VMD-L Mailing List

From: Felipe Montecinos (fmontecinos_at_gmail.com)
Date: Mon May 02 2016 - 09:49:21 CDT

Dear Jonathan,

I totally forgot to respond to your email.

Your fix worked nicely, the sequences are now in boldface font. GREAT!

About the the secondary structure depiction.

I know how to show the secondary structural elements along with the
sequence in multiseq, I use it a lot. It's just that it always appears in
black, cannot modify it's colors. Anyway I could do this?

Thanks a lot!

On Tue, Jul 14, 2015 at 1:06 PM, Lai, Jonathan <jlai7_at_illinois.edu> wrote:

> Dear Felipe,
>
> Sorry for the delay in responding. I have modified the seqedit_widget.tcl
> file that makes the sequence letters bold face. I hope that helps.
>
> You can apply the patch as follows:
> 1) Download the tcl file.
> 2) Navigate to the plugins directory of your vmd build. On my Ubuntu
> machine, the plugins directory was found here:
> /usr/local/lib/vmd/plugins/noarch/tcl/seqedit1.1
> 3) Copy the new tcl file and replace the seqedit_widget.tcl
>
> As for the secondary structure, you can click on the little "r" button
> that is next to the sequence name. That should show the secondary
> structure.
>
> Best,
> Jonathan
> ------------------------------
> *From:* Felipe Montecinos [fmontecinos_at_gmail.com]
> *Sent:* Friday, July 10, 2015 1:16 PM
> *To:* Lai, Jonathan
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: Multiseq display settings
>
> Thanks a lot!
>
> Looking forward for those fixes.
>
> Enjoy your weekend!
>
> On Fri, Jul 10, 2015 at 1:57 PM, Lai, Jonathan <jlai7_at_illinois.edu> wrote:
>
>> Dear Felipe,
>>
>> I am current working on the Multiseq plugin. I'll take a look this
>> weekend to see what can be done to make the display better.
>>
>> Cheers,
>> Jonathan
>>
>> ------------------------------
>> *From:* owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of
>> Felipe Montecinos [fmontecinos_at_gmail.com]
>> *Sent:* Friday, July 10, 2015 11:28 AM
>> *To:* vmd-l_at_ks.uiuc.edu
>> *Subject:* vmd-l: Multiseq display settings
>>
>> Hi VMD people,
>>
>> I have two questions for the VMD/Multiseq community:
>>
>> 1. How to change fonts in the multiseq sequence display. The current
>> configuration/settings uses a font that looks very dim, not good.
>>
>> 2. How to color secondary structure representation, by secondary
>> structure element, in the multiseq display.
>>
>> Finally, the ultimate goal is to make the multiseq window/screenshoot to
>> look good for publication and/or presentations.
>>
>> Any suggestions?
>>
>> PD: I'm not a programmer/robot
>> --
>>
>> *Felipe Montecinos F.*
>>
>>
>
>
> --
>
> *Felipe Montecinos F.*
>
> 

-- 
*Felipe Montecinos F.*