- modeller_usage - salilab.org

Reading in water residues
by Sajeewa Pemasinghe 25 Sep '12

25 Sep '12

Hi everyone, I want to read in hydrogens, heteroatoms and water molecules into my modeller-modeled protein structure. In the manual it says: to read in the heteroatoms, put env.io.hetatm=true and to use '.' characters in the alignment sequences. to read in the waters, put env.io.water=true and to use 'w' characters in the alignment sequences. Usually in a pdb file the 'ligand' heteroatoms are given as HETATM 843 FE1 SF4 A 107 14.698 20.785 10.230 1.00 13.78 FE and waters are given as HETATM 858 O HOH A 109 23.833 10.228 18.799 1.00 17.80 O so both of them use 'HETATM' . So my question is if we have asked the modeller to read ALL HETATM records by setting env.io.hetatm=true, do we have to specifically say again, to add waters by env.io.water=true. Can't we just read all the heteroatom records (including waters) and use '.' for both normal heteroatoms and waters? Thank you Sajeewa Dewage

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meaning of "env.io.atom_files_directory"
by Sajeewa Pemasinghe 22 Sep '12

22 Sep '12

Hi everyone, I am working on the tutorial in http://salilab.org/modeller/wiki/Missing%20residues. I have my pdb files in C:\Users\Sajeewa\Desktop\protease_project\modeller_practice directory. In the script to generate the model with all residues # directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files'] should this be changed as env.io.atom_files_directory = ['C:/Users/Sajeewa/Desktop/protease_project/modeller_practice'] ? I don't understand what it means by '.', '../atom_files' Could you please explain? Thank you Sajeewa Dewage

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sequence file produced is different from the one shown in the tutorial
by Sajeewa Pemasinghe 21 Sep '12

21 Sep '12

Hi everyone, I am working on the example given in the modeller tutorial http://salilab.org/modeller/wiki/Missing%20residues. I used the exact same script to generate the sequence file. Instead of the given pdb1qg8.ent , I used the 1qg8.pdb downloaded from www.rcsb.org. When I ran the script it resulted in the following sequence file (1qg8.seq) >P1;1qg8 structureX:1qg8: 2 :A:+238 :A:MOL_ID 1; MOLECULE SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA; CHAIN A; ENGINEERED YES; OTHER_DETAILS GLYCEROL MAGNESIUM:MOL_ID 1; ORGANISM_SCIENTIFIC BACILLUS SUBTILIS; GENE SPSA; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_STRAIN BL 21: 1.50: 0.16 PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNDIVKETVRPAAQVTWNAP CAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITEFVRNLPPQRNC RELRESLKKLGMG* In the field 5, it says +238 whereas in the tutorial, in the resulting 1qg8.seq file it shows 256. Have I done any mistake? Would the above sequence file work just as fine as the one shown in the tutorial? Thank you Sajeewa Dewage

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Fwd: PIR file format
by Nanda Pandey 21 Sep '12

21 Sep '12

Thanks for the reply, Troubling you with one more query though.... "PIR files are just plain text, so they're very easy to make manually in a text editor or with some simple scripting." I have read in the forum that one needs to input PDB structure details also while changing the format, Please let me know if this is required for query sequence also or only while submitting the alignment as input (changed to PIR). Thanks and Regards, Nanda On Fri, Sep 21, 2012 at 6:00 PM, Modeller Caretaker < modeller-care(a)salilab.org> wrote: > On 9/21/12 6:26 AM, Nanda Pandey wrote: > >> Do i need to convert my sequence to PIR file format in order to use it. >> > > If by "use it", you mean you want to build a comparative model, then yes. > > > If yes, how do i do it?? >> > > PIR files are just plain text, so they're very easy to make manually in a > text editor or with some simple scripting. > > > Is it recommended to generate alignment from external sources and then >> perform modelling using modeller or I can generate my model for a >> sequence using only modeller. >> > > You can do it either way. The alignment you use for modeling doesn't have > to be generated by Modeller. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/**modeller/<http://www.salilab.org/modeller/> > Modeller mail list: http://salilab.org/mailman/**listinfo/modeller_usage<http://salilab.org/mailman/listinfo/modeller_usage> >

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PIR file format
by Nanda Pandey 21 Sep '12

21 Sep '12

Hi, I am new to modeller so have a basic question : Do i need to convert my sequence to PIR file format in order to use it. If yes, how do i do it?? Is it recommended to generate alignment from external sources and then perform modelling using modeller or I can generate my model for a sequence using only modeller. Getting confused with the tutorials. Thanks, Nanda.

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Modeling a missing loop without any template strand
by Sajeewa Pemasinghe 20 Sep '12

20 Sep '12

Hi everyone, I am quite new to modeller (My first time posting). I have a pdb file in which a loop (11 residues long) is missing. I DO NOT have a template strand which contains these missing residues. Can I use modeller to build these for me from scratch? Thank you Sajeewa Dewage

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Regarding CASP9 Targets
by Ashish Runthala 17 Sep '12

17 Sep '12

Dear Modellers, Is there a way to get the information about CASP9 Targets, i.e. which of the CASP9 targets are TBM-HA (High Accuracy) targets? Unlike CASP9 page, CASP8 results page gives such information. Please show me the path. CASP abstract details also don't reveal such information, however 50 such targets were discussed in the meeting, as per their added information. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Building in missing residues from a known structure
by Joshua Adelman 12 Sep '12

12 Sep '12

I've looked through the mailing list archives and online documentation, but I'm having some trouble wrapping my head around the proper way to accomplish the following. I have two PDB files of a protein in different conformations, where in one of the two PDBs, a short stretch of residues are missing, but in the other the complete coordinates in that region are known. Both PDBs have different missing residues throughout their chain, but I'm only interested at this time in modeling that small section that's present in one and not in the other. My alignment file looks something like: >P1;A structureX:A: 1 :A:149 :A:::-1.00:-1.00 ---------FIRIMVFAIYVALPIGV--------------------AGKSLPWYAVGASLIAANISAEQFIGGMS SAYSIGLAIASYRWMSALTLIIVGKYFLPIFIEKGIYTIPEFVRKRSNKKLLTILAVFWISLYIFVNLTSVLYL* >P1;B structureX:B:1 :A:149 :A:::-1.00:-1.00 --------SFIRIMVFAIYVALPIGVGLWV-------------------SLPWYAVGASLIAANISAEQFIGGMS SAYSIGLAIASYRWMSALTLIIVGKYFLPIFIEKGIYTIPEFVRKRS----LTILAVFWISLYIFVNLTSVLYL* In B the sequence `NKKL` is missing. Because they are in different conformations, I want to use the PDB for B as an initial model. In each of the PDB files, the residues follow the number in the above sequence alignment, and only contain coordinates for the residues that are not marked with a `-`. My script looks like: ----------------------------------------------------- ----------------------------------------------------- # Modeling using a provided initial structure file (inifile) from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../structures'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('123', '126')) a = MyModel(env, alnfile='../sequences/alignments.ali', # alignment filename knowns='A', # codes of the templates sequence='B', # code of the target inifile='B.pdb') # use 'my' initial structure a.starting_model = 1 # index of the first model a.ending_model = 1 # index of the last model a.make() # do homology modeling ----------------------------------------------------- ----------------------------------------------------- If in my alignment file, I specify that each structure starts at residue 1, I get an error: > No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 1", chain " A"; atom file name: ../structures/A.pdb However if I change the starting residue to 10 in A and 9 in B, Modeller runs, but it builds a different set of residues than I intended, because I think it is numbering the residues in sequential order as they are read in from the PDBs, ignoring the missing residues (determined by running the small script in FAQ #17). I've seen advice on renumbering residues on the mailing list, but I'm not sure if I'm missing something more basic. Any suggestions or pointers would be most appreciate. Josh

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Regarding Modelling
by Ashish Runthala 12 Sep '12

12 Sep '12

Is there a way that i can ask MODELLER to exactly copy the topology of backbone,CA atoms of all the aligned residues and model the same for the other unaligned loop chunks. But it should not add the side chains. Is there a way that the side chain addition can be stopped after the desired initial backbone, CA construction. Best Regards Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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A small query regarding modelling
by Ashish Runthala 08 Sep '12

08 Sep '12

Respected Sir, First of all, congratulations for the MODELLER's 9.11 release. I have a small query. For a considered well reliable template, is it possible that i can also use the side chain information exactly the same way from the template, i.e. MODELLER uses the complete backbone and side-chain information for the aligned residues from the considered template, and accordingly the MODELLER then predicts the left over residues through the earlier considered reliable scaffolds? Please guide me the same way. Sincerely, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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