September 2012 - Rnatoolbox-help - SimTK Mailing Lists

Re: SV: clashes in exercise 0
by Samuel Flores 04 Sep '12

04 Sep '12

Hi Emma, Well it will be a one-day class sometime after 19 September. It's part of a longer Uppsala course (several weeks) -- but you wouldn't need to stay for all that. But the other possibility is that you walk yourself through exercises 1-3 or so and then come for a visit so we can work on your problem specifically. I have a public calendar with my engagements (http://xray.bmc.uu.se/flores/Calendar.html) which should give you an idea of when I'm in town and so on. Sam > Hi Samuel, > > Thank you very much for your reply. I did not get any announcement from the email list about your reply though. > > I tried exercise 1 and it seems to work fine. I thought that de-clashing was included also in the first exercise as the final output figure in the tutorial document looks ok. However, now when I read in the commands.hairpin-short.dat file about how clashes are treated I understand more; I was a bit fast in sending my problem to the email list, I realize that now. > > I will continue the exercises and I think that things will work out fine. > > Thank you for the suggestion about the MMB workshop. When will it take place and what will be the main topics? Two of my collegues went to the course that you had in Uppsala last week and it was actually from them that I found out about MMB and that it can be used for predicting RNA 3D structures. I am trying different programs fo this purpose and it will be interesting to try how well MMB works. I will mainly use it for predicting structures of small RNAs. > > Thank you again. > > Best regards, > Emma Eriksson > > Postdoctoral associate > Department of Chemistry and Molecular Biology > University of Gothenburg > 412 96 Göteborg > Sweden > > ________________________________________ > Från: Samuel Flores [samuelfloresc(a)gmail.com] > Skickat: den 4 september 2012 15:27 > Till: Emma Eriksson > Ämne: Re: clashes in exercise 0 > > Did you get this message? I'm not entirely sure that the email list is functioning correctly. > > thanks > > sam > >> Hi Emma, >> >> That example does not have sterics turned on. It is merely intended to make sure you have installed MMB correctly (which you have). >> >> Try exercise 1 to see an example that includes de-clashing. >> >> If you tell me more about your problem I can help guide you to use MMB most effectively. >> >> Are you interested in an MMB workshop? We are running one soon in Uppsala, and I have been thinking about setting one up in Gothenburg (thought that might be some time from now). >> >> Sam >> >> >>> Send Rnatoolbox-help mailing list submissions to >>> rnatoolbox-help(a)simtk.org >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://simtk.org/mailman/listinfo/rnatoolbox-help >>> or, via email, send a message with subject or body 'help' to >>> rnatoolbox-help-request(a)simtk.org >>> >>> You can reach the person managing the list at >>> rnatoolbox-help-owner(a)simtk.org >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of Rnatoolbox-help digest..." >>> >>> >>> Today's Topics: >>> >>> 1. Tutorial problem - Unrealistic RNA structure generated >>> (Emma Eriksson) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Tue, 4 Sep 2012 07:31:26 +0000 >>> From: Emma Eriksson <emma.eriksson(a)chem.gu.se> >>> Subject: [RNABuilder-help] Tutorial problem - Unrealistic RNA >>> structure generated >>> To: "rnatoolbox-help(a)simtk.org" <rnatoolbox-help(a)simtk.org> >>> Message-ID: >>> <E7E706508AD8CC4CA0E362089D784E9C0351AF(a)thane.ita.chalmers.se> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Hi all, >>> >>> >>> >>> I am new to the MMB software and I am going through the tutorials in order to learn how the program works. However, I am not even able to complete the first tutorial (Exercise 0 with commands.singlebasepair.dat). The files last.1.pdb and trajectory.1.pdb are generated but the RNA structure is unrealistic, with overlapping bases, like if they did not feel each other's presence. The folding to this conformation happens very early in the trajectory. >>> >>> I am following the exact instructions from the tutorial and I have not made any changes. I am running on Windows 7. What am I doing wrong? >>> >>> I would really appreciate some help. Thank you! >>> >>> >>> >>> Best regards, >>> >>> Emma >>>

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test -- please disregard
by Samuel Flores 04 Sep '12

04 Sep '12

testing email list mailed at 16:22 CET, 4 sept 2012

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clashes in exercise 0
by Samuel Flores 04 Sep '12

04 Sep '12

Hi Emma, That example does not have sterics turned on. It is merely intended to make sure you have installed MMB correctly (which you have). Try exercise 1 to see an example that includes de-clashing. If you tell me more about your problem I can help guide you to use MMB most effectively. Are you interested in an MMB workshop? We are running one soon in Uppsala, and I have been thinking about setting one up in Gothenburg (thought that might be some time from now). Sam > Send Rnatoolbox-help mailing list submissions to > rnatoolbox-help(a)simtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://simtk.org/mailman/listinfo/rnatoolbox-help > or, via email, send a message with subject or body 'help' to > rnatoolbox-help-request(a)simtk.org > > You can reach the person managing the list at > rnatoolbox-help-owner(a)simtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rnatoolbox-help digest..." > > > Today's Topics: > > 1. Tutorial problem - Unrealistic RNA structure generated > (Emma Eriksson) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 4 Sep 2012 07:31:26 +0000 > From: Emma Eriksson <emma.eriksson(a)chem.gu.se> > Subject: [RNABuilder-help] Tutorial problem - Unrealistic RNA > structure generated > To: "rnatoolbox-help(a)simtk.org" <rnatoolbox-help(a)simtk.org> > Message-ID: > <E7E706508AD8CC4CA0E362089D784E9C0351AF(a)thane.ita.chalmers.se> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > > > I am new to the MMB software and I am going through the tutorials in order to learn how the program works. However, I am not even able to complete the first tutorial (Exercise 0 with commands.singlebasepair.dat). The files last.1.pdb and trajectory.1.pdb are generated but the RNA structure is unrealistic, with overlapping bases, like if they did not feel each other's presence. The folding to this conformation happens very early in the trajectory. > > I am following the exact instructions from the tutorial and I have not made any changes. I am running on Windows 7. What am I doing wrong? > > I would really appreciate some help. Thank you! > > > > Best regards, > > Emma >

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Tutorial problem - Unrealistic RNA structure generated
by Emma Eriksson 04 Sep '12

04 Sep '12

Hi all, I am new to the MMB software and I am going through the tutorials in order to learn how the program works. However, I am not even able to complete the first tutorial (Exercise 0 with commands.singlebasepair.dat). The files last.1.pdb and trajectory.1.pdb are generated but the RNA structure is unrealistic, with overlapping bases, like if they did not feel each other's presence. The folding to this conformation happens very early in the trajectory. I am following the exact instructions from the tutorial and I have not made any changes. I am running on Windows 7. What am I doing wrong? I would really appreciate some help. Thank you! Best regards, Emma

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