"No known/registered attribute seq_conservation" in conservation tutorial
Hi all,
I am following the coloring sequence by conservation tutorial https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html but ran into some unexpected behavior. I used the the exact commands, but when I ran the "color byattribute seq_conservation" command, I got an error, "No known/registered attribute seq_conservation." The association was successful so I don't know why the seq_conservation attribute is not being set. See below for the log of my commands.
I also tried using my own structure and msa but ran into the same "No known / registered attribute seq_conservation" issue, despite associating with 0 mismatches.
Am I somehow missing something, or is something wrong? I am using a version of ChimeraX downloaded in November 2020, running on Windows 10.
*open 121p*
*121p title:*
Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal verkuerzten menschlichen krebsproteins P21-H-ras [more info...]
Chain information for 121p #1 Chain Description A H-ras P21 protein Non-standard residues in 121p #1 GCP — phosphomethylphosphonic acid guanylate ester MG — magnesium ion 121p mmCIF Assemblies 1 author_defined_assembly
*hide solvent* *style ligand ball*
Changed 32 atom styles
*open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.a... https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln* Summary of feedback from opening // www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
fetched from https
notes Fetching 121p-consurf(1).aln from https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.a... Downloaded 121p-consurf.aln to C:\Users\selua\Downloads\121p-consurf(1).aln Alignment identifier is 121p-consurf(1).aln Associated 121p chain A to Input_pdb_SEQRES_A with 0 mismatches Opened 150 sequences from 121p-consurf(1).aln *color byattribute seq_conservation*
No known/registered attribute seq_conservation
[image: image.png]
Thanks for any help, Etowah
Hi Etowah, First doublecheck that you have ChimeraX version 1.1 released August 2020 or newer (1.2 daily build). Version should be shown in the Log when you start up, or you can use ChimeraX command "version" to report it in the Log. Although you said when you got it, this is the most reliable way to check the version.
Otherwise, I have no idea why it wouldn't work. I certainly checked each step carefully several times when I wrote that tutorial. If you have ChimeraX 1.1 or newer and still have the problem, please use menu: Help... Report a Bug and attach a session file from right after you get the error. Please include a short description in the report, as well as your e-mail address if you would like feedback about what we find.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 16, 2021, at 8:34 PM, Etowah Adams etowah.adams@yale.edu wrote:
Hi all,
I am following the coloring sequence by conservation tutorial but ran into some unexpected behavior. I used the the exact commands, but when I ran the "color byattribute seq_conservation" command, I got an error, "No known/registered attribute seq_conservation." The association was successful so I don't know why the seq_conservation attribute is not being set. See below for the log of my commands.
I also tried using my own structure and msa but ran into the same "No known / registered attribute seq_conservation" issue, despite associating with 0 mismatches.
Am I somehow missing something, or is something wrong? I am using a version of ChimeraX downloaded in November 2020, running on Windows 10.
open 121p 121p title: Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal verkuerzten menschlichen krebsproteins P21-H-ras [more info...]
Chain information for 121p #1 Chain Description A H-ras P21 protein Non-standard residues in 121p #1 GCP — phosphomethylphosphonic acid guanylate ester MG — magnesium ion 121p mmCIF Assemblies 1 author_defined_assembly
hide solvent style ligand ball Changed 32 atom styles open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.a... Summary of feedback from opening //www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln fetched from https notes Fetching 121p-consurf(1).aln from https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.a... Downloaded 121p-consurf.aln to C:\Users\selua\Downloads\121p-consurf(1).aln Alignment identifier is 121p-consurf(1).aln Associated 121p chain A to Input_pdb_SEQRES_A with 0 mismatches Opened 150 sequences from 121p-consurf(1).aln color byattribute seq_conservation No known/registered attribute seq_conservation
<image.png>
Thanks for any help, Etowah
Sorry for the late reply. I managed to get it working with the 1.1 version with no hiccups. Thank you for the help!
Best, Etowah
On Wed, Feb 17, 2021 at 10:56 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Etowah, First doublecheck that you have ChimeraX version 1.1 released August 2020 or newer (1.2 daily build). Version should be shown in the Log when you start up, or you can use ChimeraX command "version" to report it in the Log. Although you said when you got it, this is the most reliable way to check the version.
Otherwise, I have no idea why it wouldn't work. I certainly checked each step carefully several times when I wrote that tutorial. If you have ChimeraX 1.1 or newer and still have the problem, please use menu: Help... Report a Bug and attach a session file from right after you get the error. Please include a short description in the report, as well as your e-mail address if you would like feedback about what we find.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 16, 2021, at 8:34 PM, Etowah Adams etowah.adams@yale.edu wrote:
Hi all,
I am following the coloring sequence by conservation tutorial but ran
into some unexpected behavior. I used the the exact commands, but when I ran the "color byattribute seq_conservation" command, I got an error, "No known/registered attribute seq_conservation." The association was successful so I don't know why the seq_conservation attribute is not being set. See below for the log of my commands.
I also tried using my own structure and msa but ran into the same "No
known / registered attribute seq_conservation" issue, despite associating with 0 mismatches.
Am I somehow missing something, or is something wrong? I am using a
version of ChimeraX downloaded in November 2020, running on Windows 10.
open 121p 121p title: Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal
verkuerzten menschlichen krebsproteins P21-H-ras [more info...]
Chain information for 121p #1 Chain Description A H-ras P21 protein Non-standard residues in 121p #1 GCP — phosphomethylphosphonic acid guanylate ester MG — magnesium ion 121p mmCIF Assemblies 1 author_defined_assembly
hide solvent style ligand ball Changed 32 atom styles open
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.a...
Summary of feedback from opening //
www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
fetched from https notes Fetching 121p-consurf(1).aln from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.a...
Downloaded 121p-consurf.aln to
C:\Users\selua\Downloads\121p-consurf(1).aln
Alignment identifier is 121p-consurf(1).aln Associated 121p chain A to Input_pdb_SEQRES_A with 0 mismatches Opened 150 sequences from 121p-consurf(1).aln color byattribute seq_conservation No known/registered attribute seq_conservation
<image.png>
Thanks for any help, Etowah
participants (2)
-
Elaine Meng -
Etowah Adams