August 2003 - modeller_usage

Modeller input alignment file
by christos Kouriniadis 26 Jan '04

26 Jan '04

Hello everybody, I am doing a project on comparative modelling, by using modeller. My problem is the following: I am trying to make an input file with PDB structures aligned in PIR format. However, when I am reading the modeller manual, I see that the worked example is in the form: P1;2ald structureX:2ald:2:@:363:@:aldolase:human muscle:2.00:0.17 * If you go to the section "display/download file", in the PDB website, you will get the usual big file. But when I have a look at this file, I see that ATOM has three coordinates: -20.521 45.890 70.464 How from these coordinates I get the :2:@:363:@: ??? Is there a formula that transforms it? I would be grateful if you could give me a hint on this. Thanks, Christos Kouriniadis _________________________________________________________________ Add photos to your e-mail with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail

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FW: building a new residue
by Modeller Care 28 Aug '03

28 Aug '03

------ Forwarded Message From: Tom Burghardt <burghardt(a)mayo.edu> Date: Thu, 28 Aug 2003 14:40:36 -0500 (CDT) To: Modeller Care <modeller-care(a)salilab.org> Subject: building a new residue Dear Modellers, I defined a new residue type following the instructions (a-d) of FAQ17 in the Modeller handbook. I did not do the last step (e) because I need to run the program first to see what needs to be done. To allow Modeller to recognize the new residue single letter code in the sequence file (FAQ17 part d) I modified the residue type library 'modlib/restyp.lib' with a new entry at the end of the file (index=142). When I run Modeller I get the message: read_al_375E> Unknown residue type,position,sequence: U 84 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 implying I guess that it does not recognize the one letter code I assigned my modified residue. Everything runs OK if I replace the modified residue with a BLK residue in the alignment file. My top file is below. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log SET ALNFILE = 'seq-sk_sk_T1_short_gly.ali' # alignment filename SET KNOWNS = '2tnx' # codes of the templates SET SEQUENCE = '2tns' # code of the target SET TOPOLOGY_MODEL = 3,HETATM_IO=ON SET TOPLIB = '${LIB}/top_heav.lib' SET PARLIB = '${LIB}/par.lib' READ_RESTYP_LIB RESTYP_LIB_FILE='${LIB}/restyp.lib' SET ATOM_FILES_DIRECTORY = './' # directories for input atom files SET STARTING_MODEL= 1 # index of the first loop model SET ENDING_MODEL = 1 # index of the last loop model CALL ROUTINE = 'model' # do homology modelling Thanks Tom Burghardt ------ End of Forwarded Message

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More weight for user distance restraints
by Modeller Care 28 Aug '03

28 Aug '03

Forwarded by list-owner ------ Forwarded Message From: "Thorsten Schweikardt" <thorsten(a)mail.uni-mainz.de> To: <modeller_usage(a)salilab.org> Subject: More weight for user distance restraints Date: Thu, 28 Aug 2003 16:28:34 +0200 Hi to all, I have a problem with user defined distance restraints, I want to model the n-terminus of a protein that's available as pdb with the help of measured distances. So far, it works, but one little problem remains: the distance-requirements are not met entirely, because modeller does not distort the rest of the protein at all, is there a possibility to force it to add more weight to these distance restraints, even if it means distorting the template protein? Thanks, Thorsten University of Mainz My Top-File: ----------------------------- INCLUDE SET ALNFILE = 'alignment.ali' SET KNOWNS = 'protein1' SET SEQUENCE = 'protein1plusnterm' SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL= 1 SET ENDING_MODEL = 20 SET LIBRARY_SCHEDULE = 4 SET FINAL_MALIGN3D = 1 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS = 'OG:3' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 30.0 10.0 SET ATOM_IDS = 'OG:116' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 0.0 SET ATOM_IDS = 'CA:42' 'CA:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 1.0 SET ATOM_IDS = 'CA:3' 'CA:42' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 21.0 4.0 SET ATOM_IDS = 'CA:3' 'CA:116' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 50.0 1.0 RETURN END_SUBROUTINE ------ End of Forwarded Message

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loop modeling
by Moshe Amitay 27 Aug '03

27 Aug '03

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.

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Multidomain protein alignment
by Morgane Agez 27 Aug '03

27 Aug '03

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 structures appropriatly before the modeling? Thank you very much! With best regards, Morgane

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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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