February 2003 - modeller_usage

FW: modeller in CCP4 (fwd)
by Andrej Sali 03 Mar '03

03 Mar '03

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org -----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] Sent: Wednesday, February 26, 2003 4:18 PM To: Andrej Sali Subject: modeller in CCP4 (fwd) ---------- Forwarded message ---------- Date: Fri, 21 Feb 2003 14:32:44 -0300 From: Frederico Moraes Ferreira <fredi(a)if.sc.usp.br> To: bozidar(a)salilab.org Subject: modeller in CCP4 Dear Sir, I have been trying to run Modeller6v2 on the CCP4 interface unsuccessfully. The file $MODINSTALL6v2/script/setmodeller is missing or do not take part of this version anymore. So I am writing to ask you how to overcome this problem for the Modeller6v2 or take a previus Modeller version. Thanks in advance. Frederico Moraes Ferreira

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FW: rationale for assigining the coordinates with a break ( | )
by Modeller Care 28 Feb '03

28 Feb '03

------ Forwarded Message From: "Dr.Shyam Charan Mallena" <shyam(a)gvkbio.com> Reply-To: shyam(a)gvkbio.com Date: Fri, 28 Feb 2003 12:23:09 +0530 To: bozidar(a)salilab.org, modeller-care(a)salilab.org Subject: rationale for assigining the coordinates with a break ( | ) Sir, {Sub : To know how or what considerations are followed to model a protein with breaks} It is a common occurance to get breaks in reference proteins "|" whis is due to non availability of a certain number of coordinates in the reference protein. In the assigining of coordinate manually this reference is not acceptable many a times. But it works many a times with modeller (I've used Modeller from insight II (Accelrys) at bioCampus - a subsidary of gvkBio Sciences - Hyderabad India). What is the rationale for assigining the coordinates with a break ( | ) in reference protein in modeller. Also how exactly is the minimization or dymanics done (If at all) in modeller. What are the considerations for such an approach ? Regarding model with a loop : In Modeller : Consider the following example : PDF Violations Energy Model 1 : 6693.9 392.083 Model 2 : 960.0 749.346 which model is prefferable to the other and the rationale. thanking you, Dr. SHYAM CHARAN MALLENA CALL # +91 -40 5551 9990 Ext : 149 210, My Home Tycoon, Kundanbagh, Begumpet Hyderabad - 500016 . ------ End of Forwarded Message

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It`s alive!!!
by Luis Rosales 27 Feb '03

27 Feb '03

Hi to all: I just made modeller work!!!! I still don`t know what my problem was, but as I can run the examples just fine, I figured the problem were my files. Briefly, I just delete my old files and created them from scratch with nedit... My final files looked like this: (model.top, my script): INCLUDE # Include the predefined TOP routines SET ALNFILE = 'aln.ali' # alignment filename SET KNOWNS = '1cx1' # codes of the templates SET SEQUENCE = '1dnj' # code of the target SET ATOM_FILES_DIRECTORY = '../bin/modeller6v2/examples/atom_files/' # directories SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 2 # index of the last model # (determines how many models to calculate) SET DEVIATION = 4.0 # have to be >0 if more than 1 model SET RAND_SEED = -12312 # to have different models from another TOP file CALL ROUTINE = 'model' # do homology modelling (aln.ali, my alignment file) C; First alignment >P1;1cx1 structureX:1cx1:FIRST:A:LAST:A:template:HCV: 2.50:-1.00 GSVVIVGRIILSGSGSITAYSQQTRGLLGCIITSLTGRDKNQVEGEVQVVSTATQSFLATCVNGVCWTVYHGAGSK TLAG PKGPITQMYTNVDQDLVGWQAPPGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLS-------PRPVSYL KGSS GGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVP AAYA AQGYKVLVLNPSVAATLGFGAYMSKAHGID------PNIRTGVRTITTGAPVTYSTYGKFLADGGCSGGAYDIIIC DECH STDSTTILGIGTVLDQAETAGARLVVLATATPPGSVTVPHPNIEEVALSNTGEIPFYGKAIPIEAI--RGGRHLIF CHSK KKCDELAAKLSGLGINAVAYYRGLDVSVIPT---IGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTF TIET TTVPQDAVSRSQRRGRTGRGRRGIYRFVTPGERPSGMFDSSVLCECYDAGCAWYELTPAETSVRLRAYLNTPGLPV CQDH LEFWESVFTGLTH-IDAHFLSQTKQAGDNFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLH---GPTPLLY RLGA VQNEVTLTHPITKYIMACMSADLEVVT* >P1;1dnj sequence:1dnj:FIRST:@:LAST:@:model:dengue: 2.50:-1.00 GSSPILSITISEGSGS----AGVLWDVPSPPPVGKAELEDGAYRIKQRGILGYSQIGAGVYKEGTFHTMWHVTRGA VLMH KGKRIEPSWADVKKDLISYGG---GWKLEGEWKEGEEVQVLALE-PGKNPRAVQ-TKPGLFKTNTGTIGAVSLDFS PGTS GSPIVDRKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIEDD-------IFRKKRLTIMDLHPGAGKTKRYL PAIV REAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPV-RVPNYNLIIM DEAH FTDPASIAARGYISTRVEMGE-AAGIFMTATPPGSRDPFPQ-SNAPIMDEEREIPERSWNSGHEWVTDFKGKTVWF VPSI KAGNDIAACLRKNGKKVIQLSRKTFDSEYVKTRANDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILT-DGEER VILA GPMPVTHSSAAQRRGRIGRNPKNENDQYI---------YMGEPLENDEDCAHWKEAKMLLDNINTPEGIIPSMFEP EREK VDAIDGEYRLRGEARKTFVDLMRRG---DLPVWLAYRVAAEGINYADRRWCFDGIKNNQILEE-NVEVEIWTKEGE RKKL KPRWLDARIYSDPLALKEFKEFAAGRK* Hope this helps, Holton... And thanks to all for your help!!!! Luis

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gap creation and extension penalties
by Chris de Graaf 27 Feb '03

27 Feb '03

Dear Modellers, I am working on a structural alignment between 6 protein structures with an average seq. identity of approx. 25 % and average homology of approx. 45 %. Usage of default values for gap creation and extension penalties for structure/structure superposition (0.0 and 1.75 respecrtively) result in the introduction of multiple (relatively) large gaps in the multiple sequence alignment. Of course I can "avoid" this by increasing both gap creation and extension penalties, but what I would like to know which penalty values are "reasonable" in this case. Thanking you in advance and with kind regards, Chris de Graaf -- drs. C. de Graaf LACDR - Division Molecular Toxicology Department Pharmacochemistry Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam Tel. (31) 020-4447608 Fax. (31) 020-4447610

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FW: modeller problem (fwd)
by Andrej Sali 26 Feb '03

26 Feb '03

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org -----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] Sent: Wednesday, February 26, 2003 4:29 PM To: Andrej Sali Subject: modeller problem (fwd) ---------- Forwarded message ---------- Date: Tue, 18 Feb 2003 10:40:55 +0200 From: Liisa laakkonen <llaakkon(a)pcu.helsinki.fi> Reply-To: liisa.laakkonen(a)helsinki.fi To: bozidar(a)salilab.org Subject: modeller problem Hello, and good luck in the new place, I have a heteroatom problem. The system is as follows: the template (actually 3 but I try first one) the sequence the alignement includes one chain of the template only and the middle part only e.g. structureX:templ:25:A:400:A:undefined:undefined:1.00:1.0 The prosthetic groups are defined as a separate chain, X, and they are observed in the unknown structure, too. I've included: set hetatm_io = on -----/.., in the alignement BLK residue for fixed unknown structure (+ have ch27 topology files for it) DON'T KNOW how to mark two chains in the alignment Is it possible? Clearly, the program would like to get the number of residues right, and and complains about the dots in the alignemnt, OR about the missing backbone atoms in the BLK, whichever I edit. The only way I can see possibly working is to edit styronly the pdb files, cut away the C-termini, mark heteroatoms to belong to the subunit A, and change their numbering. I would not like to do this, because I might need the tails later, and eliminating true residue numbers nearly always causes trouble. Any help would be most welcome. Sincerely, Liisa Laakkonen University of Helsinki

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FW: Ask for help. (fwd)
by Andrej Sali 26 Feb '03

26 Feb '03

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org -----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] Sent: Wednesday, February 26, 2003 4:26 PM To: Andrej Sali Subject: Ask for help. (fwd) ---------- Forwarded message ---------- Date: Thu, 20 Feb 2003 17:23:10 From: Chengbing Wang <wangcb(a)moiza.chonnam.ac.kr> To: bozidar(a)salilab.org Subject: Ask for help. Dear Bozidar, I try to use the MODELLER for my work. But there is a problem to run it when I am installing it although I required the KEY WORD, and I input it also. It is reported as in the attached file. Thanks for your help. Best Regards. Sincerely Chengbing Wang Chengbing Wang Hormone Research Center Chonnam National University Kwangju 500-757 South Korea

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FW: Help - syntax problem (fwd)
by Andrej Sali 26 Feb '03

26 Feb '03

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org -----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] Sent: Wednesday, February 26, 2003 4:18 PM To: Andrej Sali Subject: Help - syntax problem (fwd) ---------- Forwarded message ---------- Date: Fri, 21 Feb 2003 19:17:52 +0100 From: Anita Bentley <anita.bentley(a)lure.u-psud.fr> To: bozidar(a)salilab.org Subject: Help - syntax problem Dear Modeller experts, I have been trying to use Modeller for a very specific task. It gives me really interesting answers and I would like to go a bit further. Here is what I do: I have a PDB coordinate file for the N-terminus and a new X-ray structure we have just solved for the C-terminus of another protein. The homology is high, so that I can get a quite satisfactory model for the "long" protein. It turns out both domains contain a Zn ion, well characterised in the coordinate files. I would like to model both ions in the target structure. For the N-terminal part this involves slightly different ligands in the target. I therefore prepared a list of added restraints in order to ensure the ion stays in the right place. And this is where things start going funny: the C-terminal zinc ligands stay bound to the ion and all is fine. But the N-terminal zinc ligands move away, as if the restraints were ignored! Here is the file I use: # PRIMER: STEP 5 # INCLUDE # Include the predefined TOP routines SET ALNFILE = 'adca_2.ali' # alignment filename SET KNOWNS = 'psa' 'yoda' # codes of templs SET SEQUENCE = 'ADCA' # code of the target #SET ATOM_FILES_DIRECTORY = '/home/users/anita/work/yoda' # directories for input SET TOPOLOGY_MODEL = 1, HETATM_IO = on SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 2 # index of the last model # (determines how many models to calculate) SET DEVIATION = 4.0 # have to be >0 if more than 1 model SET RAND_SEED = -12312 # to have different models from another TOP file CALL ROUTINE = 'model' # do homology modelling CALL ROUTINE = 'special restraints' SUBROUTINE ROUTINE = 'special restraints' ADD_RESTRAINT ATOM_IDS = 'NE2:42' 'ZN2:481' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:119' 'ZN2:481' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:183' 'ZN2:481' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1 ADD_RESTRAINT ATOM_IDS = 'OE1:258' 'ZN2:481' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.1 0.1 ADD_RESTRAINT ATOM_IDS = 'OE2:258' 'ZN2:481' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.1 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:431' 'ZN2:482' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:440' 'ZN2:482' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:442' 'ZN2:482' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1 RETURN It is the first 5 restraints that pose problems. Any suggestions? Best regards, Anita Anita Lewit-Bentley LURE Bât. 209D, Centre Universitaire Paris-Sud BP 34, 91898 Orsay Cedex France tel: (33-1) 64 46 80 50 fax: (33-1) 64 46 41 48 e-mail: anita.bentley(a)lure.u-psud.fr

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New to... (cont!!!!)
by Luis Rosales 26 Feb '03

26 Feb '03

Hi: So far, I know: 1) structureX or structure didn´t make a difference (I used both) 2) As far as the manual goes, the minimum second line of a sequence can be: "structure:1cx1" or as complex as "structure:1cx1: : : : : : : :" or "structureX:1cx1:FIRST:@:LAST:@" anyway none of they works.... 3)However, I can run the examples and get the apropriate result on them (doing the "Run_tests" or "mod6v2 topfile.top"). And I used to think of the Xplor language as complicated.... ;) Thanks, Luis ----- Original Message ----- From: "Guittet, Muriel" <Guittet(a)vegmail.ucdavis.edu> To: "Luis Rosales" <ludwig(a)biomedicas.unam.mx> Sent: Wednesday, February 26, 2003 5:27 PM Subject: RE: New to mod6v2 (cont...) > Hi, > I'm sorry... At first look I don't know what could be wrong. > I just saw once in the users' list that it was better to use "structureX" than "structure" alone (but I know it should work with structure...) > I cannot read exactly if there isn't a blank after 1cx1 in your aln file (I don't know if it is important or not, but I encountered some tricky problems like using caps or not, or because my file was an rtf file instead of a txt one... so) > At least, aren't you supposed to precise the name of the chain even if it is FIRST:@:LAST:@ > good luck > Muriel >

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heteroatoms & loop_select
by Modeller Care 26 Feb '03

26 Feb '03

Forwarded to modeller_usage from the listowner. ------ Forwarded Message From: Liisa laakkonen <llaakkon(a)pcu.helsinki.fi> Reply-To: liisa.laakkonen(a)helsinki.fi Date: Wed, 26 Feb 2003 12:30:50 +0200 To: modeller-care(a)salilab.org Subject: heteroatoms & loop_select Dear Modeller-Man, A question about loops. I cannot get the atom selection for loops to work. I SET DO_LOOPS = 1 and then select_loops as in example 3. Whatever numbers I put in for the loops (from the beginning of the chain, or from the middle), the whole protein is "initialized" to a neat straight polypeptide chain. Any suggestions? I also include a question from two weeks ago, for the case it was lost during your move. ---------------------------- I have a heteroatom problem. The system is as follows: the template (actually 3 but try first one) the sequence the alignement includes one chain of the template only and the middle part only e.g. structureX:templ:25:A:400:A:undefined:undefined:1.00:1.0 The prosthetic groups are defined as a separate chain, X, and they are observed in the unknown structure, too. I've studied: set hetatm_io = on -----/.., in the alignement BLK residue for fixed unknown structure (+ have ch27 topology files for it) DON'T KNOW how to mark two chains in the alignment Is it possible? Clearly, the program would like to get the number of residues right, and and complains about the dots inthe alignemnt, OR about the missing backbone atoms in the BLK, whichever I edit. The only way I can see possibly working is to edit stronly the pdb files, cut away the C-termini, mark heteroatoms to belong to the subunit A, and change their numbering. I would not like to do this, because I might need the tails later, and eliminating true residue numbers nearly always causes trouble. Any help would be most welcome. Sincerely, Liisa Laakkonen University of Helsinki liisa.laakkonen(a)helsinki.fi ------ End of Forwarded Message

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New to mod6v2 (cont...)
by Luis Rosales 26 Feb '03

26 Feb '03

Hello again: Still stranded on this one, so I send you my aln file (called 01mod.ali): >P1;1cx1 structure:1cx1 :::::::2.5:0.20 GSVVIVGRIILSGSGSITAYSQQTRGLLGCIITSLTGRDKNQVEGEVQVVSTATQSFLAT CVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSLTPCTCGSSDLYL VTRHADVIPVRRRGDSRGSLLS-------PRPVSYLKGSSGGPLLCPSGHAVGIFRAAVC TRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYA AQGYKVLVLNPSVAATLGFGAYMSKAHGID------PNIRTGVRTITTGAPVTYSTYGKF LADGGCSGGAYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLATATPPGSVTVPH PNIEEVALSNTGEIPFYGKAIPIEAI--RGGRHLIFCHSKKKCDELAAKLSGLGINAVAY YRGLDVSVIPT---IGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTFTIET TTVPQDAVSRSQRRGRTGRGRRGIYRFVTPGERPSGMFDSSVLCECYDAGCAWYELTPAE TSVRLRAYLNTPGLPVCQDHLEFWESVFTGLTH-IDAHFLSQTKQAGDNFPYLVAYQATV CARAQAPPPSWDQMWKCLIRLKPTLH---GPTPLLYRLGAVQNEVTLTHPITKYIMACMS ADLEVVT* >P1;1dnj sequence:1dnj :::::::0.0:0.0 GSSPILSITISEGSGS----AGVLWDVPSPPPVGKAELEDGAYRIKQRGILGYSQIGAGV YKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGG---GWKLEGEWKEGEEVQV LALE-PGKNPRAVQ-TKPGLFKTNTGTIGAVSLDFSPGTSGSPIVDRKGKVVGLYGNGVV TRSGAYVSAIAQTEKSIEDNPEIEDD-------IFRKKRLTIMDLHPGAGKTKRYLPAIV REAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMR LLSPV-RVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGE-AAGIFMTATPPGSRDPFP Q-SNAPIMDEEREIPERSWNSGHEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQL SRKTFDSEYVKTRANDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILT-DGEERVILA GPMPVTHSSAAQRRGRIGRNPKNENDQYI---------YMGEPLENDEDCAHWKEAKMLL DNINTPEGIIPSMFEPEREKVDAIDGEYRLRGEARKTFVDLMRRG---DLPVWLAYRVAA EGINYADRRWCFDGIKNNQILEE-NVEVEIWTKEGERKKLKPRWLDARIYSDPLALKEFK EFAAGRK* Again, the top file goes like this: SET ALNFILE = '01mod.ali' # alignment filename SET KNOWNS = '1cx1' # codes of the templates SET SEQUENCE = '1dnj' # code of the target SET ATOM_FILES_DIRECTORY = './:../PDB:./atom_files' # SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 2 # index of the last model SET DEVIATION = 4.0 # have to be >0 if more than 1 model SET RAND_SEED = -12312 # CALL ROUTINE = 'model' # do homology modelling ************************************************* Let me know if you found something weird on my ali file.... I tried with the MINT script from Dr Andrew, (it complied and run fine) but I still get the same error as with my own script: check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Thanks in advance, Luis Rosales

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