deepti wrote: > I am trying to construct a model for a protein having a known > structure for the purpose of learning Modeller. > The pdb structureis in form of protein-NAD adduct. My aim is to build a > similar model. > Using the templates I have built a model, please tell me how to > incorporate NAD and water in my model. I have read the manual 'faq' , > but am confused how to change my alignment (including '.' for BLK > residues and 'w' ). How do I change the template pdb files for this? > How do I make my own restraint file?

There is no need to change your PDB file, or define custom restraints. You simply tell Modeller to read in the HETATM and water residues from the PDB (env.io.hetatm = True and env.io.water = True) and then list all of those residues in your template sequence in your alignment (. for HETATM, w for water). You can then use the target sequence alignment as per usual to list the residues you want to appear in your final model (generally people use a 1:1 alignment for the . and w residues).

There is a fully functional example in the manual at http://salilab.org/modeller/manual/node18.html (you can find the model-ligand.py and align-ligand.ali inputs in the examples/automodel directory). Alternatively, the advanced modeling tutorial at http://salilab.org/modeller/tutorial/advanced.html goes into some detail on ligand modeling, complete with custom restraints.

If this information is not clear, please let me know.

Ben Webb, Modeller Caretaker

Do you have to use the modeller alignment script? I have been using ebi software to create a .pir file.

After reading the modeller files and tutorials i am still at a loss as to how to use these 'blk' characters. I am trying to get a molecule of fad that is present in my template into my model.

>From: Joel Tyndall joel.tyndall@otago.ac.nz >To: deepti s_pinkbutterfly@rediffmail.com, modeller_usage@salilab.org >Subject: Re: [modeller_usage] How to incorporate NAD and water in my model >Date: Thu, 15 Mar 2007 11:27:59 +1300 > > >Hi Deepti, > >I recently looked at a similar complex that included ATP and Mg. You can >add a # to your alignment file for NAD. See the response to my post >below (just replace ATP with NAD). > >Cheers > >J > >Hi Joel > Have you tried to include an @ in your alignment file?according to >restyp.lib (in mollib directory) it should correspond to ATP. I dont know >how about the quality of the parameters are, but its a starter. And theres >a starter for tweaking in top_heav.lib. If theres no ATP (or similat >molecule) in you template You'll need to add some constraints to some atoms >between your protein and ATP to restrict it to a position near the binding >site. > >Happy Modelling >Esben Bjerrum > > >deepti wrote: > > > > > > Dear Modeller caretakers, > > I am trying to construct a model for a protein having a known > > structure for the purpose of learning Modeller. > > The pdb structureis in form of protein-NAD adduct. My aim is to build > > a similar model. > > Using the templates I have built a model, please tell me how to > > incorporate NAD and water in my model. I have read the manual 'faq' , > > but am confused how to change my alignment (including '.' for BLK > > residues and 'w' ). How do I change the template pdb files for this? > > How do I make my own restraint file? > > My alignment file is(generated by align2d.py):- > > > > >P1;1qsgA > > structureX:1QSG.pdb: 2 :A: 259 :A:undefined:undefined:-1.00:-1.00 > > >GFLS-GKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQND--KLKGRVEEFAAQLGSDIVLQCDVAEDASIDT > > >MFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLG > > > > >AERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAASGIK--------DFRKMLAHCEAVTP > > IRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMNEL* > > > > >P1;1eny > > sequence:1eny: : : : ::: 0.00: 0.00 > > >AGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAG > > >RVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDP > > >S-RAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQR > > APIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL* > > > > > > > > > > I got a lesser objective function while using the alignment generated > > by clustalw. Which would be a better option? > > Also please suggest me ways to further refine my model so as to make > > it almost like the pdb structure. > > > > > > Thanks and Regards, > > Deepti > > > > > > > > dreams > > >http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/1120029_1114336/1119254/1?PARTNER=3&OAS_QUERY=null%20target=new%20 > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage@salilab.org > > https://salilab.org/mailman/listinfo/modeller_usage > > > >-- >Joel Tyndall, PhD > >Lecturer >National School of Pharmacy >University of Otago >PO Box 913 Dunedin 9054 >New Zealand > >Pukenga >Te Kura Taiwhanga Putaiao >Te Whare Wananga o Otago >Pouaka Poutapeta 913 Otepoti 9054 >Aotearoa > >Ph / Waea +64 3 4797293 >Fax / Waeawhakaahua +64 3 4797034 > > >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >https://salilab.org/mailman/listinfo/modeller_usage

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>Charlie Allerston wrote: >>Do you have to use the modeller alignment script? I have been using ebi >>software to create a .pir file. > >No, you do not need to use Modeller to make your alignment file. However, >since there are no standard one-letter codes for ligands, you will likely >have to edit your original alignment in a text editor to put in the >ligands. >

This is what I am not getting. Where to put the ligand in the alignment, regardless of what character to use. Take this for instance. trying to model something from the template 1VDC http://www.rcsb.org/pdb/explore.do?structureId=1VDC Looking at the PDB file it has 316 residues then it had a molecule of FAD tacked on at a position designated 400. So when I align this to some target like below (cropped).

--------------------------MNGLETHNTRLCIVGSGPAAHTAAIYAARAELKP LLFEGWMANDIAPGGQLTTTTDVENFPGFPEGILGVELTDKFRKQSERFGTTIFTETVTK VDFSSKPFKLFTDS---KAILADAVILAIGAVAKRLSFVGSGEVLGGFWNRGISACAVCD GAAPIFRNKPLAVIGGGDSAMEEANFLTKYGSKVYIIHRRDAFRASKIMQQRALSNPKID VIWNSSVVEAYGDGERDVLGGLKVKNVVTGDVSDLKVSGLFFAIGHEPATKFLDGGVELD SDGYVVTKPGTTQTSVPGVFAAGDVQDKKYRQAITAAGTGCMAALDAEHYLQEIGSQEGK SD- * >P1;fake1

DASGLSVAAAATLSQKSTPYYQSEIHTIGKRRMHSKVVIIGSGPAAHTAAIYLARAELKP VLYEGFMANGVAAGGQLTTTTEVENFPGFPEAVTGQELMDKMRAQSERFGTVIVSETVGK LDLSKRPFEYSTEWSPDTVMTADAVILATGASARRLGLPGED----KYWQNGISACAVCD GAVPIFRNKPLVVIGGGDSAAEEAIFLTKYGSHVTVLVRRDKLRASSIMARRLLAN---- ------------------------------------------------------------ -------------KKVTGLFAAGDVQDKRYRQAITSAGTGCMAALDAEKYLEELEDEQAD GKL *

Where should I stick the fad? At the end? How many blk characters should I tack on? 1 because there is only one molecule? Is there a specific character for FAD?

These are my stumbling blocks.

regards

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Charlie Allerston wrote: > This is what I am not getting. Where to put the ligand in the > alignment, regardless of what character to use. > Take this for instance. trying to model something from the template 1VDC > http://www.rcsb.org/pdb/explore.do?structureId=1VDC > Looking at the PDB file it has 316 residues then it had a molecule of > FAD tacked on at a position designated 400.

...followed by a bunch of waters from residue 500 to 945, followed by an SO4 at 440. (There are actually more than 316 residues, too.)

Modeller always reads PDB residues in order, so if the ligand is at the end of the PDB file, you put the blk residue at the end of the sequence in the alignment too. If you turn env.io.hetatm on to True, all of the HETATMs in the model (at least in the range specified by model_segment) will be read, so they must all be listed in your alignment.

> So when I align this to some target like below (cropped). > > > --------------------------MNGLETHNTRLCIVGSGPAAHTAAIYAARAELKP > LLFEGWMANDIAPGGQLTTTTDVENFPGFPEGILGVELTDKFRKQSERFGTTIFTETVTK > VDFSSKPFKLFTDS---KAILADAVILAIGAVAKRLSFVGSGEVLGGFWNRGISACAVCD > GAAPIFRNKPLAVIGGGDSAMEEANFLTKYGSKVYIIHRRDAFRASKIMQQRALSNPKID > VIWNSSVVEAYGDGERDVLGGLKVKNVVTGDVSDLKVSGLFFAIGHEPATKFLDGGVELD > SDGYVVTKPGTTQTSVPGVFAAGDVQDKKYRQAITAAGTGCMAALDAEHYLQEIGSQEGK > SD- > * >> P1;fake1 > > DASGLSVAAAATLSQKSTPYYQSEIHTIGKRRMHSKVVIIGSGPAAHTAAIYLARAELKP > VLYEGFMANGVAAGGQLTTTTEVENFPGFPEAVTGQELMDKMRAQSERFGTVIVSETVGK > LDLSKRPFEYSTEWSPDTVMTADAVILATGASARRLGLPGED----KYWQNGISACAVCD > GAVPIFRNKPLVVIGGGDSAAEEAIFLTKYGSHVTVLVRRDKLRASSIMARRLLAN---- > ------------------------------------------------------------ > -------------KKVTGLFAAGDVQDKRYRQAITSAGTGCMAALDAEKYLEELEDEQAD > GKL > * > > Where should I stick the fad? At the end?

That's not a complete alignment file, so I can't tell which is supposed to be the 1vdc sequence. But the true 1vdc sequence can be obtained by Modeller using the script at http://salilab.org/modeller/FAQ.html#18 (merely modified by setting env.io.hetatm = True):

>P1;1vdc structureX:1vdc: 1 : :+324 : :undefined:undefined:-1.00:-1.00 LETHNTRLCIVGSGPAAHTAAIYAARAELKPLLFEGWMANDIAPGGQLTTTTDVENFPGFPEGILGVELTDKFRK QSERFGTTIFTETVTKVDFSSKPFKLFTDSKAILADAVILAIGAVAKRLSFVGSGEVLGGFWNRGISACAVCDGA APIFRNKPLAVIGGGDSAMEEANFLTKYGSKVYIIHRRDAFRASKIMQQRALSNPKIDVIWNSSVVEAYGDGERD VLGGLKVKNVVTGDVSDLKVSGLFFAIGHEPATKFLDGGVELDSDGYVVTKPGTTQTSVPGVFAAGDVQDKKYRQ AITAAGTGCMAALDAEHYLQEI.#*

Since the FAD comes after the regular amino acids in the PDB file, the blk residue (.) comes immediately after the regular sequence. You can also see a # residue there - that's the SO4. You can see which HETATMs Modeller has codes for by looking at modlib/restyp.lib, but if in doubt use blk (.) since that'll match everything.

You will often see a chain break (/) immediately preceding blk residues in alignments. That's only necessary if you want to force the ligands to have a different chain ID to the amino acids. (If you want them in the same chain, leave out the chain break.)

> How many blk characters > should I tack on? 1 because there is only one molecule?

HETATM residues are treated in exactly the same way as ATOM residues, so one character per PDB residue.

What you get in your model, of course, depends on what is in your target sequence. For example, you may want to build a model containing FAD but not the SO4. In this case, you would align a blk residue in the model to the corresponding FAD blk residue in the template, but align a gap to the SO4.

Ben Webb, Modeller Caretaker