- modeller_usage - salilab.org

To add "loop restraints" or ignore the template restraints in a specific region.
by Baptiste Legrand 09 Feb '10

09 Feb '10

Hi all, It is possible to add helical or strand restraints but is it possible to add loop/coil restraints? For example in one part of my alignment, I have this type of structural alignment: StructureX: CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Sequence: CCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCC Is there a command to add a coil/loop restraint or a trick to ignore the template restraints in the misalign part? Thanks. Best wishes, Baptiste

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Re: [modeller_usage] Modeling a larger protein with multiple templates
by nornik 09 Feb '10

09 Feb '10

Hello again I might have misunderstood something then. When I used salign with several templates I noticed that the *fit_fit* files have new coordinates. I assumed that MODELLER tried to place them in the same coordinate system according to the sequence alignment produced by salign to get "better" starting positions before energy minimization. I have compared the different *fit* "clusters" and, to me, it seems like the first fit sort of places the main (top) template in some sort of origo and the following fits (*fit_fit*, *fit_fit_fit*) align the other templates with the main one according to the sequence alignment produced by salign. Due to these observations I assumed that you had to transpose the template pdb files so that they were sort of placed "correctly" with respect to eachother. The first FAQ entry (as you probably know :) ) says: "If no additional information is available about the relative orientation of the two domains the resulting model will probably have an incorrect relative orientation of the two domains when the overlap between A and B is non-existing or short. To obtain satisfactory relative orientation of modeled domains in such cases, orient the two template structures appropriately before the modeling." But with sufficient overlaps you think I can just use the original template pdb files and disregard the fit steps performed by salign? Thank you very much Niklas

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Modeling a larger protein with multiple templates
by nornik 08 Feb '10

08 Feb '10

Hello I have sent this query before, but noone replied so I will send it again, hoping for some assistance. I am wondering if anyone can help me with this problem I have. I am modeling a large protein and I am using five different templates on different regions of the protein. Let's say the alignment looks like this: MMMMMMMMSMMMMMMMMMMSMMMMMMMMMMMMMMMMMMMSMMMMMMMSMMMMMMMMMSMMMMSMMMM Model AAAAAA----------------AAAAAAAAAAAAAA-------------AAAAAAAASAA------- core template ----BBBBSBBBBBBB--------------------------------------------------- template2 ----------CCCCCCCCCSCCCCC------------------------------------------ template3 ----------------------------------DDDDDSDDDDDDDSDDDDDD------------- template4 ----------------------------------------------------------EEEESEEEE template5 sulfur bridge sulfur bridge sulfur bridge Overlaps and sequences are of course much longer. The problem is getting the different templates in the same frame of reference, since the alignment is created manually and not by Modeller. The model sequence has very high identity to the core template so what i would like to do is first model with only the core template and then remodel the three large "inserts" with the other four templates and still maintain the sulfur bridges. Any other suggestions are of course also welcome in trying to solve this problem. Thank you

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Conversion of L-isomers to their D-isomeric form
by abdullah ahmed 04 Feb '10

04 Feb '10

Bonjour, I have a protein in PDB format that I have used successfully, to make a model (using the command "a.very_fast()"). However, whenever optimization is carried out (even by the default optimization in "model-full.py") some of the residues convert to their D-isomeric form. To avoid this I have tried the following: Making a series of models rather than just one to avoid problems caused by randomization. Turning randomization off using the "deviation=None" command in the "allhmodel" parameters. Using a number of cycles of optimization with a small number of iterations rather than one optimization step with many iterations.Finally I tried using 2 files from the RCSB protein data bank, with post numeration (ie atoms are labelled HD1 rather than 1HD). This was to check if the error was from my PDB file. This did not fix the problem. Further information regarding the problem is as follows: The conversions only take place after VTFM optimization is conducted in the "model-full.py" file. Using "a.very_fast" does not cause conversions. The conversions occur in a random fashion. My original PDB file contains 10 identical chains, one on top of another. Conversions that occur in one chain do not occur at the same location or residue in other chains.Residue type does not affect the chances of a residue becoming converted. Finally, I get these warnings in the ".log" file: mdtrsr__446W>..... getf__W> RTF restraint not foundiup2crm_279W> IUPAC atom not found in topology library Thank you in advance for your help, and Happy modelling, Abdullah Ahmed PS I have attached two PDB files as an example of the problem. If the two files are super-imposed on each other (using pymol, for example), you will find that residue number 9, GLU has switched to a D-isomer. Is is evident by the fact that Hydrogen atom in this residue is rotated 180° with respect to the other file. _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

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Re: [modeller_usage] should I use T-COFFEE alignment or generate one with alignmnent() module
by Thomas Evangelidis 04 Feb '10

04 Feb '10

Actually I used compare.py as a means to narrow down the list with the 8 potential templates, not to generate an alignment for comparative modelling. As for the consensus alignment (48 sequences and templates in total), it looks very good, all the conserved motifs from each sequence coincide. The problem is that sequence matches not necessarily imply structure matches, something that was denoted by malign3d when I fed the 8 template sequences as they were aligned in the consensus alignment. Certainly my option 3 (letting Modeller align the sequences) is not a good idea as T-COFFEE's method is more sophisticated and incorporates structural information. So I'm between 1. and 2. 1. edit my T-COFFEE-generated consensus alignment by leaving only the 4 sequences I need, and create an alignment for Modeller 2. generate a new structure-based alignment with T-COFFE with only the selected 4 sequences and feed it to Modeller Which of those 2 will be more accurate? 2010/2/4 Modeller Caretaker <modeller-care(a)salilab.org> On 2/3/10 5:52 PM, Thomas Evangelidis wrote: > >> I have a protein domain with very low sequence identity to PDB >> structures (37%), therefore I created a nice consensus alignment with >> T-COFFEE which includes both sequences and templates. After carefully >> inspecting the alignment, discarding bad matches, and realigning, I >> ended up with 8 potential templates which all look good to me. Thus I >> tried to adapt the compare.py script used in the basic tutorial, to help >> me select the best templates. >> > ... > > You don't have to use Modeller to generate your alignment - you can > generate it however you like (e.g. manually, with your favorite program, > etc.). There is also no requirement to align your templates with malign3d > (as you noted, that won't work unless the templates have a lot of structural > overlap anyway). So if you like your T-COFFEE alignment, by all means use > that directly (subject only to modifying the file format so that Modeller > can read it). > > 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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should I use T-COFFEE alignment or generate one with alignmnent() module
by Thomas Evangelidis 03 Feb '10

03 Feb '10

Dear Modellers, I have a protein domain with very low sequence identity to PDB structures (37%), therefore I created a nice consensus alignment with T-COFFEE which includes both sequences and templates. After carefully inspecting the alignment, discarding bad matches, and realigning, I ended up with 8 potential templates which all look good to me. Thus I tried to adapt the compare.py script used in the basic tutorial, to help me select the best templates. Initially I tried to feed my consensus alignment instead of aligning the templates with aln.malign() command, but that failed when executing aln.malign3d() because the overlap between the template sequences is very small (I got an error about the number of equivalent positions being insufficient). So I eventually aligned the template with aln.align() and selected 3 of them for comparative modelling. Now, after that observation, I 'm a bit confused. Should I : 1. edit my T-COFFEE-generated consensus alignment by leaving only the 4 sequences I need, and create an alignment for Modeller 2. generate a new structure-based alignment with T-COFFE including only the selected 4 sequences and feed it to Modeller 3. use alignment() module to align the 4 sequences Which is the best option? Any suggestion will be greatly appreciated. Tom

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docking and modeling peptid.
by Knut J Bjuland 03 Feb '10

03 Feb '10

Hi Can the latest version of modeller do docking of a peptide into an active site. In case modeler can not do this kind of docking, which particular program is best suited for doing peptid protein docking. Knut J _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

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Amino acid Isomers
by abdullah ahmed 02 Feb '10

02 Feb '10

Hello, My question is related to optimization. I increased the default optimization in "model-full.py" using the following code: # High VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 5000 Optimization does occur, however a few amino acids are changed from their L-isomeric forms to the D-isomers. To check if this was caused by problems with the PDB file I was using, I used a file(2KDV) from the protein databank. The same thing happens to it as well. Also if a lower amount of optimization is used, the change from L to D forms does not occur. Thank you in advance for the help, Abdullah Ahmed _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

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MOULDER protocol
by frank peelman 02 Feb '10

02 Feb '10

Dear all, Is/are the MOULDER protocol (s) available for local use ? kind regards, Frank

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How can I get restraint energies of initial structure without building a model.
by Lee, Jinhyuk 28 Jan '10

28 Jan '10

Dear All, The following one after the main text is my script to get energies. I put my restraint file (L001.rsr) and my initial structure (init.pdb). I want to see the energies on initial structure without building (energy minimization) a model so that I include "max_var_iterations=0" in the script. However, Modeller complained like that. > Summary of failed models: T0388.B99990001.pdb ddihedr_262E> Central bond too short: 0.0000 Is there any other scripts to do the same job? Thanks alot ----Script from modeller.automodel import * # Load the automodel class log.verbose() env = environ() env.io.atom_files_directory = './' templates=('3gb1') a = automodel(env,alnfile = 'L001.ali',knowns= templates,sequence='L001',inifile='init.pdb',csrfile = 'L001.rsr') a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.max_molpdf=10000000000000.0 a.max_var_iterations=0 a.make() # do homology modelling

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