- modeller_usage - salilab.org

gap characters corresponding to the missing residues,
by AMARA JABEEN AMARA JABEEN 24 May '17

24 May '17

hi i just want to know if there is any script available in modeller that put in dashes (gap character) instead of missing residues when sequence is read from pdb. I am using following script: from modeller import *# Get the sequence of the 1qg8 PDB file, and write to an alignment filecode = '1qg8'e = environ()m = model(e, file=code)aln = alignment(e)aln.append_model(m, align_codes=code)aln.write(file=code+'.seq') it is giving me file without missing residues but i need to have dashes in place of missing residues please reply thank you

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Loop Refinement
by SHC160059 STUDENT 04 Apr '17

04 Apr '17

Hi all, I have a protein structure with 394 amino acids. I tried to add some missing residues from aa 395-400, obviously at the terminal end. It was successful. Q1: After loop refinement (non-missing residues did not move), the global DOPE score was improved, however PROCHECK analysis showed a minor decrease ( <1% only) in the overall quality of the model. I also noticed that the added residues were 'pointing' outwards in all the built models. Before refinement, they were close to other residues. In this case, does it mean that loop refinement is not necessary? Or just ignore PROCHECK analysis? Since I'm not building a new homology model, but insertion of few residues only. Q2: In homology modeling, does DOPE score always correlate with the quality of stereochemistry? Hope to get some feedback and learn from you all. Thank you. Regards, Adam Lim Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia.

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protein in a complex
by Mohammad Goodarzi 23 Mar '17

23 Mar '17

Hello, I would like to know whether I am doing something right or not. I have a complex which few proteins are in there. I am trying to do the homology modeling between all members and I picked only one protein as template Does it make any sense? or should I do it differently ? Many thanks Mo

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Using Clustal alignment
by Eugene Radchenko 20 Mar '17

20 Mar '17

Hello, I have a problem trying to use external alignment (from Clustal Omega, converted to PIR format). However, Modeller refuses to read the PDB template. After several rounds of iterative correction, I specified only the residues and numbers actually present in the PDB file in alignment: >P1;5u09A structure:5u09A: 100 :A:+478 :A:::: ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------E NFMDIECFMV LNPSQQLAIA VLSLTLGTFT VLENLLVLCV ILHSRSLRCR But I get the following error: read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 11) Alignment .....E.NFMDIECFMV.LNPSQQLAIA.VLSLTLGTFT.VLENLLVLCV.ILHSRSLRC PDB IECFMVLNPSQQLAIAVLSLTLGTFTVLENLLVLCVILHSRSLRCRPSYHFIGSLAVADL Match ***** ** ** * * * ** Alignment residue type 4 (E, GLU) does not match pdb residue type 18 (V, VAL), for align code 5u09A (atom file 5u09A), pdb residue number "110", chain "A" That is, it somehow skips the first 5 residues from the PDB but adds 5 dots to the alignment sequence, and then (unsurprisingly) everything breaks =( What is wrong? Thank you in advance Eugene

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model.loops crosses chains
by Shyam Saladi 23 Feb '17

23 Feb '17

Hello -- In the process of using model.loops to identify regions that I will need to model in a multi-chain situation, I have noticed that it returns insertions between chains as a single loop. Furthermore, when specifying insertion_ext > 0, if the loop is at the N- or C-terminus of a chain in the middle of the molecule, the extension crosses to the next chain. Are these two intended behaviors? For the first case, this complicates things for me since I would like to apply restraints to each loop separately (which means I need to split up a couple of the loops returned). For the second case, I feel like this may not be the intended behavior since the C terminus of one chain and the N terminus of the next can be far apart in space. Thanks, Shyam ## Reproducible for the first case (can be modified to show the second) ## wget https://files.rcsb.org/download/5KXI.pdb ## remove residues A 74 and B 1 # contents of alignment file: 5xki_fill.aln >P1;2abx structureX:2abx: 1 :A:+148 :B:MOL_ID 1; MOLECULE ALPHA-BUNGAROTOXIN; CHAIN A, B; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC BUNGARUS MULTICINCTUS; ORGANISM_COMMON MANY-BANDED KRAIT; ORGANISM_TAXID 8616; TISSUE VENOM: 2.50: 0.24 IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQP-/ -VCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG* >P1;2abx_fill sequence::::::::: IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG/ IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG* # modeller code from modeller import environ, selection from modeller.automodel import automodel class MyModel(automodel): # only refine loop regions def select_atoms(self): aln = self.read_alignment() loops = self.loops(aln, minlength=1, maxlength=100, insertion_ext=0, deletion_ext=0) for i in loops[0]: print(i) raise ValueError("stop here") return selection(loops).only_std_residues() env = environ() env.io.atom_files_directory = ['.'] a = MyModel(env, alnfile = '2abx_fill.aln', # alignment filename knowns = '2abx', # codes of the templates sequence = '2abx_fill') # code of the target a.starting_model = 5 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling

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Excluded volume/Planar spatial restraint
by Shyam Saladi 22 Feb '17

22 Feb '17

Hello, I am trying to model missing residues from a solved structure of a membrane protein to prepare it for MD simulations. Some of these residues (~10) are follow a transmembrane segment at the C-terminus of the protein. After loop refinement, these residues always end up in the "membrane region" that I know from the solved TMs in the structure. However, I know these loop residues are soluble and should not be in this region. I would like to specify some sort of planar spatial restraint to describe where the residues can be, e.g. residues allowed above 10 A in the z direction? Is there a way to specify this? I appreciate any help in advance. Thanks, Shyam

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Modeller 9.18 release
by Modeller Caretaker 22 Feb '17

22 Feb '17

The new version of Modeller, 9.18, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.18 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.18 is primarily a bugfix release relative to the last public release (9.17), although it also adds support for Python 3.6. See the Modeller manual for a full change log: https://salilab.org/modeller/9.18/manual/node40.html If you encounter bugs in Modeller 9.18, please see https://salilab.org/modeller/9.18/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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Distance restraint violations
by Albers, Thomas 04 Jan '17

04 Jan '17

Hello! I'm trying to model a certain membrane protein. There are two template structures with decent sequence similariry (~ 40 %) and not-so-great resolution (~ 3 angstrom). When building a model against either template nothing in particular sticks out in the logfile, but when building a model model against both templates combined there are lots of distance violations (CA-CA and N-O) in the log, however this model gives the lowest DOPE score. What gives? Thomas

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EXTREME BOND LENGTHS IN OPTIMIZED MODELS
by Mahesh Velusamy 19 Dec '16

19 Dec '16

Dear All, I have tried to do build single point mutant models (n=100) along with separate optimization step on the neighbor residues around the mutated residue.I can able to get 98 models without any issue out of 100 models but in some models, the bond lengths of longer residues(ARG,LYS,TYR) became extreme than original value. For example: IN ARG residue, the distance between (CZ & NH1) or (CZ & NH2) was extreme (3.4Å) than the original value (1.5Å ) which makes the bonds disappear. I really don't understand that what makes these issue and I use the default MD&SA parameters which used in mutate_model.py with Lenard-Jones potential. *I don't get this issue if I change the restraint from Lenard-Jones into soft-sphere potential. So, kindly give me some suggestion about the parameters that I can tune to resolve this issue. Thanking you in advance With Regards Mahesh V

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Difference between dynamic_sphere and lennard-jones potential restraints ?
by Mahesh Velusamy 12 Dec '16

12 Dec '16

Dear All, This might be very basic question and also I have read this from the manual https://salilab.org/modeller/9v8/manual/node102.html but still I am curious to know the answer for the following questions: 1.what is the difference between these two restraints in terms (when to use) usage ? 2.Which one do we need to prefer with respect to mutate_model.py? 3.Why dynamic_sphere kept as False in this script https://salilab.org/modeller/wiki/Mutate%20model ? 4.Is it good idea if I use dynamic_sphere in mutate_model.py ? Thanking you in advance With Regards Mahesh V

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