Allow specifying frame start, stop and step when opening DCD trajectory to limit memory use

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202105180049 (2021-05-18 00:49:36 UTC)
Description
When opening a DCD file it would be handy to be able to specify start, stop, and step frame parameters so that the whole possibly enormous file does not need to be read into memory.  Big trajectories are common.

The case I am looking at now is a 5 Gbyte DCD file which causes ChimeraX to use 13 Gbytes of memory.

Log:
UCSF ChimeraX version: 1.3.dev202105180049 (2021-05-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/Downloads/6vsb_1_1_1.pdb

Chain information for 6vsb_1_1_1.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> show atoms

> select all

72990 atoms, 74307 bonds, 4407 residues, 1 model selected  

> select clear

> select ligand

14040 atoms, 14559 bonds, 588 residues, 1 model selected  

> select clear

> open /Users/goddard/Downloads/6vsb_1_1_2.pdb

Chain information for 6vsb_1_1_2.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vsb_1_1_1.pdb, chain C (#1) with 6vsb_1_1_2.pdb, chain C (#2),
sequence alignment score = 6588.2  
RMSD between 1233 pruned atom pairs is 0.176 angstroms; (across all 1273
pairs: 1.351)  
  

> hide #1 models

> show #1 models

> hide

> show ligand

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> style ligand sphere

Changed 28080 atom styles  

> close #2

> usage open

open names [format format] [fromDatabase fromDatabase] [name a text string]
[format/database-specific arguments]  
— read and display data  
names: file names to open; a name of 'browse' will bring up a file browser  
format: one of aln, amber, amira, apbs, bild, brix, ccd, ccp4, cellpack, cmap,
cmd, collada, com, compiled python, cube, dat, dcd, defattr, delphi, dicom,
dock, dsn6, dv, emanhdf, fasta, fchk, fsc, gltf, gopenmol, gro, hdf, hssp,
html, ihm, images, imagic, imod, imodmap, ims, log, macmolplt, markers, mmcif,
mmtf, mol2, mrc, msf, mtz, netcdfmap, obj, out, pdb, pdbqt, pfam, photo, pif,
pir, positions, priism, profec, pseudobonds, python, rmf, rsf, schrodinger
maestro, sdf, segger, session, sff, situs, smiles, spider, stl, stockholm,
storm, swc, tom_em, trr, uhbd, uniprot, vtk, web fetch, xplor, xtc, or xyz  
fromDatabase: one of ccd, cellPACK, eds, edsdiff, emdb, ftp, help, http,
https, pdb, pdbdev, pdbe, pdbe_bio, pdbj, pubchem, rcsb_bio, smiles, or
uniprot  
format/database-specific arguments: format- or database-specific arguments; to
see their syntax use 'usage open format format' or 'usage open database
database' commands respectively, where format and database are as per the
above  

> usage open format dcd

open names [structureModel a structure specifier] [replace true or false]  
— read and display data  
names: file names to open; a name of 'browse' will bring up a file browser  

> close

> open /Users/goddard/Downloads/6vsb_1_1_1_traj_dcd/initial/prot_gly_memb.pdb

Summary of feedback from opening
/Users/goddard/Downloads/6vsb_1_1_1_traj_dcd/initial/prot_gly_memb.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG)  
  
Ignored bad PDB record found on line 2  
REMARK INPUT FILES FOR EQUILIBRATION  
  
Ignored bad PDB record found on line 3  
REMARK DATE: 8/30/20 22:40:33 CREATED BY USER: kyo  
  
Ignored bad PDB record found on line 332716  
TER 332713 DPPS 2342  
  
Chain information for prot_gly_memb.pdb #1  
---  
Chain | Description  
? | No description available  
  

> open /Users/goddard/Downloads/6vsb_1_1_1_traj_dcd/initial/prot_gly_memb.pdb

Summary of feedback from opening
/Users/goddard/Downloads/6vsb_1_1_1_traj_dcd/initial/prot_gly_memb.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG)  
  
Ignored bad PDB record found on line 2  
REMARK INPUT FILES FOR EQUILIBRATION  
  
Ignored bad PDB record found on line 3  
REMARK DATE: 8/30/20 22:40:33 CREATED BY USER: kyo  
  
Ignored bad PDB record found on line 332716  
TER 332713 DPPS 2342  
  
Chain information for prot_gly_memb.pdb #2  
---  
Chain | Description  
? | No description available  
  

> close #2

> open /Users/goddard/Downloads/6vsb_1_1_1_traj_dcd/trj_nos.dcd

Must specify a structure model to read the coordinates into  

> open /Users/goddard/Downloads/6vsb_1_1_1_traj_dcd/trj_nos.dcd structureModel
> #1

Replaced existing frames of prot_gly_memb.pdb #1 with 1283 new frames  

> coordset slider #1

> select all

332712 atoms, 324902 bonds, 6757 residues, 1 model selected  

> select clear

> select ligand

272003 atoms, 264355 bonds, 2938 residues, 1 model selected  

> select :POPE

52875 atoms, 50219 bonds, 423 residues, 1 model selected  

> select :POPE,PSM

112565 atoms, 107377 bonds, 893 residues, 1 model selected  

> select :POPE,PSM,POPC

131459 atoms, 125467 bonds, 1034 residues, 1 model selected  

> select :POPE,PSM,POPC,DPPE

165581 atoms, 157876 bonds, 1316 residues, 1 model selected  

> select :POPE,PSM,POPC,DPPE,POPS

183488 atoms, 174986 bonds, 1457 residues, 1 model selected  

> hide :POPE,PSM,POPC,DPPE,POPS

> hide :POPE,PSM,POPC,DPPE,POPS,DPPS

> hide :POPE,PSM,POPC,DPPE,POPS,DPPS,CHL1

> hide :POPE,PSM,POPC,DPPE,POPS,DPPS,CHL1,DPPC

> lighting soft

> lighting full

> lighting simple

> lighting soft

> select @@serial_number=10608

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

97 atoms, 97 bonds, 6 residues, 1 model selected  

> select up

332712 atoms, 324902 bonds, 6757 residues, 1 model selected  

> select clear

> hide protein

> show protein ribbons

> lighting simple

> usage namesel

"namesel" is not a command name  

> usage name

name name [text]  
— Define specifier name as a string  
name: a text string  
text: the rest of line

name delete name  
— Remove user-defined specifier name  
name: a text string

name frozen name objects  
— Define specifier name as atoms in current session matching a string  
name: a text string

name list [builtins true or false]  
— List user-defined specifier names  

> name mem :POPE,PSM,POPC,DPPE,POPS,DPPS,CHL1,DPPC

> show mem

> hide mem

> style ligand & ~mem sphere

Changed 14040 atom styles  

> show mem

> hide mem

> preset cartoons/nucleotides cylinders/stubs

Changed 59232 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> graphics triangles
    
    
    7286830 total triangles in 1 models and 5 drawings
    #1 prot_gly_memb.pdb 7286830
      atoms 4820022 in 7281 instances, 662 each
      ribbons 2466808
        prot_gly_memb.pdb # ribbon tethers 0
      bonds 0
    

  

> graphics quality

Quality 1, atom triangles 662, bond triangles 160, ribbon divisions 20  

> graphics quality atomTriangles 60

> graphics quality

Quality 1, atom triangles 60, bond triangles 160, ribbon divisions 20  

> usage grap qual

graphics quality [quality] [atomTriangles atomTriangles] [bondTriangles
bondTriangles] [totalAtomTriangles an integer] [totalBondTriangles an integer]
[ribbonDivisions ribbonDivisions] [ribbonSides an integer] [colorDepth an
integer]  
— Set graphics quality parameters  
quality: a number  
atomTriangles: default or an integer  
bondTriangles: default or an integer  
ribbonDivisions: default or an integer  

> graphics quality ribbonDivisions 2

> graphics triangles
    
    
    782980 total triangles in 1 models and 5 drawings
    #1 prot_gly_memb.pdb 782980
      atoms 436860 in 7281 instances, 60 each
      ribbons 346120
        prot_gly_memb.pdb # ribbon tethers 0
      bonds 0
    

  

> graphics quality ribbonSides 4

> graphics quality

Quality 1, atom triangles 60, bond triangles 160, ribbon divisions 2  

> graphics triangles
    
    
    503900 total triangles in 1 models and 5 drawings
    #1 prot_gly_memb.pdb 503900
      atoms 436860 in 7281 instances, 60 each
      ribbons 67040
        prot_gly_memb.pdb # ribbon tethers 0
      bonds 0
    

  

> graphics quality atomTriangles 12

> graphics triangles
    
    
    154412 total triangles in 1 models and 5 drawings
    #1 prot_gly_memb.pdb 154412
      atoms 87372 in 7281 instances, 12 each
      ribbons 67040
        prot_gly_memb.pdb # ribbon tethers 0
      bonds 0
    

  

> graphics quality ribbonSides 8

> graphics quality atomTriangles 24

> color protein gray

> color protein lightgray

> color C & ligand & ~mem yellow

> set bgColor white

> graphics silhouettes true

> set bgColor black

> graphics silhouettes false

> color protein #999999

> lighting simple

[Repeated 1 time(s)]




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1554.100.64.0.0 (iBridge: 18.16.14556.0.0,0)

Software:

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      Kernel Version: Darwin 19.6.0
      Time since boot: 42 days 22:01

Graphics/Displays:

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      Chipset Model: Intel UHD Graphics 630
      Type: GPU
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      Revision ID: 0x0002
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      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

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      Type: GPU
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      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
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      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
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          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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[Eric Pettersen]

Duplicate of #4501