix  




OpenGL version: 3.3.0 NVIDIA 388.16
OpenGL renderer: GeForce GTX 1060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Acer
Model: Predator G3-572
OS: Microsoft Windows 10 Home Single Language (Build 18362)
Memory: 17,057,812,480
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Eric Pettersen]

Hi Santiago,

The "coord true" argument is only legal when opening a multi-model PDB or mmCIF file and you want it to open as a trajectory rather than individual models. It is not legal when opening an .xtc file. So, just omit it from your open command: "open C:\Users\Santiago\Escritorio\gromacs\protein_md_corrected.xtc structureModel #1".
Since "coord true" wasn't legal, the open command interpreted "coord" as another file name that you wanted to open, which is why you got the error you did.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[santiago.jus.are@…]

Is there a form in ChimeraX to plot distance between atoms by frame in a
trajectory as in Chimera?


El jue., 6 ago. 2020 1:09 p. m., ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
escribió:

[Eric Pettersen]

MD analysis is one of the areas where ChimeraX is still far behind Chimera. The only "builtin" things you can do with a trajectory is play it back and record it as a movie. You could use a combination of the "coordset", "perframe", and "distance save" commands to write a series of files with distance information for each frame.

--Eric

[santiago.jus.are@…]

ok, thank you very much for the indication

Em qui., 6 de ago. de 2020 às 11:53, ChimeraX <
ChimeraX-bugs-admin@cgl.ucsf.edu> escreveu: