Hello, I am exploring ModBase to build a model for the REcQ2 of arabidopsis Thaliana(swiss prot acc: Q9FT73). ModBase found 2 structures matching this target and after downloading the coordinates file and also the showfile.chimerax file, I was able to visualize with chimera both structures with apparently a satisfactory relative orientation. Below I copy-paste the target coverage:

2v1xA (63-592) crystal structure of human recq-like dna helicase 1wudA (531-602) e. coli recq hrdc domain

I wanted to know if there is an optimization step in the ModBase pipeline to achieve this and if it is referenced somewhere....and if not, which modules-scripts are available?

Thanks for your attention, Maria Persico

Quoting modeller_usage-request@salilab.org:

> Send modeller_usage mailing list submissions to > modeller_usage@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: restraining secondary structure (Modeller Caretaker) > 2. Re: BLK usage => mainy chains (Modeller Caretaker) > 3. Re: Loop Modeling (Modeller Caretaker) > 4. Loop modeling while restraining the secondary structure > (bharat lal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 24 Jan 2011 14:49:01 -0800 > From: Modeller Caretaker modeller-care@salilab.org > Subject: Re: [modeller_usage] restraining secondary structure > To: bharat lal monu46010@yahoo.com > Cc: modeller modeller_usage@salilab.org > Message-ID: 4D3E01DD.9030008@salilab.org > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 1/24/11 1:00 AM, bharat lal wrote: >> I am using the following script for restraining the beta strands in my >> protein (after searching the mailing archives):- > > Your script will not work because you are using the automodel class > rather than your custom 'mymodel' class. Replace > a = automodel(env, > with > a = mymodel(env, > > This also looks like a very old Modeller script (perhaps for Modeller > 8). The way secondary structure restraints are defined has changed. See > http://salilab.org/modeller/9v8/manual/node27.html > for the correct syntax for adding a secondary structure restraint. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 2 > Date: Mon, 24 Jan 2011 14:51:01 -0800 > From: Modeller Caretaker modeller-care@salilab.org > Subject: Re: [modeller_usage] BLK usage => mainy chains > To: Isaure Chauvot de Beauchene ichauvot@lbpa.ens-cachan.fr > Cc: modeller_usage@salilab.org > Message-ID: 4D3E0255.1050307@salilab.org > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 1/24/11 6:56 AM, Isaure Chauvot de Beauchene wrote: >> I try to build a modele with 2 protein templates. I want to modelise >> just one loop of 1pkg, part of it on the template 3A2M, the rest of the >> loop de novo. The rest of 1pkg must not be changed, so I put it as BLK: > > BLK residues are really designed for modeling ligands and other things > that are not proteins. If you only want Modeller to optimize part of > your protein, see > http://salilab.org/modeller/9v8/manual/node23.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 3 > Date: Mon, 24 Jan 2011 14:56:19 -0800 > From: Modeller Caretaker modeller-care@salilab.org > Subject: Re: [modeller_usage] Loop Modeling > To: bharat lal monu46010@yahoo.com > Cc: modeller modeller_usage@salilab.org > Message-ID: 4D3E0393.2020703@salilab.org > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 1/24/11 12:01 AM, bharat lal wrote: >> I want to graft the loop from some other protein taken from pdb to my >> protein structure. > > You could use multiple-template modeling to achieve this. Alternatively, > you could manually combine the two PDB files, using a PDB viewer or even > by editing the files in a text editor. > >> I tried modeling it on my own but some parts of the >> secondary structure (beta sheet) also change into loop while loop >> modeling .. > > That is hardly surprising - loop modeling does not use any information > from the template. > >> So I want to fix those two ends of the beta sheet where the >> loop is present so that these end should not change to loop region. > > If you don't want to subject the beta sheet to loop modeling, simply > don't select those residues in the select_loop_atoms function: > http://salilab.org/modeller/9v8/manual/node34.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 4 > Date: Tue, 25 Jan 2011 11:18:50 +0530 (IST) > From: bharat lal monu46010@yahoo.com > Subject: [modeller_usage] Loop modeling while restraining the > secondary structure > To: modeller modeller_usage@salilab.org > Message-ID: 274112.20221.qm@web94710.mail.in2.yahoo.com > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > Thanks for the help regrading model-loop-define.py script. I have > one doubt in model selection .. The number of residues that has to > be mentioned for restraining should according to the target sequence > only know ?? .. > Also, I generated some 5 models while restraining some portion of > the sequence as beta strands ?and after seeing all the structures I > found that its model 3 that is having perfectly restrained beta > sheets as compared to others but its DOPE score is ?more as compared > to other structures . In this type of situation how do we have to > select the correct model ?? Here's the list of energies that I got : >>> Summary of successfully produced models:Filename ? ? ? ? ? ? ? ? ? >>> ? ? ? ?molpdf ? ? DOPE score ? ?GA341 >>> score----------------------------------------------------------------------target.B99990001.pdb ? ? ? ? ?1552.05176 ? -25341.12891 ? ? ? ?1.00000target.B99990002.pdb ? ? ? ? ?1485.22974 ? -25387.23438 ? ? ? ?1.00000target.B99990003.pdb ? ? ? ? ?1559.28723 ? -25382.83984 ? ? ? ?1.00000 (perfectly restrained str.)target.B99990004.pdb ? ? ? ? ?1483.82568 ? -25213.86523 ? ? ? ?1.00000target.B99990005.pdb ? ? ? ? ?1402.83508 ? -25525.49023 ? ? ? >>> ?1.00000 > > Also, I would like to ask one more thing about restraining structure > that while giving the residue range generally last 2 or some times > 1 residue/s doesnot retain the restrained structure .. In that case > what do i need to do ?? > After doing the restrained modeling is it required to do loop > refinement .. as I am doing loop refinement also by generating some > 50 structures and then finally selecting the one with low DOPE score > .. Is this strategy right or wrong ??? > > > -------------- > Bharat > > > >