[Feature-users] Re: Evan MAsutani IRTA update

Fri Oct 10 10:36:29 PDT 2014

Dear Michael and simtk.org,

Thank you very much for your reply!  I currently have feature-3.1.0 running
and it's great!  Installing it, however, had a few kinks that I thought
might be worth asking about.  As a bit of background, I am a bioengineer by
training and am not all that familiar with Macs (my work computer is a Mac
running OS X 10.9.5) and am a mediocre programmer at best, so my apologies
if I say something dumb.  For ease of reading, I have put the issues I
encountered into a list below:
1) The dssp link in the manual is broken.  After the fact, I might've seen
the dssp program in the feature folder but was not sure.  What I ended up
doing was downloading dssp-2.2.1
2) The Mac I am working on did not have Boost installed and it was
necessary to run dssp-2.2.1; using Macports resulted in some downstream
errors, but using Homebrew worked well.
3) There were some other peculiarities with dssp-2.2.1 but I realize that
this is outside the scope of FEATURE, but will be happy to give more input
if you would like.
4) For whatever reason, only standard FEATURE could install on my Mac and
it might be because I am running clang?  I am not sure, but it works fine
otherwise.
5) make install feature does not add the examples folder to the directory;
only README, bin, data, and tools are there
6) After fiddling around I (if I remember correctly, but not really
relevant) managed to try the serine protease example by changing
directories to a separate feature-3.1.0 folder on my desktop.  When I
looked at the output, however, they differed from the output given.  For
one, curiously, FEATURE only returned the top 2 scoring hits and I double
checked the command in the terminal.  When I opened the .hits.sorted file,
there were the same number of entries as with the example output.  Even
more curiously, however, the output values themselves did not match.  I
have pasted the outputs below:
Manual Output (omitted other 3 entries):
Env_1bqy_31 149.060025 35.096 9.444 145.234 # SER195:B at OG
Env_1bqy_14 176.033218 19.642 39.631 59.232 # SER195:A at OG
My Output:
Env_1bqy_31 144.728524 35.096 9.444 145.234 # SER195:B at OG
Env_1bqy_14 154.566672 19.642 39.631 59.232 # SER195:A at OG

To the best of my knowledge, I followed the directions properly, so this
result is puzzling.  I was wondering if it had to do with the fact that I
am using a different version of dssp?

Thank you very much for your time!  I really appreciate it and apologize
for any ignorant comments.  Have a great weekend!

Sincerely,
Evan Masutani

On Thu, Oct 9, 2014 at 2:57 PM, Michael Wong <mikewong at sfsu.edu> wrote:

>  Hi Evan,
>
>  Thanks for using the FEATURE software! Your feedback helps improve
> FEATURE as a solid basis for computational protein research.
>
>  You can post to feature-users at simtk.org and/or directly e-mail me your
> suggestions to improve the installation process; I suggest that you e-mail
> feature-users at simtk.org and cc me (I will get both e-mails) so we can
> track and resolve the issues you raise.
>
>  Best regards,
>
>  - m.
>  __________________________________
> Mike Wong, Staff Research Associate
> Center for Computing for Life Sciences (CCLS)
> San Francisco State University
> 1600 Holloway Avenue, Hensill Hall 302, SF, CA 94132
> (415) 405-2119
> mikewong at sfsu.edu
>
>  On Oct 8, 2014, at 7:15 PM, Russ B Altman <russ.altman at stanford.edu>
> wrote:
>
> You should be able to post things on the discussion part of simtk.org but
> I am cc’ing Mike Wong who helps with managing the code base, in case he has
> a better place for you to put your info.  I’m also cc’ing a grad student in
> my lab, Weizhuang, who has built a Ca++ site recently and may be useful to
> you for advice.
>
> Thanks!
> Russ
>
>
> On Oct 7, 2014, at 4:12 PM, Evan Masutani <evmasuta at gmail.com> wrote:
>
> Dear Prof. Altman,
>
> Thank you very much for your encouraging email!  I am going to give it a
> shot and build a model for Mg++ sites.  I am still getting the
> software/dependencies set up, so I will play around with FEATURE for a bit
> before soliciting further advice.  I am running it on a Mac and had some
> difficulties as well as work-arounds with the installation and was
> wondering if/where I should post this information.  In particular, getting
> dssp was rather painful, although I did manage to do so in the end.  Thank
> you very much!
>
> Sincerely,
> Evan Masutani
>
> On Fri, Oct 3, 2014 at 6:17 PM, Russ B Altman <russ.altman at stanford.edu>
> wrote:
> Evan,
>
> Nice to hear from you!  Very interesting--yes we have a MG++ finder for
> RNA, but have never built one for proteins.   This is chiefly because Ca++
> and Mg++ are very very similar and we are not sure that we have good gold
> standards because depending on which of them is in the buffer when a
> protein is crystallized they can often occupy each other's sites.  So--you
> are right:  the Ca++ models can sometimes be good Mg++ finders.   I am
> going to cc a BioE grad student in my lab who has just built the definitive
> Ca++ model, and used Mg++ as a test for specificity.  He may have ideas (or
> code) for building a MG++ specific model that might be fun--if you are
> interested.  I'm not sure he wants to do this because the Ca++ model was
> just a side project and not his main PhD project, but I will let him
> comment.
>
> Building FEATURE models not that hard:  you find N good Mg++ sites that
> you trust and M good "non-sites" (Weizhuang is expert at this) and then you
> run FEATURE to get a model, cross-validate it, and then go to town!  All
> the FEATURE code is available at simtk.org
>
>
> Thanks!
> Russ
>
>
> On Oct 3, 2014, at 1:01 PM, Evan Masutani <evmasuta at gmail.com> wrote:
>
> Dear Prof. Altman,
>
> I hope that you are well and that the new academic year is off to a good
> start!  I am writing to inform you that all is well at my postbac position
> at the NIH.  I will be working with magnesium transporters; as it turns
> out, as part of the lab's projects, we are trying to identify magnesium
> binding sites on some proteins.  The first thing I thought of when I heard
> that was FEATURE.  I decided to try and take a look at webFEATURE and ran a
> few proteins.  I noticed that the database lacks model proteins for
> magnesium binding sites; however, when I was looking at the results of
> H-Ras (which has magnesium binding sites), I saw that there were a number
> of predicted Ca2+ and ferritin/iron binding sites.  If you have time, I
> would really appreciate any advice on how I should go about looking for
> magnesium binding sites bioinformatically, as well as your opinion about
> possible crossover between predicted Ca2+/ferritin binding sites and Mg2+
> binding sites.  Thank you very much and have a great weekend!
>
> Sincerely,
> Evan Masutani
>
>
>
>
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: https://simtk.org/pipermail/feature-users/attachments/20141010/de303ee6/attachment.html