Hi Elaine, Thanks for the reply. I ended up using Modeler, which after much frustration, gave me some reasonable models. Thank you and best wishes, Maja On Oct 18, 2013, at 3:29 AM, Elaine Meng wrote:

Dear Dr Maja Divjak, Sorry, Chimera does not do de novo modeling. Although the Chimera-Modeller interface does include untemplated loop-building, that is more appropriate for shorter missing segments within an existing protein, not entire domains or proteins. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>

I can only recommend you do some searching of web resources and perhaps literature, as I am sure there are many programs for that kind of modeling. I have not done it myself, so I don't have any specific recommendations. Other than that, you might try asking for recommendations of what program(s) to use on some more general forum such as the computational chemistry list, CCL.net : <http://ccl.net/cgi-bin/ccl/send_ccl_message> Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 16, 2013, at 12:04 AM, Maja Divjak <divjak.m@wehi.EDU.AU> wrote:

...

Hello Chimera,

I have looked high and low for the propeptide domain of IL-1 beta, but it does not exist as a PDB. I was therefore wondering what is the best approach to generating a 3d structure for the propeptide domain using the protein sequence and Chimera? If you could please outline a possible process, I would very much appreciate it. I see you have tutorials for comparative modeling, but in this case there is nothing to compare it to except other homologous sequences from the IL-1 family.

I look forward to your reply!

Thank you and best wishes,

Dr Maja Divjak, WEHI, Melbourne, Australia

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Hello Maja, It depends if there are atoms of overlap between the two parts. If there are overlapping parts, for example one structure is residues 1-15 and the other is residues 12-500: you can position the structures relative to each other by superimposing just the overlapping atoms using the "match" command (for example, something like "match #0:12-15@n,ca,c,o #1:12-15@n,ca,c,o"). Note the numbering won't necessarily be the same in the two structures, so you need to check on exactly which residues should be superimposed. Then you would delete the overlapping atoms from one structure (since the "same" atoms are already in the other structure), combine the two structures into one model, and then add a bond between the two parts. This could all be done in Chimera (see commands "delete" "combine" "bond", or graphical interfaces for the latter two are Favorites...Model Panel "copy/combine" function and Tools...Structure Editing... Build Structure, Adjust Bonds tab), OR it could be done by manually text-editing PDB files, after the matching step described above and then saving one structure as PDB "relative to" the other structure. Documentation for commands, command-line atom specification, and Build Structure: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> If there are not overlapping parts, for example one structure is residues 1-15 and the other is residues 16-500, you would just use the Join Models tab in the Build Structure tool mentioned above: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join> YOu can see there are fewer steps in the latter, but it can be hard to fully specify the correct geometry at the join. Thus when overlapping atoms in similar conformations are available, that more complicated overlapping procedure may produce better results than simply deleting the redundant atoms and using the second approach. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 18, 2013, at 2:26 AM, Maja Divjak wrote:

Hello again Elaine,

And further to that, how do I put the two molecules together please, now that I have a possible propeptide for IL-1beta? I had a go using MatchMaker with best-aligning pair of chains and everything else at default, but I'm not sure if this is the best approach? The propeptide bound via it's N-terminus to the C-terminus of IL-1 (in rainbow depiction) and the propeptide is supposed to be at the N-terminus of the whole. Apologies it this seems totally lame, but protein structure is not my forte...

I look forward to your reply,

Thank you and best wishes,

Maja

On Oct 18, 2013, at 7:28 PM, Maja Divjak wrote:

...

Hi Elaine,

Thanks for the reply. I ended up using Modeler, which after much frustration, gave me some reasonable models.

Thank you and best wishes,

Maja

Hello Elaine and Darrell, Thank you both so much for your help, I have managed to join the two molecules together using build, join models to give a convincing structure. Now I just need to get it out as a PDB that Maya can read. Problems every step of the way. Grrrr! You're both brilliant! Have a great weekend, Maja On Oct 19, 2013, at 4:28 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:

Hi Maja,

At the risk of straying too much from the Chimera listserv,if you are willing to go outside of Chimera, there are some additional tools that you could try:

(1) For the homology modeling, give the Protein Model Portal a try: http://www.proteinmodelportal.org

(2) For the assembly of the complex, you can follow Elaine's excellent instructions below and then accommodate the overlapping portions using a "perturbation docking" server, such as the docking server at ROSIE: http://rosie.graylab.jhu.edu

Hope that helps, Darrell

-- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit<https://twitter.com/niaidbioit>

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From: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Reply-To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Mailing List" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Date: Friday, October 18, 2013 1:02 PM To: Maja Divjak <divjak.m@wehi.EDU.AU<mailto:divjak.m@wehi.EDU.AU>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> List" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>>, Maja Divjak <divjak.m@wehid.wehi.edu.au<mailto:divjak.m@wehid.wehi.edu.au>> Subject: Re: [Chimera-users] Create a protein model using Chimera?

Hello Maja, It depends if there are atoms of overlap between the two parts.

If there are overlapping parts, for example one structure is residues 1-15 and the other is residues 12-500: you can position the structures relative to each other by superimposing just the overlapping atoms using the "match" command (for example, something like "match #0:12-15@n,ca,c,o #1:12-15@n,ca,c,o"). Note the numbering won't necessarily be the same in the two structures, so you need to check on exactly which residues should be superimposed. Then you would delete the overlapping atoms from one structure (since the "same" atoms are already in the other structure), combine the two structures into one model, and then add a bond between the two parts. This could all be done in Chimera (see commands "delete" "combine" "bond", or graphical interfaces for the latter two are Favorites...Model Panel "copy/combine" function and Tools...Structure Editing... Build Structure, Adjust Bonds tab), OR it could be done by manually text-editing PDB files, after the matching step descr! ibed above and then saving one structure as PDB "relative to" the other structure. Documentation for commands, command-line atom specification, and Build Structure: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>

If there are not overlapping parts, for example one structure is residues 1-15 and the other is residues 16-500, you would just use the Join Models tab in the Build Structure tool mentioned above: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>

YOu can see there are fewer steps in the latter, but it can be hard to fully specify the correct geometry at the join. Thus when overlapping atoms in similar conformations are available, that more complicated overlapping procedure may produce better results than simply deleting the redundant atoms and using the second approach.

Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 18, 2013, at 2:26 AM, Maja Divjak wrote:

Hello again Elaine, And further to that, how do I put the two molecules together please, now that I have a possible propeptide for IL-1beta? I had a go using MatchMaker with best-aligning pair of chains and everything else at default, but I'm not sure if this is the best approach? The propeptide bound via it's N-terminus to the C-terminus of IL-1 (in rainbow depiction) and the propeptide is supposed to be at the N-terminus of the whole. Apologies it this seems totally lame, but protein structure is not my forte... I look forward to your reply, Thank you and best wishes, Maja On Oct 18, 2013, at 7:28 PM, Maja Divjak wrote: Hi Elaine, Thanks for the reply. I ended up using Modeler, which after much frustration, gave me some reasonable models. Thank you and best wishes, Maja

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