- modeller_usage - salilab.org

coulomb energy
by abdullah ahmed 19 Apr '10

19 Apr '10

Dear modeller users, I incorrectly wrote, "However, this is not the case after optimization (the single charge has a higher energy value)" in my previous mail. This should have been "the single charge has a lower energy value." Sorry about the inconvenience, Abdullah From: abdullah_renk_ahmed(a)hotmail.com To: modeller_usage(a)salilab.org; andrey.kajava(a)crbm.cnrs.fr Subject: coulomb energy Date: Mon, 19 Apr 2010 16:11:58 +0600 Dear Modeller users, I am working on two structures where the insides of the structure do not have access to water. One structure contains a charged Lysine and a charged Glutamic acid residue facing each other, with distances favorable for electrostatic interactions. The other contains a negatively charged residue only. There are no other charges in either molecule, but there are a large number of Glutamines. The dielectric constant is set to 1. Theoretically, the structure with two opposite charges should have a higher coulomb energy. However, this is not the case after optimization (the single charge has a higher energy value). I would like to know if this is because: 1) I haven't used the coloumb energies properly? (I used the following line in the optimization.py script to switch it on: "env.edat.dynamic_coulomb= True") 2) Modeller calculates the electrostatic energies in a different way to what I has excepting? Thank you in advance for your reply, Abdullah Ahmed Hotmail: Free, trusted and rich email service. Get it now. Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969

1 0

model with ligand
by Knut J Bjuland 15 Apr '10

15 Apr '10

I am useing modeller to do modell protein. There are some point that I do not get in adding the ligand. Is it possible to add the lign in the alignment witouth adding manual to the aln file. How do I instruct t saling to add the ligand. I have tried add env.io.hydrogen = True env.io.water = True env.io.hetatm=True with out much success. Knut J _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969

2 5

question about unusual bond length, bond angle, Chirality deviations
by Song, Hyundeok (songhk) 15 Apr '10

15 Apr '10

Dear Modeller users I generated the dimer by Modeller. Fasta sequence number of model(400) is 70 less than Fasta sequence number of template(470). Sequence identity between template and model is 24%. after selecting the template, I aligned them, and then I did loop modeling. (I attached the code at the bottom.) Finally I got final pdb structure, but when I checked my model, I found the below warning message. "Unusual bond length, unusual bond angle, Chirality deviations " I am a beginner, so I don't what should I do to correct above warning message. Please help me, Any suggestions or comments are welcomed. Thanks. Hyun. ---align2d.py---- from modeller import * env = environ() aln = alignment(env) mdl = model(env, file='****', model_segment=('FIRST:A','LAST:B')) aln.append_model(mdl, align_codes='******', atom_files='*****') aln.append(file='******.ali', align_codes='*****') aln.align2d() aln.write(file='**************.ali', alignment_format='PIR') aln.write(file='**************.pap', alignment_format='PAP') ---model-loop.py----- # Homology modeling by the automodel class from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = loopmodel(env, alnfile = '***************.ali', # alignment filename knowns = '*******', # codes of the templates 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.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 50 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() # do homology modeling

2 3

Mutant models
by Alfonso Mendez 14 Apr '10

14 Apr '10

Hello: I am building a protein model using a script that has been cited several times. http://salilab.org/modeller/wiki/Mutate%20model I started to work on it using Modeller9v2 on a Windows XP machine. After some tries, I noted that I can use the script with the next command for example: mod9v7 mutar.py 1dxt 85 TYR A However, I needed to delete lines 2 and 165 of the script because the "import os" command is not recognized by the python version that is included with modeller. The script seems to work and autogenerates a log file and the mutant model of course. I am working with a model of hemoglobin (1DXT). However, after looking the log file there some messages that are intriging for me: a) Some atoms were not found in params file: generat_607W> Cannot find params in params file: CHARMM atoms : NPH FE NP1 CPA IUPAC atoms : NA FE NB C1B Atom indices : 4406 4405 4407 4414 Residues : HEME HEME HEME HEME As this is hemoglobin model HEME groups are important b) Serious non-bounded atoms contacts at the end of the script report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 650 4405 2.247 serious non-bonded atom clash: 1778 4448 2.197 serious non-bonded atom clash: 2850 4491 2.252 serious non-bonded atom clash: 3978 4534 2.101 c) The modelling was produced in few seconds. Can the model produced by this script be optimized even more? (even if the script takes more running time) Also I am interested in create a mutant model but without optimize it. Then I want to compare the energy of the mutant model before and after the optimization. How can I produce the mutant model without the optimization? I am attaching the log file of my previous model. Thanks Dr. Alfonso Méndez Tenorio

2 1

Re: [modeller_usage] Alignment of the sequences
by Thomas Evangelidis 12 Apr '10

12 Apr '10

Your question is answered in the FAQs: http://salilab.org/modeller/FAQ.html#17 use that code to get the sequence from .pdb (as MODELLER reads it), and realign it with the rest of your sequences to generate a new .pir file. Otherwise just align it with the original sequence to spot discrepancies. Tom 2010/4/12 piyush diyora <yellow_piyu46(a)yahoo.co.in> > Hi, > I am new to modeller. > Before building a model, we have to first modify the sequence present in > the PIR file. PDB file and PIR file may have few different sequences. So is > there any way or software which can align both the sequences (from PDB file > and PIR file) so that the sequence present in PIR can be modified. > > Thank you, > Piyush Diyora > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >

1 0

Alignment of the sequences
by piyush diyora 12 Apr '10

12 Apr '10

Hi, I am new to modeller. Before building a model, we have to first modify the sequence present in the PIR file. PDB file and PIR file may have few different sequences. So is there any way or software which can align both the sequences (from PDB file and PIR file) so that the sequence present in PIR can be modified. Thank you, Piyush Diyora

1 0

generated models superimposition
by Белалов Илья 12 Apr '10

12 Apr '10

Dear Modeller Caretaker and Modeller users, I want Modeller to fit generated models by dope_loopmodel class. But only structures derived from the same IL000* file are superimposed to it. Also templates are aligned, but not to generated models. Thanks in advance, Ilya. I used following: class MyModel(dope_loopmodel): def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['21'], self.residues['92'])) log.very_verbose() env = environ() env.io.atom_files_directory = ['.', '../'] a = MyModel(env, alnfile='../mulalignment.ali', knowns=('1', '2','3'), sequence='d6', assess_methods=assess.DOPE, loop_assess_methods=assess.DOPE) a.starting_model = 1 a.ending_model = 3 a.md_level = refine.very_fast a.loop.starting_model = 1 a.loop.ending_model = 3 a.loop.md_level = refine.very_fast a.final_malign3d = True a.make()

2 1

dihedral phi psi restraint
by Armin Meier 12 Apr '10

12 Apr '10

Hi, in a Modeller-generated .rsr file, I have lines like this one: R 9 3 4 25 8 18 2 5 4 4 7 9 10 12 9 10 12 14 0.1295 0.3250 0.5455 -1.0908 -0.7138 -1.1903 2.5360 -2.3 3880 387 2.5656 0.0908 0.1065 0.2059 0.2164 0.5271 0.3072 -0.2541 3880 -0.4199 -0.6670 I suppose it's a restraint on phi-psi angles, but I cant find a description for Feature "4" (third number in first line) in the Modeller documentation (http://salilab.org/modeller/manual/node447.html) Moreover, why are there two features for this restraint (numb_feat=2) and what does Modal2 = 5 stand for? Are restraints of this type (i.e. Group=25, dihedral) always generated by default (Modeller version >= 9.5)? Thanks a lot in advance Armin Meier

2 1

evaluation of a region with DOPE z-score
by Thomas Evangelidis 12 Apr '10

12 Apr '10

Dear Modeller Caretaker, I have generated several models with different template combinations and want select the best with regard to some regions of interest (i.e. the ATP binding site). In the case of the binding site my residue selection is not contiguous (roughly all residues within 10 A. from the ATP). Does the resulting score make sense? Also if you look into the profile plot you will notice that the line is also curved in regions outside the binding cavity, and that happens even if the residue selection is conti. I think DOPE score is affected by neighboring atoms. If that's true what's the best way to assess a model region? thanks, Tom PS: the class to evaluate the cavity is pasted below. from modeller import * from modeller.parallel import task from modeller.scripts import complete_pdb import os class Evaluate_Cavity(task): """A task to evaluate a model with the DOPEHR method""" def run(self, template_combination, i): log.minimal() # request minimal output env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters # read model file mdl = complete_pdb(env, "/home/thomas2/Documents/PfMDR1_AAA1/new_alignment_"+template_combination+"/modeller/target.B999900"+str(i)+".pdb") # Select all residues except for the loop s = selection(mdl.residue_range('8', '20'), mdl.residue_range('34', '53'), mdl.residue_range('210', '212'), mdl.residue_range('242', '244'), mdl.residue_range('258', '261')) # Assess with DOPE: os.chdir("/home/thomas2/Documents/PfMDR1_AAA1/new_alignment_"+template_combination+"/modeller/") score = s.assess_dopehr(output='ENERGY_PROFILE NO_REPORT', file="model_"+str(i)+"_"+template_combination+".profile", normalize_profile=True, smoothing_window=15) return [str(i), score]

2 1

Error when reading the alignment PIR file.
by Daniel Fernandez 12 Apr '10

12 Apr '10

Hi, Please help me if possible, I have been stuck few days by now :-( I am trying a very basic approach to use modeller, but in this case I am using my own global alignment from clustalW. I am trying a very basic protein, target: 1aho, and only one template 2kbh_A ClustalW outputs the alignment in PIR format ( http://www.bioinformatics.nl/tools/crab_pir.html) but is a different PIR format than the one required by modeller. Actually the main difference is that clustalW does not provide the *start residue*:*start chain code*:*endresidue :end chain code: parts.* I do not know how to get that information and modeller apparently does not know either. Here I copy and paste the clustalW PIR format, the PIR modeller format and the errors I get from the model_simple.log. *CLUSTALW PIR format - sequencealn.pir* >P1;1AHO_A|PDBID|CHAIN|SEQUENCE VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK LPDHVRTKGPGRCH-- * >P1;2KBH_A|PDBID|CHAIN|SEQUENCE VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK LPDDARIMKPGRCNGG * *MODELLER INPUT (does not work, not sure why)* >P1;1aho sequence:1aho: : : : ::: 0.00: 0.0 VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK LPDHVRTKGPGRCH--* >P1;2kbhA structureX:2kbh.pdb: : : : ::: 0.00: 0.0 VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK LPDDARIMKPGRCNGG* *ERROR MODELLER GIVES ME:* get_ran_648E> Alignment sequence not found in PDB file: 1 2kbh.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these fr the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). Traceback (most recent call last): File "hoModeller-clustalaln.py", line 14, in <module> a.make() # do the homollogy modelling File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line 98, self.homcsr(exit_stage) File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line 411, aln = self.read_alignment() File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line 401, aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/n/sw/modeller-9v7/modlib/modeller/alignment.py", line 79, in append allow_alternates) _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not found i I am aware that the error advice me to put the start and ending residues numbers but I am still not sure how to solve the issue. Any help will be strongly appreciated, I need to use modeller as soon as possible to do some progress in my research. Best, -- Daniel F. Department of Statistics, Harvard University 1 Oxford Street, Cambridge, MA 02138

3 3