- Chimera-users - RBVI Mailing Lists

Fitmap: correlation about the mean for global search
by Michele Lunelli 25 Sep '18

25 Sep '18

Dear people, I want to do a global search of an atomic model into an EM map, using the correlation about the mean (cam) as metric. I use a command like this: fitmap #0 #1 resolution 6 metric cam search 100 radius 150 However, only the correlation about zero is reported in the final fit list (and used to rank the solutions). Where can I find the cam values for all the fits? Thank you Michele

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MatchMaker
by Ward, Miriam L. (CDC/OID/NCIRD) 24 Sep '18

24 Sep '18

Hello, I used MatchMaker to superimpose a couple of models. Now when I open any .pdb files, they automatically superimpose. How can I "turn off" MatchMaker so it doesn't automatically superimpose everything? Thanks, Leanne M. Leanne Ward, MEd. Microbiologist II Cherokee Nation Assurance contractor Rotavirus Surveillance and Molecular Epidemiology Team Gastroenteritis Viruses Branch Division of Viral Diseases, NCIRD, CDC Mailstop G04 1600 Clifton Rd. N.E. Atlanta, Georgia 30329 U.S.A. Phone: (404) 639-3265 Email: mrw0(a)cdc.gov<mailto:mrw0@cdc.gov>

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Hiding AutoDock Vina Search Volume (frame)
by leifepeterson＠sbcglobal.net 24 Sep '18

24 Sep '18

Using Select-->Chains-->(no ID), I can select the AutoDock Vina Search Volume structure after performing a docking, but once it's selected (highlighted in green), I can't seem to remove it from the molecular plot. What is the recommend way to remove the square frame?

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Re: [Chimera-users] Placing Autodock Vina Pocket around AA residues from RaptorX
by Leif Peterson 20 Sep '18

20 Sep '18

Hi Elaine, Thanks for the tip on the center command, and looking up the Swiss-Prot method. Leif Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Placing Autodock Vina Pocket around AA residues from RaptorX
by leifepeterson＠sbcglobal.net 20 Sep '18

20 Sep '18

Couple newbie questions: 1. I don't know if any users have run RaptorX (U-Chicago) for ligand-residue pocket prediction, but the results simply tell you the specific AA residues are which are close to the pocket For example the locations could simply be e.g. the residues K252, Q256, and K260 in the input PDB file. So my question in terms of AA annotation in Chimera is, how could I center Autodock Vina's pocket box around residues something like K252, Q256, and K260? I looked through the select options and didn't see where numbered residues could be selected. 2. For 3D modeling when x-ray crystallography results are not available in PDB, I commonly will submit a protein's FASTA sequence to SWISS-MODEL, and then download the PDB and go through dock prep for the receptor and minimization of the ligand(and adding e.e. hydrogens, etc.) Isn't the SWISS-MODEL approach an alternative for using the MODELLER add-on for homology modeling. The MODELLER run I just went through was really using a lot of core resources, and the BLAST template results were complexes between receptors and ligands, and sometimes DNA. So isn't there an advantage to inputting a FASTA from Uniprot into SWISS-MODEL to obtain the predicted 3D structure, when compared with the BLAST results required during MODELLER runs?

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chimerax mesh commands doesn't work
by Yehuda Halfon 20 Sep '18

20 Sep '18

Hi all, I wanted to use chimeraX to use some commands on mesh display. Some works like meshLightning but others like lineThickness doesn't I use volume #1 lineThickness 10 (or any other integer) but nothing seems to change. What am I doing wrong? Yehuda Halfon

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change the center of a pdb model
by C.J. 19 Sep '18

19 Sep '18

Dear specialists, When I opened two pdb files of icosahedral model(two structures of the same virus), I found both center didn't overlap. My question is how to change the origin of a pdb model to overlap both. Thank you! -- Best regards! Jianhao Cao

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How to show ligand pocket as wireframe mesh
by leifepeterson＠sbcglobal.net 19 Sep '18

19 Sep '18

I ran a ligand-receptor prediction for a protein at Site-hound, and downloaded all the files. Is there a Chimera tutorial which shows how to display the volume a selected cluster inside the protein as a wireframe mesh? My guess is that the volume will be between all the AA residues in the given cluster(?) Once I can show the mesh, I will then go through the Autodock Vina run using ligands in a mol2 file, to sort their energies.

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FW: Question for using Chimera 1.8
by Williams, Joanne 17 Sep '18

17 Sep '18

From: Shabnam Nadjafi <shabnam.nadjafi(a)gmail.com> Date: Monday, September 17, 2018 at 12:29 AM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Question for using Chimera 1.8 Dear Manager I am a pharmacologist and I decide to publish a book about drugs and some biochemicals by in silico evaluation of the chemical structures with biologic targets. I have to use the impressive software "Chimera 1.8". Would you please give me some information about this? Is it enough to cite "Chimera 1.8" in "Foreword" or "Preface" sections of the book? Is it free to use "Chimera 1.8" for publishing a book? Sincerely Yours Shabnam Nadjafi M.D. PhD of Pharmacology Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran

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Add to discussion group
by Ayala Carl 17 Sep '18

17 Sep '18

To whom this may concern, I am a chimera user and have been having some difficulty opening structural measurement file. I would like to join the discussion group to post a question regarding this topic. Thanks, Ayala

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