[chimerax-users] "No known/registered attribute seq_conservation" in conservation tutorial

[Etowah Adams]

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 at 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 at 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.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.aln
> > 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
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210223/961cbc2a/attachment.html>