[Chimera-users] matchmaker and MSA

Tue Oct 6 06:48:48 PDT 2020

Thank you Elain, you are right, I was using the wrong menu.

Now I have an issue with chimera for OSX I had already submitted a help request long time ago but it has not been solved yet.

When I go into full screen clicking on items in menu becomes a guess game usually I need to click lower from where the actual item is.

I am on the latest Daily build and this happens in all items I wish to click on.

Should I open a new ticket again, or can you help or pass this through?

Thanks,
Zaher

On 25/09/2020, 18:28, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

    Hi Zaher,
    It sounds like you are using the wrong menu item from the sequence alignment.  Do not use File... Save, instead use sequence alignment menu item Headers... Save.
    Best,
    Elaine

    > On Sep 24, 2020, at 7:55 PM, arrafzaher at campus.technion.ac.il wrote:
    >
    > Thank you again.
    > They seem like plain text alright. But for some reason I am not able to save the header data vs alignment position, actually the files show only sequence and they are not arranged in columns.
    >
    > The other way you suggested using “Render by Attribute” tool does produce a plain text file with columns and header value.
    >
    > Maybe I am missing something?
    >
    > Best,
    > Zaher
    >
    >
    >
    > From: Elaine Meng <meng at cgl.ucsf.edu>
    > Sent: Thursday, September 24, 2020 6:52 PM
    > To: Zaher Arraf
    > Cc: Chimera
    > Subject: Re: [Chimera-users] matchmaker and MSA
    >
    > Hi Zaher,
    > They are plain text files, so you can view them in any text editor.  These files were not really meant for other apps, just Chimera, but since they have tabs between columns, so they might be OK in Excel.
    >
    > In my tests, both of these file types (which are almost exactly the same as each other) worked in Excel if I named them ending with ".txt" before opening them in Excel.  Optionally, before opening in Excel you could use a text-editor to delete the information lines at top and/or bottom, the lines that don't have numbers in them.
    >
    > I tried
    > Best,
    > Elaine
    > -----
    > Elaine C. Meng, Ph.D.
    > UCSF Chimera(X) team
    > Department of Pharmaceutical Chemistry
    > University of California, San Francisco
    >
    > > On Sep 24, 2020, at 2:48 AM, arrafzaher at campus.technion.ac.il wrote:
    > >
    > > Hi Elaine,
    > > In the second method I am able to open that file in Excel.
    > >
    > > I can’t figure out Which file format I need to save into in order to be able to open the file saved from the first method?
    > >
    > > Thanks,
    > > Zaher
    > >
    > > From: Elaine Meng <meng at cgl.ucsf.edu>
    > > Reply-To: Chimera <chimera-users at cgl.ucsf.edu>
    > > Date: Friday, 18 September 2020 at 23:07
    > > To: Zaher Arraf <arrafzaher at campus.technion.ac.il>
    > > Cc: Chimera <chimera-users at cgl.ucsf.edu>
    > > Subject: Re: [Chimera-users] matchmaker and MSA
    > >
    > > Hi Zaher,
    > > First use the Multalign Viewer (sequence window) Headers menu to show the RMSD histogram(s) that you want: CA, backbone, and/or full.  Then use that same Headers menu "Save..." option to save to file with RMSD vs. alignment position.
    > >
    > > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fmultalignviewer%2Fframemav.html&data=02%7C01%7Carrafzaher%40campus.technion.ac.il%7C6ff563a64790468f905e08d86167b80e%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637366445389422842&sdata=t7E1cF%2FRZtQp5qMd167DBJGFmlH3BCGRXFwb6s5plSI%3D&reserved=0>
    > > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fmultalignviewer%2Fmultalignviewer.html%23headers&data=02%7C01%7Carrafzaher%40campus.technion.ac.il%7C6ff563a64790468f905e08d86167b80e%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637366445389422842&sdata=BtkSjZ4M%2ByHimG87bZSiAkDh2yn6F7iIkNdBlV435iE%3D&reserved=0>
    > >
    > > This example image shows all three RMSD histograms:
    > > <image001.png>
    > >
    > > ... or if you want the list to be RMSD vs. structure residue numbering instead of alignment numbering, start the "Render by Attribute" tool (in menu under Tools... Structure Analysis) and use that tool's File menu to save the corresponding residue attribute(s) named "mavRMSD[...]". This is possible because sequence alignment header values are automatically assigned as attributes of the associated residues.
    > >
    > > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Frender%2Frender.html%23saving&data=02%7C01%7Carrafzaher%40campus.technion.ac.il%7C6ff563a64790468f905e08d86167b80e%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637366445389422842&sdata=Y1ze0b3AFLddLOrsoMVQY60PrYHnmAOboWVqC%2BQQ5ns%3D&reserved=0>
    > >
    > > In ChimeraX, you can only show one RMSD header at a time but you can choose whether it is ca, backbone, or full.  The ChimeraX Sequence Viewer has its own menu including Headers to control this and also saving the header to file, but instead of on the top bar it is a context menu shown with right-click or ctrl-click, depending on your type of computer.   The attribute is also assigned but ChimeraX does not yet have saving attributes to file.
    > >
    > > I hope this helps,
    > > Elaine
    > >> On Sep 18, 2020, at 12:38 PM, arrafzaher at campus.technion.ac.il wrote:
    > >>
    > >> Thank you Elaine,
    > >> No worries.
    > >> One Last Question (Hopefully),
    > >> Is there a way to produce a datasheet of RMSD for each position aligned from the 3 structures?
    > >> Zaher
    > >>
    >
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