- modeller_usage - salilab.org

mutate
by Hafsa/Asmat 26 Aug '03

26 Aug '03

Dear MODELLER users I want to mutate a single residue in a model. I run the TOP file given in the tutorial (with 1fas.pdb) successfully. There are two options given: in one case the specified residue is mutated whenever it appears in the structure. This runs fine. But in case of the second option, (where a segment is specified) all the residues are mutated instead of one. Following is the part of the TOP file.( to change residue 14 to Cys) # The second example is commented out; it selects residues '1' and '10'. SET SELECTION_SEARCH = 'SEGMENT', SELECTION_FROM = 'ALL' PICK_ATOMS SELECTION_SEGMENT = '14' '14', SELECTION_STATUS = 'INITIALIZE' # Mutate the selected residues into HSD residues (neutral HIS): MUTATE_MODEL RESIDUE_TYPE = 'CYS' This works perfectly fine with 1fas.pdb but not with my model. Can you point out where I am going wrong. regards

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loop modeling
by Modeller Care 26 Aug '03

26 Aug '03

Non-member submission forwarded by list-owner ------ Forwarded Message From: Moshe Amitay <amitaym(a)mail.biu.ac.il> Organization: BIU X-Mailer: Mozilla 4.79 [en] (X11; U; IRIX64 6.5 IP35) X-Accept-Language: en MIME-Version: 1.0 To: modeller_usage(a)salilab.org Subject: loop modeling Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I whuld like your advice: I build a model of a membrane protein and I want now to do "loop modeling" to few extra cellular and intra-cellular loops. I wonder if this protocol of modeller is the right choice since the model doesn't contain the membrane and I actually ignore the influence of the polar heads. thank's Moshe Amity. -------------------------------------- Moshe Amity amitaym(a)mail.biu.ac.il Dep. of Chemistry Bar Ilan University Israel. ------ End of Forwarded Message

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FW: two attached small, pdb files
by Modeller Care 26 Aug '03

26 Aug '03

Forwarded by list-owner ------ Forwarded Message From: Michael Grabe <mgrabe(a)itsa.ucsf.edu> Date: Mon, 25 Aug 2003 12:33:05 -0700 To: modeller-care(a)salilab.org Subject: two attached small, pdb files Dear Modellers, Let me describe a minor problem I have encountered with modeller 6V2 on Mac OSX, What I do: I take a small alpha helix (25 amino acids) and I copy it and translate it. I then concatenate the two alpha helix pdb files, separating the first and the second alpha helix by a TER line. Note, the original helix is missing a capping oxygen at the last residue. Now I renumber the pdb amino acids so that they go from 1 to 50 instead of 1 to 25 and then 1 to 25 (see helices.ini). I then start to work with this pdb file without any alignment file. I run this modeller script on the two alpha helices: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% INCLUDE READ_MODEL FILE = 'helices.ini' READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' GENERATE_TOPOLOGY SEQUENCE = 'temp' WRITE_MODEL FILE = 'refine0.pdb' OPTIMIZE MAX_ITERATIONS = 100 WRITE_MODEL FILE = 'refine1.pdb' ENERGY %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Now if I look at refine0.pdb generated from modeller, I have a problem. As I mentioned before amino acids 25 and 50 are missing capping oxygens, but modeller puts them on for me and refine0.pdb has two more atoms than the initial helices.ini. ***Here is the point, the added oxygen to amino acid 25 shifts the labeling of all of the atoms and their positions in the second alpha helix. *** Look at and compare atoms 201 to 206 in the attached files to see exactly what I mean. Once you see, it will be clear that the optimization that follows has a bit of a tough time since all of the atoms in the second helix have shifted positions. Any hints about how to make this better? Thanks, Michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. Post-doctoral Fellow Howard Hughes Medical Institute University of California, San Francisco 533 Parnassus Ave. San Francisco, CA 94143 mgrabe(a)itsa.ucsf.edu tel: ++ 415.476.6585 http://itsa.ucsf.edu/~mgrabe ------ End of Forwarded Message

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multidomain protein modeling
by Modeller Care 20 Aug '03

20 Aug '03

non-member submission forwarded by list-owner ------ Forwarded Message From: "Morgane Agez" <morgane(a)iqs.es> To: <modeller_usage(a)salilab.org> Subject: multidomain protein modeling Date: Wed, 20 Aug 2003 17:31:45 +0200 Hi, I have seen in the Chapter 4 of the manual how to build a multi-domain = protein model using templates corresponding only to the individual = domain. But I think I obtain a model with an incorrect relative = orientation of the diferent domains. How can I orient the three template = structure appropriatly before the modeling? Thank you very much! With best regards, Morgane

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Advice on heteroatoms, metals and water
by Jim Procter 20 Aug '03

20 Aug '03

Hi. This is directed to : >Karsten Suhre <Karsten.Suhre(a)igs.cnrs-mrs.fr> (IGS) >Introduction of a Ca binding site >Moshe Amitay <moshe(a)noamy.ch.biu.ac.il> ("Bar-Ilan University, Ramat-Gan, >building a model with water molecules. From: Tjaart de Beer <tjaart(a)tuks.co.za> >Modelling with metals and hetero. The practical advice : Modeller treats the 'hetatm' entries as residues for much of the modelling process. By this, I mean that it is as picky as with the other residue entries when you describe them in the alignment. You can see all the types of residue entry that it knows about in the mod6v2/lib/restyp.lib file. Its always simpler to 'SET HETATM_IO', rather than change the pdb file. If modeller knows about the heteroatom residue code then it will read it, and not attempt to attach proximal metal ions to the polypeptide backbone. I was mislead by the chain break character '/', which actually introduces a chain break for your model, rather than describing a corresponding template (? not really sure here). I got away with this example : 1tem:Template:1: :3: :.:.:. WLMzz* 1hom:Homolog:1: :3: :.:.:. WITzz* Where I just used set HETATOM_IO on. The important thing is the numbering used in the PIR header for each protein sequence - this only relates to the amino acids, not the hereroatoms. I imagine that you need to use set WATER_IO on, and put in the waters, too, but the chain break didn't seem to help. Above all, look carefully at the numbers that Modeller gives you when it complains that you don't have enough residues in the PDB file or the sequence. For Moshe's case, the chain break may well have been the problem, but it can't hurt to use the unedited PDB file but setting HETATM_IO as well as WATER_IO (but maybe you could delete the un-necessary waters and heteroatoms from the pdb file just to make the alignment simpler!). As for the optimization behaviour with metal atoms - I didn't really notice modeller doing any optimization of the bonding geometry, but in my case these contacts were thoroughly conserved. However, I can't see any parameters in the MD forcefield definitions to indicate that charge/ligand geometry is taken into account, it is probably all done through restraints. Think thats it - sorry for not giving a concrete example! j-- ps. For Calcium - the HETATM's residue entry should be CAL or CA (that is, not CA2), and '3' is the alignment symbol used in the PIR file (see the restyp.lib file). _______________________________________________________________________ Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics Hamburg http://www.zbh.uni-hamburg.de/mitarbeiter/procter

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Modelling with metals and hetero
by Modeller Care 19 Aug '03

19 Aug '03

non-member submission forwarded by list-owner ------ Forwarded Message Date: Tue, 19 Aug 2003 07:27:56 +0200 From: Tjaart de Beer <tjaart(a)tuks.co.za> Reply-To: tjaart(a)tuks.co.za User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20021204 X-Accept-Language: en-us, en MIME-Version: 1.0 To: modeller_usage(a)salilab.org Subject: Modelling with metals and hetero I have followed the method in the Modeller manual on how to model with water and metals or hetero atoms. The template includes a ligand, metal atom and water molecules. I would like to know how to incorporate this into the newly built model. So far I have succeeded in adding waters during modelling but the metal atom and the ligand is still not in the model. Any help would be greatly appreciated. Thanks!! Tjaart -- Tjaart de Beer Department Biochemistry Agricultural Building Faculty of Natural Sciences University of Pretoria Lynwood rd Pretoria South Africa 0001 Tel: +27 12 420 2990 Cell: +27 83 504 7914 Fax: +27 12 362 5302 Email: tjaart(a)tuks.co.za tjaartdb(a)absamail.co.za ------ End of Forwarded Message

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comparing align. (1 attachment)
by Michael Grabe 18 Aug '03

18 Aug '03

Dear Modellers, I have three published alignments, and I want to use my models generated by Modeller to qualitatively estimate the goodness of the different alignments. I have made 100 models of my unknown sequence to the target structure using each of the three alignments. I then binned the objective energy output from the standard Modeller run (see panel A in attached pdf). I also binned the final C-alpha to C-alpha RMS for the generated models to the known homologous structure (see panel B in attached pdf). Is it true that the energy function is not the best objective measure because different alignments will have different numbers of constraints (i.e. one alignment may correspond to 100 amino acid pairs, whereas a shifted alignment may only have 98 amino acid pairs between the known and unknown sequences.) Can you easily normalize to account for this? What is the best way to do this? I would like to say that Alignment 1 below is best but I am hesitant. Hopefully this question is understandable. Thank you, Michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. Post-doctoral Fellow Howard Hughes Medical Institute University of California, San Francisco 533 Parnassus Ave. San Francisco, CA 94143 mgrabe(a)itsa.ucsf.edu tel: ++ 415.476.6585 http://itsa.ucsf.edu/~mgrabe

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CPIB Tutorial 1
by Andrew Latos 16 Aug '03

16 Aug '03

Hello Andy and Darren, thanks for the help. You were right about the composition of the pdb file containing an acetylated group. This change to the .ali file allowed the models to be generated. >P1;4mdhA structureX:4mdhA: 1 :A: 333 :A:undefined:undefined:-1.00:-1.00 SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEE IAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKE NFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFIT TVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISD-GNSYGVPDDLLYSFPVTIK-DKTWK IVEGLPINDFSREKMDLTAKELAEEKETAFEFLSSA-* >P1;TvLDH sequence:TvLDH: : : : ::: 0.00: 0.00 MSEAAHVLITGAAGQIGYILSHWIASGELYG-DRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPK AAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPE NFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHD-YVFDTFFK KIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIH VVEGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG* I appreciate your help. Andrew Latos MBB student University of Idaho

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mutate_model
by Asmat Salim 15 Aug '03

15 Aug '03

Dear MODELLER users I want to mutate a single residue in a model. I run the TOP file given in the tutorial (with 1fas.pdb) successfully. There are two options given: in one case the specified residue is mutated whenever it appears in the structure. This runs fine. But in case of the second option, (where a segment is specified) all the residues are mutated instead of one. Following is the part of the TOP file.( to change residue 14 to Cys) # The second example is commented out; it selects residues '1' and '10'. SET SELECTION_SEARCH = 'SEGMENT', SELECTION_FROM = 'ALL' PICK_ATOMS SELECTION_SEGMENT = '14' '14', SELECTION_STATUS = 'INITIALIZE' # Mutate the selected residues into HSD residues (neutral HIS): MUTATE_MODEL RESIDUE_TYPE = 'CYS' This works perfectly fine with 1fas.pdb but not with my model. Can you point out where I am going wrong. regards

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e-mail
by truename 15 Aug '03

15 Aug '03

Modeller care: I have changed my e-mail from yb_108(a)yeah.net to saint2k2k(a)yahoo.com.cn. please renew my information in the maillist simutaleously. My old mailbox will not be available now bing

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