There is also a choice on the Matchmaker dialog to open Match->Align, "After superposition, compute structure-based multiple sequence alignment." That just starts the tool, exactly the same as choosing it from the Tools menu. Elaine

On Sep 18, 2020, at 9:39 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Zaher, Yes, but it is a separate step. After all three structures are superimposed in 3D (using Matchmaker or any other method you like), then you can use the Match->Align tool to create a sequence alignment of all three. Menu: Tools... Structure Comparison... Match->Align.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.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 Sep 18, 2020, at 9:19 AM, arrafzaher@campus.technion.ac.il wrote:

Hi, Suppose I have 3 structures #0 #1 and #2. If I impose structure alignment of both #1 and #2 to #0. I receive two MSA alignment. Is there a way to view one MSA of the 3 structures and not 2 MSA of them. Thanks, Zaher

Yes, the Matchmaker dialog does have a choice to show the pairwise alignments, but the option that I mentioned is a different one. As I said, it starts the Match->Align tool. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html#final> ChimeraX does not yet have anything like the Match->Align tool, sorry. Elaine

On Sep 18, 2020, at 11:39 AM, arrafzaher@campus.technion.ac.il wrote:

Thank you Elaine, I know about the choice in the MM dialog however this runs 2 separate MSA.

The first method helped, where can I find these tools in ChimeraX?

Zaher On 18/09/2020, 19:44, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:

There is also a choice on the Matchmaker dialog to open Match->Align, "After superposition, compute structure-based multiple sequence alignment." That just starts the tool, exactly the same as choosing it from the Tools menu. Elaine

...

On Sep 18, 2020, at 9:39 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Zaher, Yes, but it is a separate step. After all three structures are superimposed in 3D (using Matchmaker or any other method you like), then you can use the Match->Align tool to create a sequence alignment of all three. Menu: Tools... Structure Comparison... Match->Align.

<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fmatchalign%2Fmatchalign.html&data=02%7C01%7Carrafzaher%40campus.technion.ac.il%7C6bfd0bf57da34de4df1a08d85bf20ba5%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637360442425122795&sdata=elzHUJySn9pfNK%2FBEBjGs5aI5OX4XLEf77c9aJNZpPM%3D&reserved=0>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Sep 18, 2020, at 9:19 AM, arrafzaher@campus.technion.ac.il wrote:

Hi, Suppose I have 3 structures #0 #1 and #2. If I impose structure alignment of both #1 and #2 to #0. I receive two MSA alignment. Is there a way to view one MSA of the 3 structures and not 2 MSA of them. Thanks, Zaher

This email is from an external mail server, be judicious when opening attachments or links

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Sigh, too much rushing. The mailing list is chimerax-users@cgl.ucsf.edu ! Elaine

On Sep 18, 2020, at 11:59 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

There is another mailing list chimerax-user@cgl.ucsf.edu specifically for ChimeraX, if you are interested!

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. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers> This example image shows all three RMSD histograms: ... 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. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving> 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@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

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@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@cgl.ucsf.edu> Reply-To: Chimera <chimera-users@cgl.ucsf.edu> Date: Friday, 18 September 2020 at 23:07 To: Zaher Arraf <arrafzaher@campus.technion.ac.il> Cc: Chimera <chimera-users@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.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers>

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.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

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@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

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@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@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@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@cgl.ucsf.edu> Reply-To: Chimera <chimera-users@cgl.ucsf.edu> Date: Friday, 18 September 2020 at 23:07 To: Zaher Arraf <arrafzaher@campus.technion.ac.il> Cc: Chimera <chimera-users@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%7Cbfff96be450f4f1bcd7a08d860a1cadb%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637365595305334463&sdata=7WjO5obq7CT8nIKh5BKjmp6BJHWBNBS%2BwymAInpegWQ%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%7Cbfff96be450f4f1bcd7a08d860a1cadb%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637365595305334463&sdata=i36REdPMEdsczVCqEaFOeUagdrVAPgzwG%2BeJgOAjNuk%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%7Cbfff96be450f4f1bcd7a08d860a1cadb%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637365595305334463&sdata=aQGb%2FvJJfTl780Fk2%2BWAcLASkpSnteBiR%2FapN4%2BoeZc%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@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

This email is from an external mail server, be judicious when opening attachments or links _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Zaher, I believe the ticket is this one <https://plato.cgl.ucsf.edu/trac/chimera/ticket/16679> ... which was closed 21 months ago and at that time, the system would have sent you an e-mail with the final comment: =-=-=-= Hi Zaher, This is fixed in the final 1.13.1 release. You are running a 1.13.1 release candidate. Please get the final release and try it -- if you still have the problem then, then please let us know! --Eric =-=-=-= So if you are still having the problem even in the new version (including daily build) then please use Chimera menu: Help... Report a Bug to describe it and include as many details as might be important, such as if you are using fullscreen mode, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 6, 2020, at 6:48 AM, arrafzaher@campus.technion.ac.il wrote:

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@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@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@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@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@cgl.ucsf.edu> Reply-To: Chimera <chimera-users@cgl.ucsf.edu> Date: Friday, 18 September 2020 at 23:07 To: Zaher Arraf <arrafzaher@campus.technion.ac.il> Cc: Chimera <chimera-users@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@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

This email is from an external mail server, be judicious when opening attachments or links _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Carrafzaher%40campus.technion.ac.il%7C6ff563a64790468f905e08d86167b80e%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637366445389422842&sdata=fwt2LG7RfMzp5pwGIfWV0QyVmsuOfz9sAI8RksrrEGs%3D&reserved=0

This email is from an external mail server, be judicious when opening attachments or links

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users