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Today's Topics:
1. Re: Volume Series tool missing (Elaine Meng)
2. Re: Volume Series tool missing (Jarrett Bowman)
3. ChimeraX Questions (Bani Kaur)
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Message: 1
Date: Fri, 30 Jun 2023 13:14:56 -0700
From: Elaine Meng <meng@cgl.ucsf.edu>
Subject: [chimerax-users] Re: Volume Series tool missing
To: Jarrett Bowman <jarrettbow@gmail.com>
Cc: chimerax-users@cgl.ucsf.edu
Message-ID: <D9C12F1F-8A96-428D-B572-4D0E83ACD5EA@cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii
Hi Jerry,
The picture shows that the video tutorial you are viewing is for Chimera, not ChimeraX. Chimera and ChimeraX are two different programs.
ChimeraX does not have a GUI tool, as you said, but it does have volume series capabilities via the "vseries" command, see both of the following and links therein:
<https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html>
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Jun 30, 2023, at 12:46 PM, Jarrett Bowman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
> I am trying to use the volume series tool on ChimeraX version 1.6.1 for Windows. It doesn't appear to be in my download of ChimeraX possibly along with other tools. A tutorial I am following shows this picture:
>
> <image.png>
>
> While this is what I have:
>
> <image.png>
>
> Any help would be greatly appreciated!
>
> Jerry Bowman
------------------------------
Message: 2
Date: Fri, 30 Jun 2023 14:49:14 -0600
From: Jarrett Bowman <jarrettbow@gmail.com>
Subject: [chimerax-users] Re: Volume Series tool missing
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Message-ID:
<CAFN=EO2pGxSNMRJ=ChH+QTG+WSH-G8oshP41fJtKbTBD=DF_aw@mail.gmail.com>
Content-Type: multipart/alternative;
boundary="000000000000d3119b05ff5ef3b8"
Elaine,
Thanks! The links helped a bunch
On Fri, Jun 30, 2023 at 2:15 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
> Hi Jerry,
> The picture shows that the video tutorial you are viewing is for Chimera,
> not ChimeraX. Chimera and ChimeraX are two different programs.
>
> ChimeraX does not have a GUI tool, as you said, but it does have volume
> series capabilities via the "vseries" command, see both of the following
> and links therein:
>
> <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html>
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jun 30, 2023, at 12:46 PM, Jarrett Bowman via ChimeraX-users <
> chimerax-users@cgl.ucsf.edu> wrote:
> >
> > Hello,
> > I am trying to use the volume series tool on ChimeraX version 1.6.1 for
> Windows. It doesn't appear to be in my download of ChimeraX possibly along
> with other tools. A tutorial I am following shows this picture:
> >
> > <image.png>
> >
> > While this is what I have:
> >
> > <image.png>
> >
> > Any help would be greatly appreciated!
> >
> > Jerry Bowman
>
>
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Message: 3
Date: Fri, 30 Jun 2023 17:39:23 -0700
From: Bani Kaur <bankaur@ucdavis.edu>
Subject: [chimerax-users] ChimeraX Questions
To: chimerax-users@cgl.ucsf.edu
Message-ID:
<CAPA-7dC=PAuAQF2XEOrzGLXvPzmMiCVLkChOV9eFzajW_uC50Q@mail.gmail.com>
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Hi,
I hope you are doing well! My name is Bani Kaur and I am an active user of
ChimeraX for a research project concerning protein modeling, specifically
with the CFTR protein. I have been running into issues with showing atoms
on my residue, specifically after I change the romater. I am not sure what
to do about this as I have downloaded the latest version of ChimeraX. I
have attached a photo where the left one is the selected residue (Thr) and
the right photo is the residue when it is changed to Ile.
[image: Screen Shot 2023-06-30 at 5.38.22 PM.png]
Additionally, I am not able to see clashes for some very reason and am
only able to see it when limit by selection is unchecked, but for my
research project, we require that it is checked in the clashes settings. I
have attached a photo of the settings.
[image: Screen Shot 2023-06-30 at 5.39.01 PM.png]
Thank you so much for your help!
Best,
Bani Kaur
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