Re: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax
------------------------------------------------------------------ From:孙业平 <sunyeping@aliyun.com> Send Time:2021年2月3日(星期三) 16:09 To:ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject:Re: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax Hi Elaine, Thank you for you help. I will send chimerax questions to chimerax mail list next time. By changing the match mode from "1-to-1" to 'any', I can also color the protein according to the entropy.txt file. If you recheck the entropy.txt file you will find that there are quite a few residues have an entropy vavle around 0.3, in addition to the 0.788 residue. Could you tell me how to generate a color gradient bar base on the entropy values in the entropy.txt file in chimerax? Best regards, Yeping ------------------------------------------------------------------ From:Elaine Meng <meng@cgl.ucsf.edu> Send Time:2021年1月28日(星期四) 00:44 To:孙业平 <sunyeping@aliyun.com> Cc:ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject:Re: [Chimera-users] how to color an model by an attribute in chimerax Hi Yeping, **Please send ChimeraX questions to the chimerax-users@cgl.ucsf.edu address, *not* to chimera-users@cgl.ucsf.edu, because that makes people confused about which program we are talking about. Two more thoughts about your file: (1) you need to make sure the residue numbers in the file all match to your structure. I don't know which structure you are using so when I test it on some other structure that doesn't have all the same residue numbers, it does not work unless I change the match mode from "1-to-1" to "any". You might want to try using match mode "any". (2) looks like one residue has a high value 0.788 and all the others are very close to zero, so when I color the whole range the structure is all the same color (used for the low end) except for the one high-value residue. E.g. coloring by attribute entropy using palette blue-white-red makes the whole structure blue except for one residue red. Elaine
On Jan 27, 2021, at 8:25 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
This is the third time you sent this question asking how to make a color key (the gradient bar) in ChimeraX. I already answered the first time and the second time. Do not keep sending the same question to the list, it is rude to everybody on the list. Please check your spam-filtered mail for my replies (or at least look in the archive to see the answers if you can't find them in your mailbox). <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/index.html> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-February/001877.html> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-February/001885.html> In the very newest daily build of ChimeraX, there is a "key" command to make a color but we are still working on it. It does not have all the features of the Chimera color key (no outlines, tick marks, etc.) and there is no GUI yet. Elaine
On Feb 3, 2021, at 11:38 PM, sunyeping <sunyeping@aliyun.com> wrote:
------------------------------------------------------------------ From:孙业平 <sunyeping@aliyun.com> Send Time:2021年2月3日(星期三) 16:09 To:ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject:Re: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax
Hi Elaine,
Thank you for you help. I will send chimerax questions to chimerax mail list next time.
By changing the match mode from "1-to-1" to 'any', I can also color the protein according to the entropy.txt file. If you recheck the entropy.txt file you will find that there are quite a few residues have an entropy vavle around 0.3, in addition to the 0.788 residue.
Could you tell me how to generate a color gradient bar base on the entropy values in the entropy.txt file in chimerax?
Best regards, Yeping
------------------------------------------------------------------ From:Elaine Meng <meng@cgl.ucsf.edu> Send Time:2021年1月28日(星期四) 00:44 To:孙业平 <sunyeping@aliyun.com> Cc:ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject:Re: [Chimera-users] how to color an model by an attribute in chimerax
Hi Yeping, **Please send ChimeraX questions to the chimerax-users@cgl.ucsf.edu address, *not* to chimera-users@cgl.ucsf.edu, because that makes people confused about which program we are talking about.
Two more thoughts about your file:
(1) you need to make sure the residue numbers in the file all match to your structure. I don't know which structure you are using so when I test it on some other structure that doesn't have all the same residue numbers, it does not work unless I change the match mode from "1-to-1" to "any". You might want to try using match mode "any".
(2) looks like one residue has a high value 0.788 and all the others are very close to zero, so when I color the whole range the structure is all the same color (used for the low end) except for the one high-value residue. E.g. coloring by attribute entropy using palette blue-white-red makes the whole structure blue except for one residue red.
Elaine
On Jan 27, 2021, at 8:25 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Hello everybody, A limited "key" command is available in the latest daily build of ChimeraX. Not yet available: drawing outlines or tick marks (or a GUI). The help page has examples, details, current options, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/key.html> There is another example at the very end of this tutorial: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#es...> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 4, 2021, at 9:13 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
In the very newest daily build of ChimeraX, there is a "key" command to make a color but we are still working on it. It does not have all the features of the Chimera color key (no outlines, tick marks, etc.) and there is no GUI yet.
Elaine
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sunyeping