April 2019 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Calculting protein dipole moment
by Elaine Meng 04 Apr '19

04 Apr '19

Hi Boaz, Yes, Chimera reads PQR files and assigns the atom attributes “charge” (used by the script, I believe) and “radius" from the corresponding columns. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#PQR> I tried an example just now. It works with either the .pqr or .pdb filename suffixes. Tested by opening the file, starting Render by Attribute, and showing the histogram for atom attribute “charge.” Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 3, 2019, at 6:31 PM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > Hi, > Is it possible to read a .pqr file from pdb2pqr to the script for calculating dipole moment (from the chimera repository) rather than running addcharge? > Thanks, > Boaz

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Sample 3d models of whole cells
by Fatlum Hajredini 04 Apr '19

04 Apr '19

Dear all, As part of one of my teaching assignments I am trying to make an educational video that will be projected on a planetarium dome. For this I need to make some movie scenes with whole cells (preferably bacteria) through Chimera. Does anyone have some generic sampole whole cell tomograms or something of the sort that would be suitable? Thank you, Fatlum

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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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