- Chimera-users - RBVI Mailing Lists

Batch mode for Chimera
by James Starlight 02 Sep '17

02 Sep '17

Dear Chimera Users! My simple bash script loops the folder with the pdbs and open it in Chimera for pdb in ${output}/xtc_proc/*.pdb ; do name=$(basename "$pdb") echo "I am sending ${name} to Chimera!" chimera $pdb done My question - can I use with chimera some batch file which will apply the following commands to each of the loaded pdbs without opening of Chimera GUI: 1- Apply "publications-2" preset 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb according to b-factor provided in the pdb file 3- make a screen-shot of the colored cartoon figure in the selected output folder. I thanks so much for the example of batch file and the syntax accepted by chimera from the linux shell. James

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B-Factor Difference Plot
by Amanda Evans Constantinides 31 Aug '17

31 Aug '17

Hello, I am plotting the B-factor differences between two similar structures. I do not understand why the plot is almost entirely on the positive side of the X-axis. If I open B factor putty models in PYMOL and in Chimera, there are some visible areas that should translate to negative B-factor differences on a quantitative plot. There is no way one structure is entirely more flexible than the other. Can you help explain this to me? Is there away to adjust the zero point to more accurately reflect these differences on the plot? Thank you, Amanda Constantinides Graduate Research Assistant Georgia State University

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Center on surface at mouse accelerator
by Daniel P Farrell 30 Aug '17

30 Aug '17

Hello, I found myself constantly needing to re-center on different regions of EM density maps, and I was originally just dropping spheres on the surface, centering on those, then deleting them. Finally I got sick of that and wrote this. It will center the window on the surface of whatever surface the mouse is currently overlaying. I found this to be a very helpful addition when looking at large EM maps, and was thinking other people might too, after using it for a while I feel as though it could be part of trunk since I use it so much. basically it would require the addition of this to standard_accelerators.py ... other accelerators.. ('zx', 'Center view on surface where mouse is located', center_on_surface_at_mouse), ... zx because it's close to where you rest your hands on the keyboard... def center_on_surface_at_mouse(): from chimera import selection, tkgui hits = [] w = tkgui.app.graphics x = w.winfo_pointerx() - w.winfo_rootx() y = w.winfo_pointery() - w.winfo_rooty() from Surface import surface_models import VolumePath.tracer as tracer hits.extend(tracer.surface_intercepts(x, y, surface_models())) xyz, model = tracer.closest_hit(hits) print(xyz) if xyz: print('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) chimera.runCommand('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) chimera.viewer.camera.center = xyz cheers! ~Dan

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Adding ions with Amber
by George Tzotzos 30 Aug '17

30 Aug '17

I’ve loaded the prmtop and inpcrd of a protein in complex with a ligand (named DE3). I’ve tried to add ions to the complex using the Amber Tool. I received the following message (see Reply log below). I wonder if I erred, in which case I would be grateful for any suggestions, or there’s a bug in the program. Many thanks in advance George Assigning chain ID A to 125 residues, e.g. ASP Assigning chain ID B to 125 residues, e.g. ASP Model 0 (complex.inpcrd) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. /Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/matplotlib/axes.py:2369: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=1, right=1 + 'left=%s, right=%s') % (left, right)) Charge model: AMBER ff14SB Assigning partial charges to residue DE3 (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.in.mol2 -fi mol2 -o /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (DE3) (DE3) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (DE3) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (DE3) Reason: image not found (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (DE3) (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (DE3) Total number of electrons: 104; net charge: 0 (DE3) (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (DE3) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue DE3 Check reply log for details

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Rainbow command
by Mark Rosenberg 28 Aug '17

28 Aug '17

Please can you provide an example of using Rainbow with Command line for a specific chain so I can see how the nomenclature works. It would be so helpful if the Chimera help files could provide more examples like this so one can adapt them to different situations. Thank you.

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Regarding getting the .pdb file of glutamine
by Dilip H N 26 Aug '17

26 Aug '17

Hello, 1] I am having difficulties in getting the Glutamine.pdb file in chimera. I tried in Build Structure - Peptide and in peptide sequence if i type GLN, i am getting peptide of glutamine...., but what i want is just glutamine molecule, and not a peptide.. So how can i generate a glutamine molecule in chimera.... 2] Another question in Diglycine peptide, i want to insert CH2 in between the molecule (say in between C=O and CA), How can i insert the methyl group there.. Any suggestions are highly appreciated -- With Best Regards, DILIP.H.N Ph.D Student <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dili…>

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Molecule Display
by 李艺宣 25 Aug '17

25 Aug '17

Dear professor: In the process of using chimera, I encountered some problems. I found Gly residues can not be shown in stick, wire, ball-and-stick and sphere presentation. Can you help me Looking for your reply All the best.

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duplicate a EM map in window by command line
by C.J. 24 Aug '17

24 Aug '17

Dear specialists, Is there a command line to creat a model copy of a opened EM map in the window? Thank you! Best regards! Jianhao

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sent to a different url
by Arthur Szabo 23 Aug '17

23 Aug '17

I am interested in a structure 1GSG deposited in 1990. The PDB index for this file shows the enzyme Gln tRNA synthetase with the usual ribbon structure, bound to tRNA(Gln). When I fetch 1GSG using either the PDB file number only, or that file number input into PDB biounit, the structure that comes up does not have the helical or β-sheet secondary structures shown as ribbons. Rather the entire protein backbone is shown without any secondary structure definition. One can see the helical segments in the worm like structure, but not in the form of the usual helical secondary structure. How can I retrieve a structure that is similar to that in the PDB index list. I have enclosed the following: [cid:image001.png@01D31C42.7C7B48F0] This is what comes up when I fetch the PDB file. [cid:image002.png@01D31C42.7C7B48F0] Thanks Arthur G. Szabo Professor Emeritus

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setting surface color of EM map in command-line
by C.J. 22 Aug '17

22 Aug '17

Dear specialists, I want to color spherical slices of different radius of my EM map in command line/script. How to set the "surface color" dialog in command-line? If anyone could give me a example? Thank you! Best regards! Jianhao

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