- Chimera-users - RBVI Mailing Lists

PDB file of D-amino acids
by Mohsen Asadbegi 04 Apr '19

04 Apr '19

Hello every one! I want to convert a sequence of d-amino acids or a sequence of d-amino acids and L-amino acids to a PDB file. How can I construct such PDB file? I know that this is possible to enter the sequence of L-amino acids in CHIMERA (uppercase characters of the amino acids for example: LFVVA), But regarding d-peptides and retro-inverso peptides I don't know the exact way of building PDB files. Regards, Mohsen Asadbegi

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Visualisation in Headless Chimera
by James Starlight 03 Apr '19

03 Apr '19

Dear Chimera users! I am using headless version of Chimera inside of my Bash script to prepare images of the pdbs. Normally I provide a pdb file with a script in loop to obrain images automatically Here are some of my questions related to the visualisation: 1) I have a problem with the "preset apply publication 1" notably Chimera is crushed when I use #set silhouette option Is it possible to make "a black border of a selected thickness" for all of the elements of secondary structure of my proteins via some another command? Actually in terms of the cartoon's style (but not a colour) I would like to obtain something like was shown here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles-contra… 2) I am using "rangecolor bfactor 2 blue 30 red 50 yellow" option to colour the structure according to the B-factor information provided in the given PDB. The problem is when I provide "key" option for it to place a colour diagram on the resulted picture I ontain a crush in headless version. Do some other methods exist for the placement of the colour legend for the B-factor colouring which could be used in the headless version? Thank you for help in avance! James

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Adding color key to hydrophobicity surface (preset 3)
by Boaz Shaanan 03 Apr '19

03 Apr '19

Hi, I find preset 3 as a very convenient tool but is it possible to add a color key to the hydrophobicity surface produced in this preset (as in the options for coloring electrostatic surface) ? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

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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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