- Chimera-users - RBVI Mailing Lists

molecular dynamics with phosphates: monobasic form unstable?
by Geoffrey Sametz 01 Apr '19

01 Apr '19

I am having my students model dipeptides where one residue is a phosphorylated serine or threonine. Molecular dynamics with the dibasic phosphate works fine. However, the student NMR data for their dipeptides is acquired at low pH, so I would like them to be able to model the monobasic form. Unfortunately, all my attempts at creating a monobasic form have resulted in the molecule "blowing up" in MD, first by crazily shaking the phosphate as if it wants to dislodge the proton, and then the entire molecule until it fragments. I have tried building these from scratch by various methods (e.g. those listed in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007068.html ) as well as using SwissSidechain and mutating residues. I have tried exporting as a .pdb, opening in PyMOL to make sure everything looks OK, resaving as .pdb and importing PyMOL's version. I have also used a protein from PDB that had a TPO residue assigned, and snipped it down to a dipeptide.For both this manner of construction, and for building the dipeptide from scratch with SwissSidechain, Chimera interprets SwissSidechain's TPO (pThr monobasic) and SEP (pSer monobasic) as their dibasic forms (TPO2 and SEP2 respectively). PyMOL interprets these structures with the correct level of protonation, however. Is there a known issue with Chimera and treatment of [-OPO3H]-1 groups, or have I managed to make the same error across multiple build methods? -- Dr. Geoffrey Sametz QDH 104 Department of Chemistry and Biochemistry University of Delaware sametz(a)udel.edu (302) 831-3621

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Hi good morning
by prasad ssv 30 Mar '19

30 Mar '19

How do i save all pdb files into a single mol2 file individually..what is the correct format of that mol2 file to proceed for docking in dock6?

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rna-protein complex
by soo khim 29 Mar '19

29 Mar '19

Hi chimera, I have a RNA-protein complex pdb file. After modeled the missing loops in the protein and saved the pdb file for remodel protein structure, the RNA is missing in the new pdb file. How should i save the remodel protein model together with its RNA? Thank you Best Regards, Chan Soo Khim

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Aligning (superimposing) chains form the same PDB files
by Jenaro Soto 28 Mar '19

28 Mar '19

Hi, Can Chimera superimpose all chains from one PDB file. If so how can this be accomplished? I have tried using the MatchMaker tool but it ask me to select at least one different reference model. I have also tried Match -> Align but it also asked me to only choose one chain per model. Any help would be appreciated. Best, Jenaro -- Jenaro Soto PhD Student UC Irvine | Department of Pharmaceutical Sciences

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New script: CREATE ALL ALTERNATIVE RECEPTOR PROTONATIONS
by Thomas Evangelidis 28 Mar '19

28 Mar '19

New script and tutorial: CREATE ALL ALTERNATIVE RECEPTOR PROTONATION STATE COMBINATIONS. Useful for those that do MD, docking, or any other structure-based drug design method. https://github.com/tevang/tutorials/tree/master/create_alternative_protonat… <https://github.com/tevang/tutorials/tree/master/create_alternative_protonat…> -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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electron density map superimposed on protein model
by Jenaro Soto 27 Mar '19

27 Mar '19

Hi Everyone, I am new to Chimera and am still getting to know the program. So far I have found the tutorials helpful, but they don't seem to have the answer to this very specific question. I want to know how I can overlay a protein structure and electron density map correctly. I am currently analyzing a published structure and would like to look at the the electron density map superimposed on the protein model. I was able to fetch the electron density map by using the 'open edsID:PDB_ID' command. However, it doesn't seem like my structure and the electron density are overlaid correctly. This might be because I moved the structure a lot before calling in the electron density map. How can I have the electron density map overlaid to the structure correctly (like the author intended it to be). Any tips will be appreciated. Best, Jenaro

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focus over N frames
by Elena Zehr 27 Mar '19

27 Mar '19

Hello, I wish to use "focus" command in a movie script. I focus on an atom range as following focus :4-6@CA I wish to bring the atoms in focus over N frames. How do I do this? Many thanks, Elena

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drawing stereographic projections for point groups in Chimera
by Arvind SHARMA 27 Mar '19

27 Mar '19

Hi, Is there a way to draw stereographic projections in chimera or chimeraX for the point groups? I want to draw these projections for icosahedral point groups (of T=3 virus), keeping the outer shell from chimera Multi-scale Models. Idea is to make something as in attached file. Would be great if someone has ideas how to do it or a script is available. Thanks a lot. Best, Arvind.

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Save multiscale model as PDB?
by Divjak Maja 27 Mar '19

27 Mar '19

Hi Elaine, Hope you're well! I'm working with measles PDB 4uft and have managed to make a multi scale model from this in Chimera. What I would like to do is save this multiscale model as a PDB and import to Maya, however, when I do this, all I get is a single subunit and not the multiscale model. I've tried looking in the Help documentation, but can't find how to save the whole multi scale model in PDB format. Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research [Description: cid:image001.jpg@01D35ECE.31407C60] Phone +61 3 8559 5961 Email maja.divjak(a)petermac.org<mailto:maja.divjak@petermac.org> 305 Grattan Street Melbourne Victoria 3000 www.petermac.org<http://www.petermac.org/> Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Change map gridding for better display
by Ahmad Khalifa 25 Mar '19

25 Mar '19

How can I change the gridding of my cryo-EM map to make it look better? I know I can resample a map in chimera on the grid of another, but I'm not sure which absolute gridding is better to view the map and how to change the gridding without a reference.

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