- modeller_usage - salilab.org

manual restaints in muultiple template modeling?
by plmallip＠mail.uh.edu 02 Dec '08

02 Dec '08

Hi, I want to build a model using two templates. One of the templates have >70% sequence homology while the other has <35% sequence homology. To the extent of my knowledge, automodel gives more weight to the template with more sequence homology. Is there any way I can manually assign more weight to the template with less sequence homology, at some of the regions? If there is, where can I get the details, as to how to do it? I appreciate any kind of suggestions/hints in this regard. Thanks & regards, Latha, Graduate student.

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Atom has GB/SA radius 0.0000.
by Joaquim Rui Rodrigues 02 Dec '08

02 Dec '08

Dear Modellers, I made some changes to the script examples/automodel/loop.py to do loop refinement with dope_loopmodel in the presence of ligands. While this used to work well with modeller 9v4, with 9v5 I am getting the following error: e_gbsa__234E> Atom 8137 (type 112) has GB/SA radius 0.0000. Radii must all be greater than zero. Please edit the library file (e.g. modlib/solv.lib) to set a correct radius for this atom type. The atom is an MG ion. From solv.lib: # RSOL GBSA ASP ASPW SCKS OONS JRF MG 0.000 0.117 0.000 0.000 0.000 0.000 0.000 ! Magnesium Ion I suppose I should change the value of RSOL. Is there any recomended value? I foresee more problems for other atom types as solv.lib seems to have radii data only for protein atom types... Many thanks, Rui Rodrigues -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)

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Re: [modeller_usage] Transfer_xyz or other methods?
by Modeller Caretaker 02 Dec '08

02 Dec '08

plmallip(a)mail.uh.edu wrote: > I appreciate for taking time and explaining in detail. Its not that I > don't want to use automodel. But I have two questions > > 1. Is modeller going to accept the .ini file (I converted it to .pdb > manually) with undefined coordinates (999 numbers) in a script described at > > http://salilab.org/modeller/manual/node26.html > # Modeling using a provided initial structure file (inifile) Sure - Modeller will accept any model provided it has the same sequence as your target sequence. > 2. If I use automodel, I will again end up with an automated model where > I loose the bacbone Calpha conformation. i.e. my goal to retain backbone > conformation (for which I used transfer_xyz) will not be achieved. You can keep some of the atoms fixed during the refinement; see http://salilab.org/modeller/9v5/manual/node23.html In your case I guess you'd want to select everything but mainchain (or just C alphas) in aligned regions. You could do that with something like the following as your select_atoms() method: def select_atoms(self): aligned_regions = selection(self.residue_range('1:', '10:'), self.residue_range('20:', '30:')) aligned_backbone = aligned_regions.only_mainchain() # or # aligned_backbone = aligned_regions.only_atom_types('CA') return selection(self) - aligned_backbone Alternatively, you could have Modeller determine your insertions automatically with model.get_insertions() - see http://salilab.org/modeller/9v5/manual/node162.html Since this returns a list of all residue ranges that are aligned with gaps in your template, it is essentially the inverse of aligned_regions above, so you could say something like aln = self.read_alignment() aligned_regions = selection(self) - \ selection(self.get_insertions(aln, 0, 100, 0)) 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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Residues in disallowed region
by Bo Yang 01 Dec '08

01 Dec '08

Hello, Modeller: The models built from Modeller 8v1 contain some residues (non-Gly and non-Pro) in the disallowed region based on Ramachandran plot. I wonder how this could happen? How to change these residues back to allowed region? I try to use energy minimization such as NAMD and Amber. After all, the minimized models had increased numbers of residues in the disallowed region. Thank you for your advice Bo

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Transfer_xyz or other methods?
by plmallip＠mail.uh.edu 01 Dec '08

01 Dec '08

Hi, I am trying to obtain a model by transfer_xyz method, using a template which have less than 30% homology. I want to copy the coordinates of the template and if there is a gap, then obtain coordinates for those regions using model.build(). But, I end up with a model in pieces i.e. Some regions are displaced and built elsewhere. Even for some of the residues for which there is template structure, I get long linear chains built. May be the .ali file is not being used in getting the model! If transfer.xyz will not work if my the alignement has gaps in between, is there any other way to achieve this? I cannot exclude the gaps because, this will not serve the pupose of getting the template coordinates at equivalent regions where my model should have. The .ali file is >P1;1UW6 structureX:1UW6.pdb: 0 :E:215:E:undefined:undefined:-1.00:-1.00 EFDRADILYNIRQTSRPDVIPTQRD-RPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTL AWNSSHS--PDQVSVPISSLWVPDLAAYN-AISKPEVLTPQLARVVSDGEVLYMPSIRQRFS CDVSGVDTESG-ATCRIKIGSWTHHSREISVDPTTE---------NSDDSEYFSQYSRFEIL DVTQKKNSVTYSCCPEA-YEDVEVSLNFR* >P1;NRmiss_210testb sequence:NRmiss_210testb:0 :E:215 :E:::-1.00:-1.00 SVMEDTLLSVLFETYNPKVRPAQTVGDKVTVRVGLTLTNLLILNEKIEEMTTNVFLNLAWTDYRL QWDPAAYEGIKKLRIPSSDVWQPDIVLMNNNDGSFEITLHVNVLVQHTGAVSWQPSAIYRSS CTIKVMYFPFDWQNCTMVFKSYTYDTSEVTLQHALDAKGEREVKEIVINKDAFTENGQWSIE HKPSRKNWR--SDDP--SYEDVTFYLIIQ* .py file is 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') aln = alignment(env, file='NRmiss_210anti_1UW6.ali', align_codes=('1UW6')) aln.malign3d(fit=False) aln.append(file='NRmiss_210anti_1UW6.ali', align_codes= 'NRmiss_210testb') md1=model(env) md1.generate_topology(aln['NRmiss_210testb']) md1.transfer_xyz(aln) md1.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') md1.write(file='NRmiss_210testb.ini') Any suggestions in this regard is appreciated. Thanks & regards, Latha, Graduate student.

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dope batch processing
by jinlian 01 Dec '08

01 Dec '08

Hi all I want to use the 'DOPE' to do the filtering the docking structure of thousands of proteins, and I want to do batch possessing, but the script can only calculate one structure: from modeller import * from modeller.scripts import complete_pdb env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # Read a model previously generated by Modeller's automodel class mdl = complete_pdb(env, '1acb.pdb') # Select all atoms in the first chain atmsel = selection(mdl.chains[0]) score = atmsel.assess_dope() I am not familiar with python, Could you tell me how to do the batch processing in the above script? Thank you very much!

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dope batch processing
by Mauricio Carrillo Tripp 28 Nov '08

28 Nov '08

This is not a python solution, perhaps there is one, but what I did was to write a bash shell script to modify the python script changing the name of the model consecutively (might have to be modified for other shells): # DOPE for c in 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15; do sed 's/NAME/Model_'${c}'/g' model-DOPE.py > tmp.py; mod9v4 tmp.py ; echo "Model "${c}": ";grep 'DOPE' tmp.log >> Models_DOPE.dat; done In the python script (model-DOPE.py in my case) replace the line mdl = complete_pdb(env, '1acb.pdb') with mdl = complete_pdb(env, 'NAME.pdb') your previously built models should be named sequentially Model_01 to Model_15 (or the last one in your case), or change the regexp in the sed command above according to your file naming. At the end you'll have a list of DOPE values in the file Models_DOPE.dat. Hope this helps... Message: 1 > Date: Thu, 27 Nov 2008 10:03:30 +0800 > From: "jinlian" <jinlian05(a)lzu.cn> > Subject: [modeller_usage] dope batch processing > To: <modeller_usage(a)salilab.org> > Message-ID: <427750030.20199(a)lzu.cn> > Content-Type: text/plain; charset="us-ascii" > > Hi all > > I want to use the 'DOPE' to do the filtering the docking structure of > thousands of proteins, and I want to do batch possessing, but the script > can > only calculate one structure: > > > from modeller import * > from modeller.scripts import complete_pdb > > env = environ() > env.libs.topology.read(file='$(LIB)/top_heav.lib') > env.libs.parameters.read(file='$(LIB)/par.lib') > > # Read a model previously generated by Modeller's automodel class > mdl = complete_pdb(env, '1acb.pdb') > > # Select all atoms in the first chain > atmsel = selection(mdl.chains[0]) > > score = atmsel.assess_dope() > > I am not familiar with python, Could you tell me how to do the batch > processing in the above script? > Thank you very much! > -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | trippm(a)scripps.edu 0 | http://www.scripps.edu/~trippm ** Aut tace aut loquere meliora silentio **

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R: R: question for a (putative?) disulfide bridge
by Anna Marabotti 26 Nov '08

26 Nov '08

Dear Ben, I'm re-sending the message below because it seems to me that you did not receive it. Sorry for duplication. Best regards Anna Marabotti -----Messaggio originale----- Da: Anna Marabotti [mailto:anna.marabotti@isa.cnr.it] Inviato: lunedì 24 novembre 2008 13.47 A: 'Modeller Caretaker' Oggetto: R: R: [modeller_usage] question for a (putative?) disulfide bridge Dear Ben, thank you for your continuous support. I'm attaching here the pdb file of the model in which I would like to create the disulfide bridge, and the scripts I used to do it. My knowledge of Python language is very very poor and so I'm doing a trial&error procedure, but at present I obtain only errors... If I understand well, I should only provide the PDB file to Modeller, since I don't see any request of alignment. The sequence then should be read from the PDB file, right? The PDB file I have attached is the one that I obtained using mutate_model: residue 55 was previously a Gly, and now is a Cys in both subunits.So, the number of the residue should be correct. I tried to model a disulfide bridge between Cys55 of the subunit A and Cys180 of the subunit B, and I tried: 1) model-patch_1.py (see attachment): here the error message: Traceback (most recent call last): File "model-patch_1.py", line 19, in ? mdl = complete_pdb(env, code, special_patches=patches) File "C:\Programmi\Modeller9v5\modlib\modeller\scripts\complete_pdb.py", line 37, in complete_pdb special_patches(mdl) File "model-patch_1.py", line 15, in patches mdl.patch(residue_type='DISU', residues=(mdl.residues['55:'], File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 226, in _ _getitem__ (self.offset, self.length, self.suffix)) File "C:\Programmi\Modeller9v5\modlib\modeller\util\modutil.py", line 19, in h andle_seq_indx int_indx = lookup_func(*args) File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 283, in _ indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 55:' 2) model-patch_2.py (see attachment): here the error message: Traceback (most recent call last): File "model-patch_2.py", line 19, in ? mdl = complete_pdb(env, code, special_patches=patches) File "C:\Programmi\Modeller9v5\modlib\modeller\scripts\complete_pdb.py", line 37, in complete_pdb special_patches(mdl) File "model-patch_2.py", line 15, in patches mdl.patch(residue_type='DISU', residues=(mdl.residues['55:A'], File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 226, in _ _getitem__ (self.offset, self.length, self.suffix)) File "C:\Programmi\Modeller9v5\modlib\modeller\util\modutil.py", line 19, in h andle_seq_indx int_indx = lookup_func(*args) File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 283, in _ indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 180:B' 3) model-patch_3.py (see attachment): here the error message: Traceback (most recent call last): File "model-patch_3.py", line 19, in ? mdl = complete_pdb(env, code, special_patches=patches) File "C:\Programmi\Modeller9v5\modlib\modeller\scripts\complete_pdb.py", line 37, in complete_pdb special_patches(mdl) File "model-patch_3.py", line 15, in patches mdl.patch(residue_type='DISU', residues=(mdl.residues['A:55'], File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 226, in _ _getitem__ (self.offset, self.length, self.suffix)) File "C:\Programmi\Modeller9v5\modlib\modeller\util\modutil.py", line 19, in h andle_seq_indx int_indx = lookup_func(*args) File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 283, in _ indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: A:55' I also obtained the .log file, that I'm attaching here. I don't understand if there is only a problem in identifying the numbers of the residues or there are other supplementary problems, anyway the disulfide bridge is not forming, and I don't see any trivial error to correct. Thank you for your help and best regards. Anna Marabotti -----Messaggio originale----- Da: Modeller Caretaker [mailto:modeller-care@salilab.org] Inviato: venerdì 21 novembre 2008 19.02 A: Anna Marabotti Cc: modeller_usage(a)salilab.org Oggetto: Re: R: [modeller_usage] question for a (putative?) disulfide bridge Anna Marabotti wrote: > thank you for your message, and sorry to bother you again. I tried to > use model.patch() to add the disulfide > bridge to my model, but I have a supplementary problem. In fact, my > protein is a homodimer and the disulfide > bridge should link two Cys residues in the two different subunits. I > tried to indicate "A" and "B" in the > script in this way: > > # Create the disulfide bond: > def patches(mdl): > mdl.patch(residue_type='DISU', residues=(mdl.residues['55:A.'], > mdl.residues['180:B'])) > > but it doesn't work. What do you mean by "it doesn't work"? You get an error message (what is it?) or everything runs but the disulfide isn't created? In the latter case, I'd need to see the full script. In the former case, you probably have the wrong residue numbers and/or chains for your two Cys residues. The first residue should probably be '55:A' rather than '55:A.' but one way to check the numbers is to run modeling first without the patch, and look at the numbers in the generated model. 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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how to build a model from a template with only CA atoms?
by Lixia Jin Day 25 Nov '08

25 Nov '08

Hi, I have a protein conformation with only alpha carbon (CA) atoms. And I want to build up the full structure without moving the position of the CA atoms. Can I do it with MODELLER? How to do it? Thanks! Lixia

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question for a (putative?) disulfide bridge
by Anna Marabotti 21 Nov '08

21 Nov '08

Dear Modeller caretaker, using mutate_model I replaced a residue in a protein with Cys. Looking at the mutant protein, I saw that this new Cys residue is near to another Cys residue that was previously in the protein. The two sulphur moieties are not facing each others as in a disulfide bridge, but are rotated away. However, manually rotating the side chains, they can approach their sulphur moieties until less than 3A of distance, so in my opinion a disulfide bridge could be formed. At present I have not experimental data to confirm if a disulfide bridge is forming or not in this mutant. How can I check with MODELLER if this newly introduced mutation is really able to form a new disulfide bridge into my protein? How can I model this new disulfide bridge? Many thanks and best regards Anna Marabotti ______________________________________________ Anna Marabotti, Ph.D. Laboratorio di Bioinformatica e Biologia Computazionale Istituto di Scienze dell'Alimentazione, CNR Via Roma 52 A/C 83100 Avellino (Italy) Tel: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabotti(a)isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm Coming soon: BBCC2008: http://bioinformatica.isa.cnr.it/BBCC/BBCC2008 ____________________________________________________ "If you think you are too small to make a difference, try sleeping with a mosquito"

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