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
On Jan 25, 2021, at 7:47 PM, sunyeping sunyeping@aliyun.com wrote:
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
Hello, Since this is a ChimeraX question, better to send to the chimerax-users@cgl.ucsf.edu address CC'd here instead of the chimera-users list.
(1) First you need to make sure the text file is the right format. It should be tabs (not just a space) before the residue number and between the residue number and the value, e.g. as described here: https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html
(2) Then (after the atomic structure is open), open the attribute file with the "open" command, e.g. with pathname of your file, or if you want use a file browser window to find the file, "open browse". It is easiest to first name the file ending in .defattr so that ChimeraX will know what kind of file it is supposed to be. https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#defattr
(3) then the Log should report that the attribute named entropy is assigned and you are ready to do the coloring. The coloring command could be something like
color byattribute entropy palette rainbow
...there are several other options, see https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
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=s...
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@aliyun.com Send Time:2021年1月26日(星期二) 11:53 To:chimera-users chimera-users@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
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@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=s...
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@aliyun.com Send Time:2021年1月26日(星期二) 11:53 To:chimera-users chimera-users@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
participants (2)
-
Elaine Meng -
sunyeping