- modeller_usage - salilab.org

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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trouble modeling ligand
by Starr Hazard 18 Jul '07

18 Jul '07

Folks, Awhile back I wanted to get MODELLER 9v1 to place template water molecules into the modeled target sequences. I added "env.io.water = True" to my python script; then in the ali file _temp ERTF/wwwwwww _target ERTY/wwwwwww and incremented the indicated length in fields 3-6 of the structureX line to account for the waters. And all went well. Attempting to generalize to apply to a single ligand, I added "env.io.hetatm = True" to my python script and in the ali file _temp ERTF/. _target ERTY/. The HETATM entries for the ligand ARE in the template PDB file. Modeller refuses to run with this and in the log file it writes that the alignment and the PDB file have different lengths EVEN THOUGH I have incremented the actual length listed in the ALI file StructureX line in fields 3-6. In this particular case, the ligand in the template is covalently attached to a residue but I will want to model non-covalently bound ligands as well.

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DOPE score question
by hori koshii 17 Jul '07

17 Jul '07

Hi all, just a short question to make sure if: the assess_dope method in MODELLER accounts for all atoms when calculating the dope energy profile for each residue? (if so, do you know/think if DOPE may be more accurate than PROSA to some extent since the latter once take into account of the Calpha and/or Cb potential only) Thanks for answering. Good day/night! --------------------------------- Food fight? Enjoy some healthy debate in the Yahoo! Answers Food & Drink Q&A.

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