VMD-L Mailing List

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Fri Apr 15 2016 - 16:07:24 CDT

thanks so much Jonathan.
I forgot to include the url in the previous message, here it is:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17207.html

thanks,
Shyno

On Fri, Apr 15, 2016 at 4:47 PM, Lai, Jonathan <jlai7_at_illinois.edu> wrote:

>
>
> *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> 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.html
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Training_Tutorials_vmd_tutorial-2Dhtml_node6.html&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=Kp9rHtV0p-uN4jdvveXjLhWPrV0OGP1NqOSh3IHIihA&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
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_mailing-5Flist_vmd-2Dl_23627.html&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=Kp9rHtV0p-uN4jdvveXjLhWPrV0OGP1NqOSh3IHIihA&m=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
> 

-- 
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