- modeller_usage - salilab.org

automated response
by charloteaux.b 06 Aug '07

06 Aug '07

Out of office => 21/8 Best regards

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total of DOPE per residues not equal to global DOPE?
by hori koshii 06 Aug '07

06 Aug '07

Hi, I have tried to add up all the DOPE score per residue but the value is not equal to the global DOPE score at all. Anyone knows the answer please? Thank you. --------------------------------- Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.

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Could you please remove my e-mail from your list? Thank you
by Omid Khalouei 03 Aug '07

03 Aug '07

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[Fwd: Re: The models miss the 40 first aa of the sequence]
by Modeller Caretaker 03 Aug '07

03 Aug '07

-------- Original Message -------- Subject: Re: [modeller_usage] The models miss the 40 first aa of the sequence Date: Thu, 02 Aug 2007 15:03:17 -0400 From: Dany Naranjo Feliciano <dany(a)censa.edu.cu> To: Modeller Caretaker <modeller-care(a)salilab.org> References: <WorldClient-F200708021350.AA50150418(a)censa.edu.cu> <46B21D98.2020806(a)salilab.org> When I visualized the models using vmd, I can't see the first 40aa of the sequence. Thanks, Dany Naranjo Feliciano Lic. Bioquímica Grupo Biología Molecular Centro Nacional de Sanidad Agropecuaria (CENSA) Apartado 10. San José de las Lajas. La Habana. CP 32700. Cuba Teléfono 53-47-863014 ext 28 -----Original Message----- From: Modeller Caretaker <modeller-care(a)salilab.org> To: Dany Naranjo Feliciano <dany(a)censa.edu.cu> Cc: modeller_usage(a)salilab.org Date: Thu, 02 Aug 2007 11:08:24 -0700 Subject: Re: [modeller_usage] The models miss the 40 first aa of the sequence Dany Naranjo Feliciano wrote: > The models miss the 40 first aa of the sequence. > What might be wrong? What do you mean by "miss the 40 first aa" ? Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage "Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu". Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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The models miss the 40 first aa of the sequence
by Dany Naranjo Feliciano 02 Aug '07

02 Aug '07

Hi list, The models miss the 40 first aa of the sequence. What might be wrong? Thanks >P1;1gmy_A.pdb structureX:1gmy_A.pdb: 0 :A: 253 :A:undefined:undefined:-1.00:-1.00 KLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDL LTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGSR-PP CTGEG-DTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVY SDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQ DHCGIESEVVAGIPRT* >P1;Q8I7B2_sequence --------------------IPDQSSCGSCWAVAGVGAMSDRVCIHSNGMMQPELSAIDL VSCC-SYCGNGCQGGSPPAAWDYWWRNGIVTGGTLENPTGCLPYPFPQCRHPGSRSQLNP CPRYTYPTPSCYPYCQAGYDKTYEKDKVYGKTSYNVDRHEYTIMEEIMKNGPVEAGFIVY TDFAVYKSGIYHHVSGRYAGKHAIRIIGWGVENGVKYWLTANSWNVGWGENGYFRILRGT DECRIESIVVAGMPR-* # Homology modelling by the automodel class from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './' a = automodel(env, alnfile = 'test_fasciola.ali', # alignment filename knowns = '1gmy_A.pdb', # codes of the templates sequence = 'Q8I7B2_sequence') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling "Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu".

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five ss bridges
by Dany Naranjo Feliciano 02 Aug '07

02 Aug '07

Hi, I´m trying to model 5 SS bridges. When I try to tell modeller 9v1 to do that,I receive the following error: Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback File "test_ssmodel_fasciola.py", line 9 def special_patches(self, aln): ^ IndentationError: expected an indented block What might be wrong? The script, #Homology modelling by the automodel class from modeller import * # Load standar Modeller classes from modeller.automodel import * # Load the automodel class #Redefine the special_patches routine to include the additional disulfides #(this routine) class mymodel(automodel): def special_patches(self, aln): # A disulfide between residues 10-51,44-47,43-110,80-114,88-100: self.patch(residue_type='DISU', residues=(self.residues['10'], self.residues['51'])) self.patch(residue_type='DISU', residues=(self.residues['44'], self.residues['47'])) self.patch(residue_type='DISU', residues=(self.residues['43'], self.residues['110'])) self.patch(residue_type='DISU', residues=(self.residues['80'], self.residues['114'])) self.patch(residue_type='DISU', residues=(self.residues['88'], self.residues['100'])) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './' a = mymodel(env, alnfile = 'test_fasciola.ali', # alignment filename knowns = '1gmy_A.pdb', # codes of the templates sequence = 'Q8I7B2_sequence') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling "Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu".

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[Fwd: five ss bridges]
by Modeller Caretaker 02 Aug '07

02 Aug '07

-------- Original Message -------- Subject: five ss bridges Date: Thu, 02 Aug 2007 10:58:11 -0400 From: Dany Naranjo Feliciano <dany(a)censa.edu.cu> To: modeller_usage-owner(a)salilab.org -----Original Message----- From: "Dany Naranjo Feliciano" <dany(a)censa.edu.cu> To: modeller_usage(a)salilab.org Date: Thu, 02 Aug 2007 10:30:42 -0400 Subject: five ss bridges Hi, I´m trying to model 5 SS bridges. When I try to tell modeller 9v1 to do that,I receive the following error: Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback File "test_ssmodel_fasciola.py", line 9 def special_patches(self, aln): ^ IndentationError: expected an indented block What might be wrong? The script, #Homology modelling by the automodel class from modeller import * # Load standar Modeller classes from modeller.automodel import * # Load the automodel class #Redefine the special_patches routine to include the additional disulfides #(this routine) class mymodel(automodel): def special_patches(self, aln): # A disulfide between residues 10-51,44-47,43-110,80-114,88-100: self.patch(residue_type='DISU', residues=(self.residues['10'], self.residues['51'])) self.patch(residue_type='DISU', residues=(self.residues['44'], self.residues['47'])) self.patch(residue_type='DISU', residues=(self.residues['43'], self.residues['110'])) self.patch(residue_type='DISU', residues=(self.residues['80'], self.residues['114'])) self.patch(residue_type='DISU', residues=(self.residues['88'], self.residues['100'])) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './' a = mymodel(env, alnfile = 'test_fasciola.ali', # alignment filename knowns = '1gmy_A.pdb', # codes of the templates sequence = 'Q8I7B2_sequence') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling Dany Naranjo Feliciano Lic. Bioquímica Grupo Biología Molecular Centro Nacional de Sanidad Agropecuaria (CENSA) Apartado 10. San José de las Lajas. La Habana. CP 32700. Cuba Teléfono 53-47-863014 ext 28 "Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu". Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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regarding simulated annealing
by vidhya sankar 01 Aug '07

01 Aug '07

can i change default simulated annealing protocol and optimizatios protocols corresponding to model-default.py --------------------------------- Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when.

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Question about a protein structure
by Ester Fusté Domínguez 30 Jul '07

30 Jul '07

Dear sir/madam, I have a problem with modeller and probably you can help me. I want to do protein structure modelling. I have the sequence of a bacterium protein, and it's known that it has tree identical chains like this: MQMKKLFPIL IGLGLTGFSA MSQAENLLQV YQQARISNPD LRKSAADRDA AFEKINEARS PLLPQLGLGA DYTYTSGFRD YKDQNSNVTS GSLQLTQVLF DMSKWRALTL QEKQAGIQDV TYQTDQQTLI LNTATAYFKG LAAIDTLSYT EAQKQAIYRQ LDQTTQRFNV GLGAITDVQN ARSQYDAVLA NEVTARNDLD NAPQKLRQGT GNYYPELGSP NGKGFKTNKP QAVNALLKEA ESRNLSLLQA RLSQDLAREQ IPQAQDGHLP TLNLNASSGV SNNRYSGSKS ISQDADVGQN KIGLSFSLPL YQGGMVNSQV KQAQYNFVGA SEQLESAHRS VVQTVRSSFN NVNASISSIN AYKQAVVSAQ SSLDAMEAGY SVGTRTIVDV LDATTTLYNA KQQLSNARYN YLINELNIKS ALGTLNEQDL VALNNTLGKS IPTSPDSVAP ENPQQDASAD GYSNTAAAKP ASARTTQTSG SNPFRQ* I don't really know what can I do to avoid the chains overlap. I have tried to copy the sequence three times but it doesn't work. This is what I did: MQMKKLFPIL IGLGLTGFSA MSQAENLLQV YQQARISNPD LRKSAADRDA AFEKINEARS PLLPQLGLGA DYTYTSGFRD YKDQNSNVTS GSLQLTQVLF DMSKWRALTL QEKQAGIQDV TYQTDQQTLI LNTATAYFKG LAAIDTLSYT EAQKQAIYRQ LDQTTQRFNV GLGAITDVQN ARSQYDAVLA NEVTARNDLD NAPQKLRQGT GNYYPELGSP NGKGFKTNKP QAVNALLKEA ESRNLSLLQA RLSQDLAREQ IPQAQDGHLP TLNLNASSGV SNNRYSGSKS ISQDADVGQN KIGLSFSLPL YQGGMVNSQV KQAQYNFVGA SEQLESAHRS VVQTVRSSFN NVNASISSIN AYKQAVVSAQ SSLDAMEAGY SVGTRTIVDV LDATTTLYNA KQQLSNARYN YLINELNIKS ALGTLNEQDL VALNNTLGKS IPTSPDSVAP ENPQQDASAD GYSNTAAAKP ASARTTQTSG SNPFRQ MQMKKLFPIL IGLGLTGFSA MSQAENLLQV YQQARISNPD LRKSAADRDA AFEKINEARS PLLPQLGLGA DYTYTSGFRD YKDQNSNVTS GSLQLTQVLF DMSKWRALTL QEKQAGIQDV TYQTDQQTLI LNTATAYFKG LAAIDTLSYT EAQKQAIYRQ LDQTTQRFNV GLGAITDVQN ARSQYDAVLA NEVTARNDLD NAPQKLRQGT GNYYPELGSP NGKGFKTNKP QAVNALLKEA ESRNLSLLQA RLSQDLAREQ IPQAQDGHLP TLNLNASSGV SNNRYSGSKS ISQDADVGQN KIGLSFSLPL YQGGMVNSQV KQAQYNFVGA SEQLESAHRS VVQTVRSSFN NVNASISSIN AYKQAVVSAQ SSLDAMEAGY SVGTRTIVDV LDATTTLYNA KQQLSNARYN YLINELNIKS ALGTLNEQDL VALNNTLGKS IPTSPDSVAP ENPQQDASAD GYSNTAAAKP ASARTTQTSG SNPFRQ MQMKKLFPIL IGLGLTGFSA MSQAENLLQV YQQARISNPD LRKSAADRDA AFEKINEARS PLLPQLGLGA DYTYTSGFRD YKDQNSNVTS GSLQLTQVLF DMSKWRALTL QEKQAGIQDV TYQTDQQTLI LNTATAYFKG LAAIDTLSYT EAQKQAIYRQ LDQTTQRFNV GLGAITDVQN ARSQYDAVLA NEVTARNDLD NAPQKLRQGT GNYYPELGSP NGKGFKTNKP QAVNALLKEA ESRNLSLLQA RLSQDLAREQ IPQAQDGHLP TLNLNASSGV SNNRYSGSKS ISQDADVGQN KIGLSFSLPL YQGGMVNSQV KQAQYNFVGA SEQLESAHRS VVQTVRSSFN NVNASISSIN AYKQAVVSAQ SSLDAMEAGY SVGTRTIVDV LDATTTLYNA KQQLSNARYN YLINELNIKS ALGTLNEQDL VALNNTLGKS IPTSPDSVAP ENPQQDASAD GYSNTAAAKP ASARTTQTSG SNPFRQ* Could you help me, please? I need to know how can I find a solution and I don't know the way to get it. When I copy the sequence three times, the program don't distinguish the three chains, and it overlap them. I'm waiting for your reply. Thank you very much. Ester

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Block Ligand stereo chemistry problem
by Andre Fischer 26 Jul '07

26 Jul '07

Hi all, I am modelling a Protein with a ligand. The Ligand comes from the pdb template as a blk. Modeller works fine and the protein model seems reasonable, except that the modelled ligand is mirrored along its length axis compared to the template ligand. Also BLK Residues are defined rigid. some stereo operations seem to be allowed. How can i get rid of those? I want the ligand only to act as a steric constraint. Thank you very much Andre (Universität Regensburg, Germany)

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