- modeller_usage - salilab.org

SequenceMismatchError when adding missing residues in LoopModel()
by Steven Truong 07 Apr '21

07 Apr '21

Dear Ben and Modeller Mailing List, Hello, I was hoping to get some help on an error I get when trying to add missing residues to a structure using the AutoModel/LoopModel classes. The error looks like: x (mismatch at alignment position 9) Alignment NSFTRVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHNPVLPFNDGVYFASTKSNIIRGWI PDB NSFTRGVYYPDKVFRSSVL.STQDLFLPFFSNVTWF.AI.VSGTNGTKRFDNPVLPFNDG Match ***** * * * Alignment residue type 18 (V, VAL) does not match pdb residue type 6 (G, GLY), for align code 6z43 (atom file structure_aligned), pdb residue number " 35", chain "A" When I check my alignment file, I can begin to see what’s going on. Here is the first entry of the alignment file: >P1;6z43 structureM:structure_aligned:27:A:+3600:C:::-1.00:-1.00 --------------------------AYTNSFTR-VYYPDKVFRSSVLHSTQDLFLPFFS NVTWFH--------------NPVLPFNDGVYFAST >P1;6z43_fill sequence:6z43_fill:.:.:.:.:::: MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFAST It appears that Modeller does not recognize the dashes “-“ as actual missing residues. Instead, it appears to read the alignment as NSFTR()V…, rather than NSFTRG. However, isn’t the dash supposed to signal AutoModel/LoopModel to treat that as a missing residue to fill? Thank you for your help! Best wishes, Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk> Cambridge University

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Adding glycans in AutoModel?
by Steven Truong 19 Mar '21

19 Mar '21

Dear Modeller Mailing List, I was hoping to ask if there is a way to automate glycan-building in Modeller. I’ve been able to get all residues/atoms built using AutoModel. However, I lose the glycan information when using AutoModel. Is there another program that interfaces well with Modeller, or is there a class in Modeller that can add glycans at known positions (e.g. if I know NAG is attached to residue 6, can I add that to the PDB output somehow?). Thank you! Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk> Cambridge University

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Modeller 10.1 release
by Modeller Caretaker 18 Mar '21

18 Mar '21

A new version of Modeller, 10.1, 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 10.1 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.1 is a minor update that adds support for Apple Silicon. The Mac installer (dmg file) is now universal and will work on both Intel Macs and the new Apple Silicon (M1 or ARM64) Macs. The Homebrew Modeller package also works on both Intel and Apple Silicon Macs. If you encounter bugs in Modeller 10.1, please see https://salilab.org/modeller/10.1/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 unsubscribe from the modeller_announce mailing list, or 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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query regarding alignment
by anuricha sharma 15 Mar '21

15 Mar '21

Hello sir, I have a query regarding the alignment, that how can I align my two pdb structures and one query sequence(xyz.ali) together using basic modelling, I am unable to to do alignment using two models and one query sequence in basic modelling as it aligns only one model and one query sequence, can you suggest any changes that I need to do in my align2d.py file. ReplyForward Sent from Mail for Windows 10

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can I add ambiguous restraints to modeller
by Li Xue 13 Mar '21

13 Mar '21

Hello all, Does modeller accept ambiguous restraints? For example, I know there is helix in a region but I am not sure where it starts. Best, Li

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Quick Question on Automodel
by Pedro Guillem 08 Mar '21

08 Mar '21

Hello all, I'm trying to model from a known template (ident 37%). The template is missing the first 3 residues in the structure. - I start reading the template at position 4. - I add 3 dashes to the beginning of the template to compensate for the missing residues. (otherwise I get a "residue mismatch" error from modeller) Now, my alignment needs 3 additional gaps at the start of the template. No matter what I do, adding 6 dashes to the beginning of the template (3 for the missing residues and 3 extra for my alignment) has no effect on the outcome and the model doesn't align with the template in the way I expect. Here is a bit of my ali file. I want the TRL of the template to align with the TRM of the sequence. When it finishes, the position of TRM has a different offset in relation to TRL Am i doing something wrong here? >P1;template structureX:template:4:A:330:A:xxxxx:xxxxxxx:2.30:0.211 ------TR*L*......................rest of seq* >P1;seq sequence:seq:.:.:.:.:::: EAARRRTR*M*........ rest of seq* Thanks in advance. Pedro

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remodelling a fragment of protein using different template.
by Yogesh Sharma 16 Feb '21

16 Feb '21

greetings readers, I am trying to model a protein with low homology. I have used ab initio methods to get a starting structure. but i want to remodel first 50-100 residues according to a different PDB template. is it possible to do so using modeller? please give some suggestions *Yogesh Sharma*

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Installation Bug issue modeller 10.0
by Henry Monteiro 07 Feb '21

07 Feb '21

Greetings, I got the keys recently but I stumbled on a problem trying to run the program. When I type and run the command "mod10.0 foo.py" (ubuntu 20.04) this come in response: "Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback FATAL ERROR: Cannot open file foo.py: No such file or directory" Could you guys have any clue how to repair this problem? Sincerely, Henry Magalhães

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Modeller 10.0 release
by Modeller Caretaker 02 Feb '21

02 Feb '21

A new version of Modeller, 10.0, 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 10.0 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.0 is a major update that adds support for residue numbers >= 10000 in PDB format files using hybrid-36 notation, assigns the chain ID 'A' to single-chain models to generate more standard PDB files, and uses CamelCase naming for all Python classes. See the Modeller manual for a full change log: https://salilab.org/modeller/10.0/manual/node40.html If you encounter bugs in Modeller 10.0, please see https://salilab.org/modeller/10.0/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 unsubscribe from the modeller_announce mailing list, or 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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Fibrillar collagen structure model 3hr2 Inbox
by Amadeus Cavalcanti Salvador de Alcântara 27 Jan '21

27 Jan '21

Dear Modeller Users, I am trying to use Modeller to model a comparative protein structure for the type I collagen. I came to this trying to reproduce a model from this paper: doi 10.1021/nl103943u ( *Nano Lett.* 2011, 11, 2, 757–766 ) It also used Modeller to create such a model. I contacted the 1st author for instructions on how he created the model, but unfortunately he said not to remember anymore (it has been 10 years since). I also want to mention that before posting this, I read the Modeller manual and several questions and answers posted in the mail listing. They helped me get to this point. In the following I will describe in some details what I have done, with what files and how: All necessary files for reproduction are attached in this email (I tried to attach all files - pdb, target fasta, outputs, etc. - , but it exceeded the limit of 100 KB). *1 - Target:* P02452 (CO1A1_HUMAN) and P08123 (CO1A2_HUMAN) from https://www.uniprot.org/uniprot/P02452 and https://www.uniprot.org/ uniprot/P08123 The Targets are in the Fasta format. I converted them to .ali files in the PIR format, as suggested by Ben Webb in https://salilab.org/archives/modeller_usage/2010/msg00072.html . (see FASTAtoPIR.py in the attached files). I manually edited the protein code and field2 of the .ali files (based on what I read in the manual - *File formats B.1 Alignment file (PIR)*) That is how it looks like now: * COL1A1.ali* ___________________________________________________________________ >P1;COL1A1 sequence:COL1A1: : : : :::-1.00:-1.00 MFSFVDLRLLLLLAATALLTHGQEEGQVEGQDEDIPPITCVQNGLRYHDRDVWKPEPCRICVCDNGKVLCDDVIC ...* ___________________________________________________________________ *2 - Template:* 3hr2.pdb from https://www.rcsb.org/structure/3HR2 It is very important to me to get a model as close to this structure as possible, since it comprises the collagen fibrillar structure. *3 - Alignment: *I decided to align each chain and sequence individually, as many answers in the mail listing suggested. First of all I tried to align the COL1A1.ali with the chain A of the 3hr2. pdb structure. I aligned the sequences using salign (align2d was taking too long). The 3hr2.pdb contains 2 non standard amino acids: HYP hydroxyproline LYZ Hydroxylysine I added - env.io.hetatm = True - in order to read them. *1A_salign.py* ___________________________________________________________________ env = environ() aln = alignment(env) env.io.hetatm = True mdl = model(env, file='3hr2', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='3hr2A', atom_files='3hr2.pdb') aln.append(file='COL1A1.ali', align_codes='COL1A1') aln.salign() aln.write(file='COL1A1-3hr2A.ali', alignment_format='PIR') aln.write(file='COL1A1-3hr2A.pap', alignment_format='PAP') ___________________________________________________________________ I added to restyp.lib: HETATM | HYP | O | | HYP | hydroxyproline HETATM | LYZ | K | | LYS | lysine, +1 I have HYP topology and parameters, but since I don't have them for LYZ I chose to treat LYZ as LYS (Lysine). I do not know if I can do it. Is it better to do so or to simply let Modeller continue with the following warning? *read_pd_459W> Residue type LYZ not recognized. 'automodel' model building will treat this residue as a rigid body.* *4 - Automodel: *I created 10 models and chose the one with lowest DOPE score (all scored 1.0 in the GA341 score), in my case, COL1A1.B99990010.pdb. I included HYP topology and parameters information to the *top_heav*.lib and *par*.lib files from the Modeller Library. Furthermore I added the HB1 (new type in HYP top) atom type information to *solv*.lib, *radii*.lib and *radii14*.lib. The HYP information was taken from *top_all36_prot_modify_res*.str and *par_all36_prot_modify_res*.str in the CHARMm FF. *2A_model-single.py* ___________________________________________________________________ from modeller.automodel import * env = environ() env.io.hetatm = True env.libs.topology.read('${LIB}/top_heav.lib') env.libs.parameters.read('$(LIB)/par.lib') # from manual a = automodel(env, alnfile='COL1A1-3hr2A.ali', knowns='3hr2A', sequence='COL1A1', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 10 a.make() ___________________________________________________________________ *5 - Final model: *I also ran the 3A_evaluate_model and 4A_plot_profiles python scripts and after that opened the 3hr2 A chain and the final model in VMD. The model looks good, however, it is not as close to the 3hr2 structured as I wished. As a mechanical engineer I am no used to those models nor to homology modeling and have been learning all here by reading the manual, instructions and mail listing. Did I make many/any mistakes? Where and what? Can the model become better (more close to the 3hr2 template structure)? If yes, how? How to know if a model is "good enough"? Can I proceed like that and create the models for the chains B and C and complete the collagen structure? I am afraid to lose the fibrillar collagen structure (which in this case is similar to a crystalline periodic structure) from 3hr2.pdb if the model is not very similar to the the 3hr2 structure. Thank you in advance for reading up to here. I am looking forward to reading your observations, suggestions and corrections. They are all very welcome. Amadeus

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