Re: [chimerax-users] [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
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
Hi Yeping, Since you didn't say what structure you were using, I just tested coloring by your entropy attribute file on some other structure. Probably my test structure did not contain the residue numbers with 0.3, so the coloring did not look interesting.
ChimeraX does not yet have the ability to draw a color key (color gradient bar with values marked), although it is being worked on now. Currently if you still want to use ChimeraX for the main image, you could use Chimera to draw the color key separately and then put them together in an image editing program (gimp, photoshop, ...).
I hope this helps, Elaine
On Feb 2, 2021, at 12:03 AM, sunyeping sunyeping@aliyun.com wrote:
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
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
I already replied to this message 24 hours ago. There is no need to send it again.
Here is the previous answer: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-February/001877.html
From: Elaine Meng meng@cgl.ucsf.edu Subject: Re: [Chimera-users] how to color an model by an attribute in chimerax Date: February 2, 2021 at 8:27:18 AM PST To: sunyeping sunyeping@aliyun.com Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Reply-To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu
Hi Yeping, Since you didn't say what structure you were using, I just tested coloring by your entropy attribute file on some other structure. Probably my test structure did not contain the residue numbers with 0.3, so the coloring did not look interesting.
ChimeraX does not yet have the ability to draw a color key (color gradient bar with values marked), although it is being worked on now. Currently if you still want to use ChimeraX for the main image, you could use Chimera to draw the color key separately and then put them together in an image editing program (gimp, photoshop, ...).
I hope this helps, Elaine
On Feb 3, 2021, at 12:08 AM, sunyeping sunyeping@aliyun.com wrote:
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
participants (2)
-
Elaine Meng -
sunyeping