February 2013 - Rnatoolbox-help - SimTK Mailing Lists

Re: Installer.2_10.CentOS64.tgz for CentOS5
by Samuel Flores 26 Feb '13

26 Feb '13

yes I think you have an out of date molmodel library issue. are you sure you're compiling against molmodel trunk? I'm on travel at the moment and am a bit tight for time .. but if you wish we can set up a skype meeting for monday or so. mmb wo tsukau, arigatou! dewa mata! sam > You have been contacted by a member of Simtk.org. > > From: shaq liu > Email: zliu(a)ifrec.osaka-u.ac.jp > > The e-mail was sent via the "contact" link on Simtk.org by the above member. It is not screened by Simtk.org or its staff. > > > *** MESSAGE BEGINS *** > > Dear Sam, > > It seems binaries inside Installer.2_10.CentOS64.tgz in your download area are for CentOS6. Could you compile it for CentOS5? Most of our compute nodes are CentOS5.2/5.3/5.4/5.4 64bit. > > We also tried to compile MMB (MacroMoleculeBuilder) from source. But failed by error like this [[ rnatoolbox/trunk/include/PeriodicPdbAndEnergyWriter.h:51: error: 'setWriteFullPrecisionLocation' is not a member of 'SimTK::PdbAtom' ]]. Please advise if you have time. Let me know if you need more input about how we compiled. > > Thank you, > Shaq Liu <zliu(a)ifrec.osaka-u.ac.jp>

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Re: MMB RNA threading
by Samuel Flores 18 Feb '13

18 Feb '13

The problem of residue 309 is with atom C5', or more precisely the angle formed with O5' and C4'. it's a bit obtuse -- 153 degrees. If it's made a little more acute (basically by moving C5' a little in the negative x,y,z directions) the problem disappears. I am working on a fix for this issue but it's actually a bit subtle. in the meantime moving the atoms in question a bit should help you work around the issue. Sam > I think I answered my own questions. I temporarily removed chains (B, C) from the last.1.pdb file. I will thread them individually and merge them later into a single pdb file. I assume coordinates will be retained. > > Right now I loaded the entire rna sequene in the input file and MMB doesn't seem to be limited by 3k. > > If this performs well I will cite you all over the place :) > > uzay > ________________________________________ > From: UGUR UZAY Sezen > Sent: Thursday, February 14, 2013 10:27 AM > To: Samuel Flores > Subject: RE: MMB RNA threading > > I managed to thread 3000nt so far. I had to delete another residue #1623. I have a few questions. > > [1] MMB tutorial says 3000nt is the upper limit for threading. My sequence is 3388nt long. How do you suggest to get over this problem? > [2] 3iz9 has 3 chains. As you see in the picture (attached) the two chains extend out without being threaded. Is there a way to thread multiple chains using the same command file? > > So far so good! > > uzay > ________________________________________ > From: Samuel Flores [samuelfloresc(a)gmail.com] > Sent: Wednesday, February 13, 2013 8:55 PM > To: UGUR UZAY Sezen > Subject: Re: MMB RNA threading > > you can delete parts of your last.1.pdb to see which pieces caused the problem. > > I would like to try to figure out why those residues are problematic -- in the meantime this way can help you at least do part of your model. > > > > sam > > >> I deleted 309 + 310 and voila! it worked until 1500's. Now I encounter the same error. How can you tell the problem bases in pdb file of 3iz9? I attached the command file for you to see. >> >> I appreciate your input. >> >> uzay >> ________________________________________ >> From: Samuel Flores [samuelfloresc(a)gmail.com] >> Sent: Tuesday, February 12, 2013 11:55 PM >> To: UGUR UZAY Sezen >> Subject: Re: MMB RNA threading >> >> I'm at a conference and am having trouble troubleshooting this properly. However I can tell you that if you delete residues 309 and 310 from last.1.pdb you remove the problem. perhaps there is some geometric issue with these residues? >> >> >> sam >> >>> Great! >>> >>> Here's the command file and the alignment. I commented out most of the sequences while playing around. >>> >>> I appreciate your guidance. >>> >>> Uzay >>> >>> Uğur Uzay Sezen >>> Post-Doctoral researcher >>> Plant Genome Mapping Laboratory >>> University of Georgia >>> Center for Applied Genetic Technologies >>> 111 Riverbend Rd., Athens, GA 30602 >>> uzay(a)uga.edu >>> tel: 706-583-0170 >>> fax: 706-583-8120 >>> http://www.plantgenome.uga.edu/ >>> http://naturedocumentaries.org/ >>> >>> ________________________________________ >>> From: Samuel Flores [samuelfloresc(a)gmail.com] >>> Sent: Tuesday, February 12, 2013 4:55 PM >>> To: UGUR UZAY Sezen >>> Cc: rnatoolbox-help(a)simtk.org >>> Subject: Re: MMB RNA threading >>> >>> Hi Uzay, >>> >>> Happy to help. Can you send me your command file? I will take a look. >>> >>> Sam >>> >>>> You have been contacted by a member of Simtk.org. >>>> >>>> From: Uzay Sezen >>>> Email: uzay(a)uga.edu >>>> >>>> The e-mail was sent via the "contact" link on Simtk.org by the above member. It is not screened by Simtk.org or its staff. >>>> >>>> >>>> *** MESSAGE BEGINS *** >>>> >>>> I successfully run MMB using the examples in tutorial. I want to thread Sorghum ribosomal RNA on wheat model (3IZ9) but can't get it to work even in short (less than 120nt) sequences in the command input file. Can anybody provide me feedback? >>>> >>>> All the best, >>>> >>>> Uzay >>>> >>>> uzay(a)uga.edu >>> >>> <commands.3iz9-threading.dat><Sbi26S-Tae28Salign.txt> >> >> >> <commands.3iz9-threading.dat> > > >

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Re: MMB RNA threading
by Samuel Flores 12 Feb '13

12 Feb '13

Hi Uzay, Happy to help. Can you send me your command file? I will take a look. Sam > You have been contacted by a member of Simtk.org. > > From: Uzay Sezen > Email: uzay(a)uga.edu > > The e-mail was sent via the "contact" link on Simtk.org by the above member. It is not screened by Simtk.org or its staff. > > > *** MESSAGE BEGINS *** > > I successfully run MMB using the examples in tutorial. I want to thread Sorghum ribosomal RNA on wheat model (3IZ9) but can't get it to work even in short (less than 120nt) sequences in the command input file. Can anybody provide me feedback? > > All the best, > > Uzay > > uzay(a)uga.edu

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