- Rnatoolbox-help - SimTK Mailing Lists

Re: Suggested fix for Pdb.cpp - Look good.
by Samuel Flores 04 Apr '13

04 Apr '13

Hi Ugur, Mike had the same problem you had and solved it by issuing: matchHydrogenAtomLocations TRUE See the explanation below. Sorry it has taken so long to get back to you. I hope to have a real solution to this issue before too long, because reading hydrogen atom locations can cause trouble if the chirality is not clear (e.g. three bonds nearly coplanar, that sort of thing). but for now this may work fine for you, as it did for Mike. Sam > Samuel! > > You are a champ! > The option: > > matchHydrogenAtomLocations True > > seems to do the trick. I've been racking my brains on this one. > > many thanks for the insight! Good luck with the grant writing! Never a fun time. > > Best regards, > Mike > > > > On 03/04/13 21:01, Samuel Flores wrote: >> Actually I think in this case the problem is more likely that molmodel has a bit of trouble creating atom positions for two hydrogens on a tetravalent atom, quite likely C5'. If the angle it forms with O5' and C4' is a bit obtuse, it can have trouble with this. Actually it's embarrassingly picky -- I've documented it puking when this angle is 153 degrees, which is really not far from the equilibrium angle. I am planning to make a more robust alternative method for this. Right now I am writing grants but have scheduled it for 22 April, with my apologies. >> >> MMB by default ignores hydrogens, so you can try to get it to read hydrogen atom positions by setting >> >> matchHydrogenAtomLocations True >> >> .. though this very often causes additional problems, because recognizing chirality is itself an issue. So I'm not confident that this will solve your problem, though it might. >> >> >> As a workaround you might try chopping out bits of your post-NAMD structure until MMB runs. This way you can identify which residue is problematic. moving the offending atom by a tenth of an Ångström might be enough to fix it. But I acknowledge that this is highly unattractive given the number of iterations you might end up going through. >> >> Sam >> >> >> >> >> >> >>

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Re: pdb write bug in MMB 2.11
by Samuel Flores 08 Mar '13

08 Mar '13

On Mar 7, 2013, at 11:45 PM, Michael Kuiper wrote: > Greetings Samuel! > > Please feel free to use any movies I send you any way you like. I hope to have some more later. > > I think I've found a bug in 2.11 with regards to writing out large pdb files. (I'm not quite sure the official way to report this) > I'm not sure i like how the fora work .. so for now writing to rnatoolbox-help(a)simtk.org is best > It seems to me that if there are more than 100000 atoms, we will see a shift in the x,y,z coordinates due to the limitations in the > pdb format in the atom number column. I've written a small python script that corrects these errors for myself but it is easier to do it in the source! If your molecules are big you should just see a reduction in the precision. Can you send me your commands.dat and input structure file? > > The error means that the large molecule trajectories are not displayed properly in vmd and also restarting from a > 'last.x.pdb' file also seems corrupted. > > For large atom numbers I use hexadecimal notation in pdb files. > > Have to run to a meeting, > chat soon! > > Mike >

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MMB 2.11 released
by Samuel Flores 06 Mar '13

06 Mar '13

Dear MMB Users, I have now posted MMB 2.11 for OSX, Windows, and Linux. The following is from the "What's New" section of the Reference Guide: In release 2.11 the length units are Ångströms rather than nanometers, consistent with molmodel’s conventions. This makes it easier to relate various stiffnesses, energies, and other physical quantities. I have created the rootMobilizer command, which for the first time allows you to connect a chain to ground using a Weld mobilizer (rather than the default Free) – this reduces the degrees of freedom of the system and saves compute time, for the often-found situation in which one or more chains are fixed to ground. There is also now a constrainChainRigidSegments command, which constrains all rigid segments in a chain either to ground or to a specified residue in the same chain (permitting center of mass motions). One application of this is to flexibilize an interface and allow (or not allow) center of mass motions, e.g. to equilibrate clashes on that interface. I welcome comments on the release. Happy modeling! Sam

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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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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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