[Chimera-users] how to color an model by an attribute in chimerax

[Elaine Meng]

Hi Sun Yeping,
To use the "open" command to open defattr format you need ChimeraX daily build from Oct 30, 2020 or newer.  Or if you are using ChimeraX 1.1, you can use the "defattr" command to open the file.  Older ChimeraX than version 1.1 cannot read this file type at all.  Changes and approximate dates are given in the Change Log:

<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>

The format is described here:
<https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 27, 2021, at 1:04 AM, sunyeping <sunyeping at aliyun.com> wrote:
> 
> Dear Elaine,
> 
> Thank you for your reply. The attribute file entropy.txt is available at 
> 
> https://drive.google.com/file/d/1oG0O4zKqw-uD5SeLTrAu16c3Jh8m3LG5/view?usp=sharing
> 
> Could you please help check whether the format is correct"?
> 
> I cannot figure out how to open this attribure file in chimera. When I input "open entropy.txt format defattr" in chimerax, I get the following error message:
> 
> Invalid "format" argument: Should be one of 'aln', 'amira', 'apbs', 'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'compiled python', 'cube', 'dcd', 'delphi', 'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imod', 'imodmap', 'ims', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mrc', 'msf', 'netcdf', 'obj', 'pdb', 'pdbqt', 'pfam', 'pif', 'pir', 'positions', 'priism', 'profec', 'pseudobonds', 'python', 'rsf', 'sdf', 'segger', 'session', 'sff', 'situs', 'smiles', 'spider', 'stl', 'stockholm', 'storm', 'swc', 'tom_em', 'trr', 'uhbd', 'uniprot', 'vtk', 'web fetch', 'xplor', or 'xtc'
> 
> Could you tell me what is the correct way to open the file?
> 
> Thank you,
> Best,
> Yeping
> ------------------------------------------------------------------
> From:孙业平 <sunyeping at aliyun.com>
> Send Time:2021年1月26日(星期二) 11:53
> To:chimera-users <chimera-users at cgl.ucsf.edu>
> Subject:[Chimera-users] how to color an model by an attribute in chimerax
> 
> Dear all,
> 
> I wish to color an model  by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following:
> 
> attribute: entropy
> match mode: 1-to-1
> recipient: residues
>  :1 0.0
>  :2 0.0014948
>  :3 0.0090952
>  :4 0.0004805
>  :5 0.1102497
>  :6 0.0095258
>  :7 0.0008226
>  :8 0.0042205
>  :9 0.0037255
>  :10 0.0006678
>  :11 0.0027988
>  :12 0.0193925
>  :13 0.0153925
>  :14 0.0052115
>  :15 0.0020136
> ..........
> 
> However, when I input the command "color byattr attr.txt", I get the following error information:
> "No known/Registered attribute attr.txt"
> 
> Could anyone tell me what is the correct way to do this?
> 
> With many thanks.
> 
> Best regards
>