- modeller_usage - salilab.org

Re: [modeller_usage] modeller_usage Digest, Vol 6, Issue 79
by vidhya sankar 17 Aug '07

17 Aug '07

can i compare th DOPE score of my mode with dope score of X-ray PDB.?if i can, what should be the DOPE SCORE difference between my model and X-ray PDB in order tobe my model is a reliable model. could you please tell some difference in score value yhanks in advance modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: superpose.py (vidhya sankar) ---------------------------------------------------------------------- Message: 1 Date: Thu, 16 Aug 2007 01:00:44 -0700 (PDT) From: vidhya sankar Subject: Re: [modeller_usage] superpose.py To: modeller_usage(a)salilab.org Message-ID: <467087.77948.qm(a)web51604.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i do not have proper PDB TEMPLATE for my 529 amino acid sequence.I have only the PDB of 53% sequence similiarity & identity. upon using this in superpose .py script i have got RMS OF 2.3337 and number of aligned equivalent positions 33 amog 115 residues will it be reliable value ? modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: log files (vidhya sankar) ---------------------------------------------------------------------- Message: 1 Date: Sat, 11 Aug 2007 04:21:41 -0700 (PDT) From: vidhya sankar Subject: Re: [modeller_usage] log files To: modeller_usage(a)salilab.org Message-ID: <267539.63819.qm(a)web51610.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i did not get any log files when i run modeller9v1 in windowsXp .what shoul i do to get log files thank you? i am expecting your reply modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: DOPE (Modeller Caretaker) 2. regarding DOPE score (vidhya sankar) 3. regrding superpose.py (vidhya sankar) 4. ref: SUPERPOSE.PY (vidhya sankar) 5. Re: regarding DOPE score (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Thu, 09 Aug 2007 12:57:42 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] DOPE To: Ester Fust? Dom?nguez Cc: modeller_usage(a)salilab.org Message-ID: <46BB71B6.8070207(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Ester Fust? Dom?nguez wrote: > How can I see the DOPE score profile? I don't know how to use > *assess_dope* command. There is an example at the end of the basic tutorial at http://salilab.org/modeller/tutorial/basic.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Fri, 10 Aug 2007 05:10:48 -0700 (PDT) From: vidhya sankar Subject: [modeller_usage] regarding DOPE score To: modeller_usage(a)salilab.org Message-ID: <835492.28231.qm(a)web51612.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i have got a DOPE score of -41275.816406 is it reliable value ? .how can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE --------------------------------- Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search.

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loop optimization in the presence of a ligand
by Thijs Beuming 16 Aug '07

16 Aug '07

Hi, I am trying to optimize a loop in close proximity to a ligand. For some reason, the intial models have the ligand present, while the loop optimized models do not. Hence, there are major clashes between some of the calculated loops and the ligand. Is it possible to optimize loops in the presence of the ligand? My input script: # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes 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 = 'MODELLER' class mymodel(loopmodel): def special_restraints(self, aln): rsr = self.restraints rsr.add(atom_ids=('CA:189', 'CA:372'), restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) rsr.add(atom_ids=('CA:189', 'CA:393'), restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) rsr.add(atom_ids=('CA:372', 'CA:393'), restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['176'], self.residues ['185'])) def select_loop_atoms(self): return selection(self.residue_range('378:', '383:')) a = mymodel(env, alnfile = 'MODELLER/alignment.pir', # alignment filename knowns = 'template', # codes of the templates sequence = 'target') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 2 # Last loop model a.make() # do the actual homology modeling Thanks, Thijs Beuming

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restraints from multiple templates
by Mathew Smith 16 Aug '07

16 Aug '07

I was wondering how modeller uses the structural information of multiple templates. Are all aligned residues of all the templates used to create the restraints and are they weighted in any way e.g. by sequence identity of template to target or by residue type (exact matches weighted more than disimilar aa's)? Also how can I alter these things so that I can tailor the restraints that I use depending on in/dels and sequence similarity etc? Thanks in advance Mat -- Mathew.Smith(a)postgrad.manchester.ac.uk G.043 Faculty of Life Sciences Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN

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Reg. Generating profile plot using GNUPLOt
by saravanan 16 Aug '07

16 Aug '07

Query regarding visualizing profile in GNUPLOT We run the evaluate_model.py which implements mdl.assess_dope function in modeller8v2. We got the DOPE score. Now we want to generate the PLOT using GNUPLOT with the output of the script. We tried in GNUPLOT, we just got a diagonal line but not like presented in the tutorial. the script looks like: from modeller import* from modeller.automodel import* log.verbose() env=environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') #env.io.atom_files_directory='./:../atom_files' mdl=model(env) mdl.read(file='1fdx.B999900001.pdb') aln=alignment(env) code="1fdx_my" aln.append_model(mdl,atom_files='1fdx.B999900001.pdb',align_codes=code) aln.append_model(mdl,atom_files='1fdx.B999900001.pdb',align_codes=code+'-ini') mdl.generate_topology(aln,sequence=code+'-ini') mdl.transfer_xyz(aln) mdl.assess_dope(output='ENERGY_PROFILE REPORT',file='1fdx_my.profile', normalize_profile=True,smoothing_window=15) Looking forward for reply -P.Saravanan ____________________________________________________________________________________ Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. http://tv.yahoo.com/collections/222

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Re: [modeller_usage] superpose.py
by vidhya sankar 16 Aug '07

16 Aug '07

i do not have proper PDB TEMPLATE for my 529 amino acid sequence.I have only the PDB of 53% sequence similiarity & identity. upon using this in superpose .py script i have got RMS OF 2.3337 and number of aligned equivalent positions 33 amog 115 residues will it be reliable value ? modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: log files (vidhya sankar) ---------------------------------------------------------------------- Message: 1 Date: Sat, 11 Aug 2007 04:21:41 -0700 (PDT) From: vidhya sankar Subject: Re: [modeller_usage] log files To: modeller_usage(a)salilab.org Message-ID: <267539.63819.qm(a)web51610.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i did not get any log files when i run modeller9v1 in windowsXp .what shoul i do to get log files thank you? i am expecting your reply modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: DOPE (Modeller Caretaker) 2. regarding DOPE score (vidhya sankar) 3. regrding superpose.py (vidhya sankar) 4. ref: SUPERPOSE.PY (vidhya sankar) 5. Re: regarding DOPE score (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Thu, 09 Aug 2007 12:57:42 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] DOPE To: Ester Fust? Dom?nguez Cc: modeller_usage(a)salilab.org Message-ID: <46BB71B6.8070207(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Ester Fust? Dom?nguez wrote: > How can I see the DOPE score profile? I don't know how to use > *assess_dope* command. There is an example at the end of the basic tutorial at http://salilab.org/modeller/tutorial/basic.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Fri, 10 Aug 2007 05:10:48 -0700 (PDT) From: vidhya sankar Subject: [modeller_usage] regarding DOPE score To: modeller_usage(a)salilab.org Message-ID: <835492.28231.qm(a)web51612.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i have got a DOPE score of -41275.816406 is it reliable value ? .how can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE --------------------------------- Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search.

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Re: [modeller_usage] dope calculations
by vidhya sankar 13 Aug '07

13 Aug '07

dear sir , i do not have proper PDB TEMPLATE for my 529 amino acid sequence.I have only the PDB of 53% sequence similiarity & identity. can i take this Template to compare My DOPE score with PDB.WILL IT BE RELIABLE value? i am expecting your reply modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: log files (vidhya sankar) ---------------------------------------------------------------------- Message: 1 Date: Sat, 11 Aug 2007 04:21:41 -0700 (PDT) From: vidhya sankar Subject: Re: [modeller_usage] log files To: modeller_usage(a)salilab.org Message-ID: <267539.63819.qm(a)web51610.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i did not get any log files when i run modeller9v1 in windowsXp .what shoul i do to get log files thank you? i am expecting your reply modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: DOPE (Modeller Caretaker) 2. regarding DOPE score (vidhya sankar) 3. regrding superpose.py (vidhya sankar) 4. ref: SUPERPOSE.PY (vidhya sankar) 5. Re: regarding DOPE score (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Thu, 09 Aug 2007 12:57:42 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] DOPE To: Ester Fust? Dom?nguez Cc: modeller_usage(a)salilab.org Message-ID: <46BB71B6.8070207(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Ester Fust? Dom?nguez wrote: > How can I see the DOPE score profile? I don't know how to use > *assess_dope* command. There is an example at the end of the basic tutorial at http://salilab.org/modeller/tutorial/basic.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Fri, 10 Aug 2007 05:10:48 -0700 (PDT) From: vidhya sankar Subject: [modeller_usage] regarding DOPE score To: modeller_usage(a)salilab.org Message-ID: <835492.28231.qm(a)web51612.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i have got a DOPE score of -41275.816406 is it reliable value ? .how can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE --------------------------------- Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search.

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Re: [modeller_usage] log files
by vidhya sankar 11 Aug '07

11 Aug '07

i did not get any log files when i run modeller9v1 in windowsXp .what shoul i do to get log files thank you? i am expecting your reply modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: DOPE (Modeller Caretaker) 2. regarding DOPE score (vidhya sankar) 3. regrding superpose.py (vidhya sankar) 4. ref: SUPERPOSE.PY (vidhya sankar) 5. Re: regarding DOPE score (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Thu, 09 Aug 2007 12:57:42 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] DOPE To: Ester Fust? Dom?nguez Cc: modeller_usage(a)salilab.org Message-ID: <46BB71B6.8070207(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Ester Fust? Dom?nguez wrote: > How can I see the DOPE score profile? I don't know how to use > *assess_dope* command. There is an example at the end of the basic tutorial at http://salilab.org/modeller/tutorial/basic.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Fri, 10 Aug 2007 05:10:48 -0700 (PDT) From: vidhya sankar Subject: [modeller_usage] regarding DOPE score To: modeller_usage(a)salilab.org Message-ID: <835492.28231.qm(a)web51612.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i have got a DOPE score of -41275.816406 is it reliable value ? .how can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE --------------------------------- Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search.

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Re: [modeller_usage] SA IN optimize.py
by vidhya sankar 11 Aug '07

11 Aug '07

i would like to implement simulated anealing protocol in optimize.py script.along with default optimization modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: DOPE (Modeller Caretaker) 2. regarding DOPE score (vidhya sankar) 3. regrding superpose.py (vidhya sankar) 4. ref: SUPERPOSE.PY (vidhya sankar) 5. Re: regarding DOPE score (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Thu, 09 Aug 2007 12:57:42 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] DOPE To: Ester Fust? Dom?nguez Cc: modeller_usage(a)salilab.org Message-ID: <46BB71B6.8070207(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Ester Fust? Dom?nguez wrote: > How can I see the DOPE score profile? I don't know how to use > *assess_dope* command. There is an example at the end of the basic tutorial at http://salilab.org/modeller/tutorial/basic.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Fri, 10 Aug 2007 05:10:48 -0700 (PDT) From: vidhya sankar Subject: [modeller_usage] regarding DOPE score To: modeller_usage(a)salilab.org Message-ID: <835492.28231.qm(a)web51612.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i have got a DOPE score of -41275.816406 is it reliable value ? .how can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE --------------------------------- Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search.

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modeller 9.2: spaghetti effect with multiple templates
by Raik Gruenberg 10 Aug '07

10 Aug '07

Hi modellers, already a while ago I have noticed that modeller tends to produce what I would call spaghetti proteins (containing knots and other fancy structures) when it is supplied with multiple templates that are far from the target (35 % or less) and also quite diverse among each other. However, Modeller 9 seems to suffer more from this effect than the previous versions: One of our test cases uses 10 templates with between 86% and 31% sequence similarity to the target. I know that this is not the optimal strategy (especially after reading this paper: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm262v1 ) but modeller 8.2 still performed quite well and all 10 models had good topology (close to the 86% template) and secondary structure. However, I now re-run our test with modeller 9.1, using the identical alignment (T-Coffee) and the same input file (below) and the result looks much worse. Most among the 10 generated models show a messed up (swaped) topology, many have knots and the different models are generally more diverse. So to what extend differs the multiple-template treatment of Modeller 9 from previous versions? Do I need to use different parameters for multi-template modeling in the new version? Or is the general default modeling protocol different now? So here is our (old-style) input file: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'final.pir_aln' SET KNOWNS = '1K2H_A' '1M31_A' '1J55_A' '1KSO_A' '1MQ1_A' '1MWN_A' '1MHO_' '1NSH_A' '1K8U_A' '1DT7_A' SET SEQUENCE = 'target' # code of the target SET ATOM_FILES_DIRECTORY = '../templates/modeller/' SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 10 # index of the last model CALL ROUTINE = 'model' I am attaching a typical result of modeller 8 and one of modeller 9 for comparison. Thanks in advance for any comments! Best regards, Raik

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making a patch work
by Starr Hazard 10 Aug '07

10 Aug '07

Folks, I have created a RESI entry in top_heav.lib for a ligand of interest to me. When run without attempting to patch anything the RESI is accepted just fine and models are made with the appropriate ligand in an appropriate location. In reality the ligand forms a covalent bond with the protein. This is a Schiff Base linkage. My RESI is an aldehyde. The covalent bond is to the NZ of a lysine. I am deleting hydrogens from the LYS and the aldehyde oxygen from from the ligand to make the bond of interest to me. I created a PRES entry based on the disulfide example. PRES ELAZ +1.0000 ATOM 1:CE CT2 -0.10000 ATOM 1:NZ NN3 1.0000 ! trying to make a protonated Schiff base ATOM 2:C15 CN2 -0.08000 ATOM 2:C14 CT1 -0.10000 DELE ATOM 1:HZ3 DELE ATOM 1:HZ2 DELE ATOM 2:O32 BOND 1:NZ 2:C15 ANGL 1:CE 1:NZ 2:C15 1:NZ 2:C15 2:C14 DIHE 1:CD 1:CE 1:NZ 2:C15 1:NZ 2:C15 2:C14 2:C13 1:CE 1:NZ 2:C15 2:C14 IC 1:CD 1:CE 1:NZ 2:C15 0.0000 0.0000 92.5000 0.0000 0.0000 IC 1:CE 1:NZ 2:C15 2:C14 0.0000 0.0000 183.0000 0.0000 0.0000 IC 1:NZ 2:C15 2:C14 2:C13 0.0000 0.0000 177.0000 0.0000 0.0000 When I perform a test run of the code patch.py from the on-line manual (where I have added "env.io.hetatm=true" to read the ligand). The program appears to run but the log file shows numerous entries of this sort r_stere_607W > Cannot find parms in parm file Then remarks indicate that it has "added" some parms; so it gets past some instances where explicit information has not been supplied. It gets to a particular dihedral involving an atom that is supposed to be deleted by the patch ( see line above- 'DELE ATOM 2:O32' is the line in top.heav.lib; this is the aldehyde oxygen) and stops. The final line reads simply: FATAL error: assertion nbndpf < mbndpf failed in r_stereo.F90, line 608 At this point that error means absolutely nothing to me. The entries in the parm.lib file are often redundant for many entries. Are the columns described somewhere? Do I need to have explicit entries in the parm file for an atom that I hope to delete? I have not deciphered how to designate bond order in either the RESI entry or the PRES entry lines. How does one specify bond order? Starr

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