From: Lai, Jonathan (jlai7_at_illinois.edu)
Date: Fri Apr 15 2016 - 15:47:58 CDT

The dots after third residue in protein 1 means there are no aligned residues at these positions. Since multiseq is considering only the alpha carbons, it's not breaking the bonds between residues 3, 4 (Ser, Glu) in protein 1, just want to confirm?

Multiseq does not modify the connectivity of any atoms so it won't break any bonds.

I see a discussion from 2011 about Multiseq in text mode, have things changed since?

I'm not sure which discussion you are referring to; however, if you are keen on using STAMP in text mode, you can directly access the Multiseq's STAMP in your vmd folder.

On my Linux machine, the STAMP executable is located here:
/usr/local/lib/vmd2/plugins/LINUXAMD64/tcl/stamp1.2

I hope that helps,
Jonathan

________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Shyno Mathew [sm3334_at_columbia.edu]
Sent: Friday, April 15, 2016 2:49 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Re: Qres portion of MultiSeq for vmd 1.9.2

Dear all,

I am using Multiseq for the first time. Here is the N-terminal portion of the aligned proteins:

protein1: M P S . . E K T
protein2: . . . M K W . M

The dots after third residue in protein 1 means there are no aligned residues at these positions. Since multiseq is considering only the alpha carbons, it's not breaking the bonds between residues 3, 4 (Ser, Glu) in protein 1, just want to confirm?

Also, I want to get the structure alignment of the protein throughout the simulation with another protein. I understand I could do this by stand alone version of STAMP. Since Multiseq uses a modified version of STAMP, I prefer using Multiseq in text mode. I see a discussion from 2011 about Multiseq in text mode, have things changed since?
Any suggestions regarding this or do you recommend another software?

thanks,
Shyno

On Wed, Apr 13, 2016 at 9:26 PM, Shyno Mathew <sm3334_at_columbia.edu<mailto:sm3334_at_columbia.edu>> wrote:
Dear all,

I am trying to compare two proteins using Multiseq. Everything works ok for the sequence alignment. However, for the structural alignment using STAMP, I am not getting the QH values when highlighting the proteins as mentioned here in step 11.

http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node6.htmlIHIihA&m=qaqiWXJDxkrt-VcLz2BBowtUrhT7mJvsktKA8Yepeik&s=Tdmy2Dn2NdP_GR1XhK8e_hbZocvtwDvkXh0BhglBV-o&e=>

While trying to color the protein according to structural identity, I am getting an error! Also, I see a discussion about similar error concluding there is a bug with Qres portion of multiseq. I am using vmd 1.9.2
Is this bug fixed in the recent versions of vmd?

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/23627.html=qaqiWXJDxkrt-VcLz2BBowtUrhT7mJvsktKA8Yepeik&s=nCkdVtZaPCCm7bGHBu2-ePs9iY_2uE47JlBGhDR-jVc&e=>

thanks,
Shyno

--
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University
--
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University