modeller_usage

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3151 discussions

Re: [modeller_usage] How to get Secondary Structure in Alignment file
by Thomas Evangelidis 26 Mar '11

26 Mar '11

On 26 March 2011 07:47, Ashish Runthala <ashishr(a)bits-pilani.ac.in> wrote: > Dear Thomas, > You mentioned the free tools in details. I appreciate that. But what i > don't understand is to manually call everyone, and then keep on doing it, is > tedious but fun it is. > So if I get it right this time, you didn't ask what commercial free tools are available to display your sequence alignment along with the secondary structure, is that correct? Could you please be more careful with your syntax cause it's kind of difficult to follow you. > I had a query that template secondary structure information is there in > templates, but with indels, that may be disturbed. I mean the native > information is deteriorated. > > So if based on indels, available in current alignment, if i can link > directly to a python script. So that my next programme to generate the > optimal alignment will become successful, as i did all of these several > times manually, to design the algorithm to generate best representative > alignment. > > So you want to write a python script that can cope with indels inside SSEs. Namely, given a structure-based alignment between your target and templates, you want to select which of the following alignments is the optimum: target > HCSIHHSC Template1> HCSIHISC Template2> HCSHHISC ------------------------------------------------------- target > HCS-IHHSC Template1> HCS-IHISC Template2> HCSH-HISC ------------------------------------------------------- target > HCSI-HHSC Template1> HCS-IHISC Template2> HCS-HHISC etc. Is this what you seek? > Will you please elaborate this time. > > Thanks, > Ashish > > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > ----- Original Message ----- > From: "Thomas Evangelidis" <tevang3(a)gmail.com> > To: "Ashish Runthala" <ashishr(a)bits-pilani.ac.in> > Cc: "modeller" <modeller_usage(a)salilab.org> > Sent: Friday, March 25, 2011 4:50:42 PM GMT +05:30 Chennai, Kolkata, > Mumbai, New Delhi > Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment > file > > Maestro from Schrodinger can display both the predicted secondary structure > elements (SSE) of the target and the SSE of the templates above the > alignment dynamically (namely if you change the alignment the SSEs are > changed accordingly). > > Alternatively you can use the following commercial free tools: > > ESPript ( http://espript.ibcp.fr/ESPript/ESPript/ ): can create an image > of your alignment with the SSEs of your templates above it. No SSE of the > target is displayed though. > > MolIDE ( http://dunbrack.fccc.edu/molide/index.php ): I have the notion > that this alignment editor (and not only) can display both the predicted SSE > of the target and the SSE of the templates. However, I didn't manage to run > it yet due to compilation problems. I intend to give it a try in the near > future. > > STRAP ( http://3d-alignment.eu/ ): it can do both but the GUI is not handy > in Linux (windows and fonts are unequal, etc.). > > Finally you can add a row with the secondary structure (as you wrote it in > your email) above each sequence in your alignment editor. I prefer Jalview > and like to play around with groups and colors. See the attached image for > an example. SSE of your templates can be retrieved from PDB (e.g. > http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2IXF&chainId=A) whereas the SSE of your target can be predicted by Jpred3 ( > http://www.compbio.dundee.ac.uk/www-jpred/ ). > > > HTH, > > Thomas > > > > > On 25 March 2011 05:47, Ashish Runthala < ashishr(a)bits-pilani.ac.in > > wrote: > > > Dear Modellers, > Suppose i have two templates, and a target sequence. Instead of sequence > alignment based file, i want to consider the secondary structure > information, like given below > > Template1> HCSIHISC > Template2> HCSHHISC > > H=Helix, C=Coil, S-Strand, I=Indels > > Is it possible to get the alignment in this case for multiple templates > against the target sequence( whose structure can also be represented as best > aligned folds) > > Thanks > Ashish > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > > > -- > > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tevang(a)bioacademy.gr > > tevang3(a)gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 55
by Ashish Runthala 25 Mar '11

25 Mar '11

Dear Thomas, You mentioned the free tools in details. I appreciate that. But what i don't understand is to manually call everyone, and then keep on doing it, is tedious but fun it is. I had a query that template secondary structure information is there in templates, but with indels, that may be disturbed. I mean the native information is deteriorated. So if based on indels, available in current alignment, if i can link directly to a python script. So that my next programme to generate the optimal alignment will become successful, as i did all of these several times manually, to design the algorithm to generate best representative alignment. Will you please elaborate this time. Thanks, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Friday, March 25, 2011 4:50:46 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 55 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. How to get Secondary Structure in Alignment file (Ashish Runthala) 2. Re: How to get Secondary Structure in Alignment file (Thomas Evangelidis) ---------------------------------------------------------------------- Message: 1 Date: Fri, 25 Mar 2011 09:17:07 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Subject: [modeller_usage] How to get Secondary Structure in Alignment file To: modeller <modeller_usage(a)salilab.org> Message-ID: <11283718.504161301024827590.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 Dear Modellers, Suppose i have two templates, and a target sequence. Instead of sequence alignment based file, i want to consider the secondary structure information, like given below Template1> HCSIHISC Template2> HCSHHISC H=Helix, C=Coil, S-Strand, I=Indels Is it possible to get the alignment in this case for multiple templates against the target sequence( whose structure can also be represented as best aligned folds) Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 2 Date: Fri, 25 Mar 2011 13:20:42 +0200 From: Thomas Evangelidis <tevang3(a)gmail.com> Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment file To: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Cc: modeller <modeller_usage(a)salilab.org> Message-ID: <AANLkTikYvKNM3qPUU4kJ=h50DE75AJS7ncZJqjMVPSdx(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Maestro from Schrodinger can display both the predicted secondary structure elements (SSE) of the target and the SSE of the templates above the alignment dynamically (namely if you change the alignment the SSEs are changed accordingly). Alternatively you can use the following commercial free tools: ESPript (http://espript.ibcp.fr/ESPript/ESPript/): can create an image of your alignment with the SSEs of your templates above it. No SSE of the target is displayed though. MolIDE (http://dunbrack.fccc.edu/molide/index.php): I have the notion that this alignment editor (and not only) can display both the predicted SSE of the target and the SSE of the templates. However, I didn't manage to run it yet due to compilation problems. I intend to give it a try in the near future. STRAP (http://3d-alignment.eu/): it can do both but the GUI is not handy in Linux (windows and fonts are unequal, etc.). Finally you can add a row with the secondary structure (as you wrote it in your email) above each sequence in your alignment editor. I prefer Jalview and like to play around with groups and colors. See the attached image for an example. SSE of your templates can be retrieved from PDB (e.g. http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2IXF&chainId=A) whereas the SSE of your target can be predicted by Jpred3 ( http://www.compbio.dundee.ac.uk/www-jpred/). HTH, Thomas On 25 March 2011 05:47, Ashish Runthala <ashishr(a)bits-pilani.ac.in> wrote: > Dear Modellers, > Suppose i have two templates, and a target sequence. Instead of sequence > alignment based file, i want to consider the secondary structure > information, like given below > > Template1> HCSIHISC > Template2> HCSHHISC > > H=Helix, C=Coil, S-Strand, I=Indels > > Is it possible to get the alignment in this case for multiple templates > against the target sequence( whose structure can also be represented as best > aligned folds) > > Thanks > Ashish > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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How to get Secondary Structure in Alignment file
by Ashish Runthala 25 Mar '11

25 Mar '11

Dear Modellers, Suppose i have two templates, and a target sequence. Instead of sequence alignment based file, i want to consider the secondary structure information, like given below Template1> HCSIHISC Template2> HCSHHISC H=Helix, C=Coil, S-Strand, I=Indels Is it possible to get the alignment in this case for multiple templates against the target sequence( whose structure can also be represented as best aligned folds) Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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modelling from 2 templates, one for major part of sequence, 1 for insertion region
by Irene Newhouse 21 Mar '11

21 Mar '11

I'm trying to model a protein that looks like a member of CIS_IPPS with reasonable homlogy for a major portion of the sequence, but with a significant insertion region that has weak homology to a portion of a different protein. I tried to build with the .py & .ali files listed below, with the result that the CIS_IPPS regions of the protein were built just fine, but the insertion region was nothing but a random coil. When I extracted the insertion region & modeled it based on the extracted portion of the other protein, I was able to model something reasonable. I could use a GUI to meld the two models together, but I'd rather have recommendations as to how to get modeller to do the build for me - I think it'd be a lot better starting structure than the result of a hand-meld. Thanks in advance! Irene Newhouse .py file: from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '/home/newhoir/rubber/'] #read HETATMS in template env.io.hetatm = True # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'rub4b.ali' , # alignment filename knowns = ('2x06', '2erx'), # codes of the templates sequence = '1cp4', # code of the target assess_methods=assess.GA341) # request model assessment a.starting_model= 1 # index of the first model a.ending_model = 20 # index of the last model # (determines how many models to calculate) a.library_schedule = autosched.slow # thorough VTFM opt a.max_var_iterations = 300 a.md_level = refine.very_slow a.make() # do the actual homology modeling The .ali file: >P1;2x06 structureX:2x06:12:A:+474:B:PDB::0.00:0.00 -------------------------KLPAHG--CRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKS---LHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVR--------------------------------------------------------------QLAEKVQQGNLQPDQIDEEMLN-----------------------------------------------QHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE----------.../-------------------------KLPAHG--CRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKS---LHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVR--------------------------------------------------------------QLAEKVQQGNLQPDQIDEEMLN-----------------------------------------------QHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE----------...* >P1;2erx structureX:2erx:16:A:+66:B:PDB::0.00:0.00 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVI------------------------------------------------------------------------------------------------------/---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVI------------------------------------------------------------------------------------------------------* >P1;1cp4 sequence:1cp4:1:A:+758:B:::0.00:0.00 MGKHSSSRVSELFGNLGSFIRACIFRVLSMGPIPNHFAFIMDGNRRYAKKENMKKGAGHRAGFLALISILKYCYELGVKYVTIYAFSIDNFKRNPDEVKDLMDLMLEKIEELLRDESIVNQYGIRVYFIGNLKLLSEPVRIAAEKVMRATAKNTNCTLLICIAYTSRDEIVHAVQGSCKNKREDILPLSFCKANNGDIEEVEDDKKVHGVSPFVFSESQKDEAGESQATIASVTCSCLARGVEGGGNKNSMVVRAVRGSYEDKW-----DNYQAVMENRTGSGVTPSEENKNMQGECSIVKLVDIEKQMYMAVAPEPDILIRSSGESRLSNFLLWQSSECLLYSPDALWPEIGLWHLVWAVLNFQRNHSYLERKKHQL.../MGKHSSSRVSELFGNLGSFIRACIFRVLSMGPIPNHFAFIMDGNRRYAKKENMKKGAGHRAGFLALISILKYCYELGVKYVTIYAFSIDNFKRNPDEVKDLMDLMLEKIEELLRDESIVNQYGIRVYFIGNLKLLSEPVRIAAEKVMRATAKNTNCTLLICIAYTSRDEIVHAVQGSCKNKREDILPLSFCKANNGDIEEVEDDKKVHGVSPFVFSESQKDEAGESQATIASVTCSCLARGVEGGGNKNSMVVRAVRGSYEDKW-----DNYQAVMENRTGSGVTPSEENKNMQGECSIVKLVDIEKQMYMAVAPEPDILIRSSGESRLSNFLLWQSSECLLYSPDALWPEIGLWHLVWAVLNFQRNHSYLERKKHQL...*

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Modeller and Fedora 14 / python 2.7
by Susan Hutchinson 21 Mar '11

21 Mar '11

I wonder if anyone could help, please. After upgrading our systems from Fedora 12 to Fedora 14 we are unable to run modeller. It installs but fails to run, reporting the following errors: Traceback (most recent call last): File "modeller_gi60681617.py", line 2, in<module> from modeller import * # Load standard Modeller classes File "/usr/lib64/python2.7/site-packages/modeller/__init__.py", line 72, in<module> import _modeller ImportError: No module named _modeller Do you know of any problems with Modeller and recent versions of Fedora? Can you confirm that Modeller will work with Python 2.7 - the version that runs on Fedora 14 systems. The package is essential for one of our research groups and I would be very grateful for any help or advice you can give me. Many thanks, Susan Hutchinson -- Susan Hutchinson hutchins(a)stats.ox.ac.uk Computing Support Specialist http://www.stats.ox.ac.uk Department of Statistics Tel : +44 (0)1865 282852 1 South Parks Road, Fax : +44 (0)1865 272595 Oxford OX1 3TG, UK.

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NaN error model generation Lennard-Jones restraints
by David Rodríguez 18 Mar '11

18 Mar '11

Hi, In order to obtain models with less clashes (and improved stereochemistry) as measured by Molprobity, I followed this thread: http://salilab.org/archives/modeller_usage/2010/msg00382.html Taking Nick's advice into account, I switched on the dynamic Lennard-Jones restraints with the simple script shown below. Some models are generated, showing improved statistics regarding clashes and stereochemical quality, but many others fail to be generated due to NaN values in the optimization process (see 'yyyy.D00000002' file attached), and shown in the .log file as: ... yyyy.B99990002.pdb Obj. func. (nan) exceeded max_molpdf (10000000.000) ... I have varied many variables (different alignments, targets, using optimization values as in the 'model_changeopt.py' example script...), but the problem remains. The .ini file looks fine, and of course switching off LJ restraints does not yied that error. I hope someone would help with this issue. Thanks in advance. Regards, -- automodel_lj.py -- # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['./'] energy_data.dynamic_lennard = True a = automodel(env, alnfile = 'file.ali', # alignment filename knowns = 'xxxx', # codes of the templates sequence = 'yyyy', # code of the target assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1 # index of the first model a.ending_model = 15 # index of the last model # (determines how many models to calculate) ## Very thorough VTFM optimization: #a.library_schedule = autosched.slow #a.max_var_iterations = 300 ## Very thorough MD optimization: #a.md_level = refine.very_slow a.make() # do the actual homology modeling -- David Rodríguez Díaz, PhD Student Fundación Pública Galega de Medicina Xenómica (SERGAS) Santiago de Compostela (Spain) http://webspersoais.usc.es/persoais/david.rodriguez.diaz <http://webspersoais.usc.es/persoais/david.rodriguez.diaz>

2 1

E-values for profile building
by Lilit Nersisyan 18 Mar '11

18 Mar '11

I have a question regarding the e-values used in the build_profile. When I set the e-value less then 6, no sequences are found, but for higher e-values (with high numbers of iterations) several sequences are found that have e-values less than 1. What is the reason? Thank you. -- Lilit Nersisyan Institute of Molecular Biology NAS RA E-mail: txgt.lilit.nersisyan(a)gmail.com Tel.: +37494 601703

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Fedora 14 and Modeller
by flavio seixas 18 Mar '11

18 Mar '11

Hi, I was trying to install modeller on an AMD AthlonX2 Fedora-14 Linux machine 64-bit x86_64 RPM version. The following error message appears: [root@NIR Downloads]# env KEY_MODELLER9v8=<my password> rpm -Uvh modeller-9v8-1.x86_64.rpm warning: modeller-9v8-1.x86_64.rpm: Header V4 DSA/SHA1 Signature, key ID 745e6093: NOKEY Preparing... ########################################### [100%] 1:modeller ########################################### [100%] restorecon reset /usr/lib/modeller9v8/lib/x86_64-intel8/libifcore.so.5 context system_u:object_r:lib_t:s0->system_u:object_r:textrel_shlib_t:s0 [root@NIR Downloads]# I tested typing: [root@NIR Downloads]# mod9v8 /usr/lib/modeller9v8/bin/mod9v8_x86_64-intel8: error while loading shared libraries: libintlc.so.5: cannot enable executable stack as shared object requires: Permission denied Is there any library missing? I did not found nothing related with libifcore or libintlc at google... Thanks for any help. Flavio

2 1

licence key for using modellar
by An＠mIk＠ SiNgH 15 Mar '11

15 Mar '11

please provide me the to get licence key for using modellar.... -- **Anamika Singh

2 1

Re: [modeller_usage] Beta strand
by Thomas Evangelidis 09 Mar '11

09 Mar '11

On 9 March 2011 15:44, Claudia Scotti <claudiascotti(a)hotmail.com> wrote: > Dear Thomas, > > Many thanks for your suggestions. > > Yes: I have already tried to remove the alignment, but the "strand" does > not become a strand and it moves away from the beta sheet against which it > is supposed to pack. > > Mmhhh... Actually, should I try the beta sheet restraints? In this case, > please, I have some doubts on the command: > It would be a good idea to try both the strand and beta sheet restraints and the leave this region unaligned. > > rsr.add(secondary_structure.sheet(at['N:1'], at['O:14'],sheet_h_bonds=-5)) > > Particuarly, please, I can't find the explanation of the syntax in > parenthesis. May you please help me with this? > You mean the hydrogen bonding pattern in a beta sheet? Here is an explanation: http://en.wikipedia.org/wiki/Beta_sheet#Hydrogen_bonding_patterns and this one from Modeller's manual: http://www.salilab.org/modeller/manual/node219.html This is an example code snippet from my archive: rsr.add(secondary_structure.strand(self.residue_range('1:', '7:'))) rsr.add(secondary_structure.strand(self.residue_range('19:', '26:'))) rsr.add(secondary_structure.strand(self.residue_range('56:', '63:'))) ##An anti-parallel sheet composed of the two strands: self.restraints.add(secondary_structure.sheet(at['N:2'], at['O:23'], sheet_h_bonds=-12)) self.restraints.add(secondary_structure.sheet(at['O:1'], at['N:59'], sheet_h_bonds=-8)) Good luck! Thomas -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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