<div dir="ltr"><div><div><div>Hi Michael,<br><br></div>Since dssp-2.2.1 looks like it might be an issue, there were a couple of other tricky things I had to do to get it to work. First, per the README, you need to manually enter ~/dssp-2.2.1/src and modify mkdssp.cpp and replace all instances of "Version" (I can't remember if it was all caps) to "2.2.1" otherwise it won't work. I am a complete newbie with C++/C so I had no idea how to get the thing to work, but fortunately: (<a href="http://macosxpostdoc.blogspot.com/2012/09/two-for-price-of-one-mac-os-x-without.html">http://macosxpostdoc.blogspot.com/2012/09/two-for-price-of-one-mac-os-x-without.html</a>) supplied me with the command: <i>c++ -O3 -o dssp -I/sw/include -L/sw/lib -Wall -Wno-multichar -lboost_thread-mt -lboost_regex-mt -lboost_filesystem-mt -lboost_program_options-mt -lboost_date_time-mt -lboost_iostreams-mt -lboost_system-mt *.cpp <br><br></i></div>It gave me some warning about an unused variable kSSBridgeDIstance and not finding a directory for -L/sw/lib. Other than that, it seemed to work fine, but was oddly clunky to use. Perhaps as a result of the above error, I could not convert .pdb files to .dssp files unless the .pdb file was in ~/dssp-2.2.1/src (and needed to include said directory in terminal when giving the conversion command). I feel like this is just an error on my part and isn't a big deal for me. Thank you very much for your reply and please let me know if you have any questions!<br><br></div>Sincerely,<br>Evan Masutani<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 10, 2014 at 3:33 PM, Michael Wong <span dir="ltr"><<a href="mailto:mikewong@sfsu.edu" target="_blank">mikewong@sfsu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Hi Evan,
<div><br>
</div>
<div>Hi Evan,</div>
<div><br>
</div>
<div>I’ll update the DSSP links in the documentation; previous versions of DSSP did *not* need the Boost libraries, so this information is very helpful. </div>
<div><br>
</div>
<div>DSSP v2.2.1 gives different results than DSSP v1, so the scores will be different. I’ve confirmed that FEATURE-3.1 gives consistent results with the old version of DSSP, so I’ll have to look more closely into what the differences are and how to manage
the change. The most logical choice would be to update to the latest version of DSSP for our nightly build tests and documentation, although I’ll have to balance that with the impact on users who have the old DSSP.</div>
<div><br>
</div>
<div>As a bioengineer, you know that software “bit rot” is a real issue. FEATURE has several dependences, so whenever a dependence changes, it always leads to a fire-fighting adventure. Thanks for your patience!</div>
<div><br>
</div>
<div>Best regards,</div>
<div><br>
</div>
<div>- m.</div>
<div><span class=""><br>
<div><span style="border-collapse:separate;border-spacing:0px"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
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__________________________________<br>
Mike Wong, Staff Research Associate<br>
Center for Computing for Life Sciences (CCLS)<br>
San Francisco State University<br>
1600 Holloway Avenue, Hensill Hall 302, SF, CA 94132<br>
<a href="tel:%28415%29%20405-2119" value="+14154052119" target="_blank">(415) 405-2119</a><br>
<a href="mailto:mikewong@sfsu.edu" target="_blank">mikewong@sfsu.edu</a></div>
</span></span></div>
<br>
</span><div><div class="h5"><div>
<div>On Oct 10, 2014, at 10:36 AM, Evan Masutani <<a href="mailto:evmasuta@gmail.com" target="_blank">evmasuta@gmail.com</a>> wrote:</div>
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<div>Dear Michael and <a href="http://simtk.org/" target="_blank">simtk.org</a>,<br>
<br>
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:<br>
</div>
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<br>
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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.<br>
</div>
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.<br>
</div>
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.<br>
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5) make install feature does not add the examples folder to the directory; only README, bin, data, and tools are there<br>
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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:<br>
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Manual Output (omitted other 3 entries):<br>
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Env_1bqy_31 149.060025 35.096 9.444 145.234 # SER195:B@OG<br>
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Env_1bqy_14 176.033218 19.642 39.631 59.232 # SER195:A@OG<br>
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<div>My Output:<br>
Env_1bqy_31 144.728524 35.096 9.444 145.234 # SER195:B@OG<br>
Env_1bqy_14 154.566672 19.642 39.631 59.232 # SER195:A@OG<br>
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<div>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?<br>
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<div>Thank you very much for your time! I really appreciate it and apologize for any ignorant comments. Have a great weekend!<br>
<br>
</div>
<div>Sincerely,<br>
Evan Masutani<br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Oct 9, 2014 at 2:57 PM, Michael Wong <span dir="ltr">
<<a href="mailto:mikewong@sfsu.edu" target="_blank">mikewong@sfsu.edu</a>></span> wrote:<br>
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<div style="word-wrap:break-word">Hi Evan,
<div><br>
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<div>Thanks for using the FEATURE software! Your feedback helps improve FEATURE as a solid basis for computational protein research.</div>
<div><br>
</div>
<div>You can post to <a href="mailto:feature-users@simtk.org" target="_blank">feature-users@simtk.org</a> and/or directly e-mail me your suggestions to improve the installation process; I suggest that you e-mail
<a href="mailto:feature-users@simtk.org" target="_blank">feature-users@simtk.org</a> and cc me (I will get both e-mails) so we can track and resolve the issues you raise.</div>
<div><br>
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<div>Best regards,</div>
<div><br>
</div>
<div>- m.<br>
<div><span style="border-collapse:separate;font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<div style="word-wrap:break-word">__________________________________<br>
Mike Wong, Staff Research Associate<br>
Center for Computing for Life Sciences (CCLS)<br>
San Francisco State University<br>
1600 Holloway Avenue, Hensill Hall 302, SF, CA 94132<br>
<a href="tel:%28415%29%20405-2119" value="+14154052119" target="_blank">(415) 405-2119</a><br>
<a href="mailto:mikewong@sfsu.edu" target="_blank">mikewong@sfsu.edu</a></div>
</span></div>
<div>
<div><br>
<div>
<div>On Oct 8, 2014, at 7:15 PM, Russ B Altman <<a href="mailto:russ.altman@stanford.edu" target="_blank">russ.altman@stanford.edu</a>> wrote:</div>
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<blockquote type="cite">You should be able to post things on the discussion part of
<a href="http://simtk.org/" target="_blank">simtk.org</a> 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.<br>
<br>
Thanks!<br>
Russ<br>
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<br>
On Oct 7, 2014, at 4:12 PM, Evan Masutani <<a href="mailto:evmasuta@gmail.com" target="_blank">evmasuta@gmail.com</a>> wrote:<br>
<br>
<blockquote type="cite">Dear Prof. Altman,<br>
<br>
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!<br>
<br>
Sincerely,<br>
Evan Masutani<br>
<br>
On Fri, Oct 3, 2014 at 6:17 PM, Russ B Altman <<a href="mailto:russ.altman@stanford.edu" target="_blank">russ.altman@stanford.edu</a>> wrote:<br>
Evan,<br>
<br>
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.<br>
<br>
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
<a href="http://simtk.org/" target="_blank">simtk.org</a><br>
<br>
<br>
Thanks!<br>
Russ<br>
<br>
<br>
On Oct 3, 2014, at 1:01 PM, Evan Masutani <<a href="mailto:evmasuta@gmail.com" target="_blank">evmasuta@gmail.com</a>> wrote:<br>
<br>
<blockquote type="cite">Dear Prof. Altman,<br>
<br>
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!<br>
<br>
Sincerely,<br>
Evan Masutani<br>
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