- modeller_usage - salilab.org

proline cis-peptide bonds
by Fan Jin 27 Jul '17

27 Jul '17

Dear all, I want to force all the prolines in a proline-rich peptide in to cis configuration , I notice in FAQ there is a script to change one by one, is there any scripts can change all the proline configuration automatically at once? Thanks a lot! Best wishes, Fan Jin

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Modeller 9.19 release
by Modeller Caretaker 26 Jul '17

26 Jul '17

A new version of Modeller, 9.19, 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 9.19 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.19 is primarily a bugfix release relative to the last public release (9.18). See the Modeller manual for a full change log: https://salilab.org/modeller/9.19/manual/node40.html If you encounter bugs in Modeller 9.19, please see https://salilab.org/modeller/9.19/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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Modelling a tetramer from Pentameric NMR structure
by Saravanan Parameswaran 18 Jul '17

18 Jul '17

Modellers, I am interested to work on a protein whose structure is determined from NMR and its in pentameric state. We believe that It should exist as tetramer in real life. Is it possible to model the tetramer from Pentameric NMR structure? If so, please let me know how to proceed? P. Saravanan

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Missing residues in PDB file
by Szymon Żaczek 12 Jul '17

12 Jul '17

Hello, I would like to perform a research on 4za7 protein. As long as using Modeller to insert missing residues is rather straightforward, the issue I have encountered is more related to PDB file itself. In the remark 465 section in the original pdb file, there are listed several missing residues: REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 ASN A 499A REMARK 465 LEU A 499B REMARK 465 GLU A 499C REMARK 465 HIS A 506 REMARK 465 HIS A 507 The problem is that I lack the knowledge on how to deal with those residues: 499A, 499B, 499C. I would most likely just insert 499A into the structure that will be further analysed but in regular residues that are normally placed in pdb file there is already a residue numbered 499. For some reason though, there are no residues 500 and 501 in the pdb file. How should I proceed with it? Should I just ignore those different options for residue number 499 and go with the one that was properly determined by X-ray experiment, or should I do something else? Any suggestions from more experienced researchers will be welcome. Kind regards, Szymon Zaczek

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hydrogen bonds with water at the interface
by bcuevas 15 Jun '17

15 Jun '17

Dear mr/mrs I am using Modeller to include mutations in the interface of protein-protein complexes. One of the crucial parts of my work here is to characterize and improve the available methods including water at the interface, and I wanted to use the restraints related with hydrogen bond energy since I think they are very important in this. However, I can not find in the documentation how to use the Physical.h_bonds as a restraint, since I don't know how this energy function is defined and what is its input. Any clue? Thanks http://bsc.es/disclaimer

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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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