March 2016 - Chimera-users - RBVI Mailing Lists

Generating small planes inside inorganic bridges
by Henrique C. S. Junior 08 Mar '16

08 Mar '16

Dear Chimera list, As a inorganic chemist sometimes I have to deal with a variety of bridges (see image attached for an example) and it'd be very useful and didactic if I could create a little plane (like a distorted square) inside this bridges to mark different properties. Is this possible in Chimera? Thank you in advance. -- *Henrique C. S. Junior* Químico Industrial - UFRRJ Mestrando em Química Inorgânica - UFRRJ Centro de Processamento de Dados - PMP

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default position in space
by Jakob Suckale 07 Mar '16

07 Mar '16

Dear Chimera team, What determines the position of objects in space? I have done some testing with tubulin (1TUB), hemoglobin (1HHO), and collagen (1BKV). They all end up in very different and seemingly random position in print space after STL export (see screenshot). Is there a way to predict how items will appear to allow one to adjust the position beforehand with move commands? This is secondary for in silico simulations within Chimera but crucial for printing of real models. If they are cut by the plane everything below will not be printed, i.e. tubulin in my example would not be printed at all without adjustments and the others would be cut. All the best, Jakob

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color surface by volume data - thickness
by R.I.Koning＠lumc.nl 04 Mar '16

04 Mar '16

Dear all, Is it possible, while coloring the surface of a sphere using volume data value, to increase the thickness of the volume that is used to color that surface? I guess now just a 1 pixel thick intersection of the sphere with the volume is used, but I would like to vary the width of this intersection. Roman Koning

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Calculate distances between ligand atoms to select the most distant pair
by Felipe Vasquez 04 Mar '16

04 Mar '16

Hi, I am interested in select those two atoms more distant into a ligand. However, how could I estimate this so I have not to calculate the distance manually for all possible pairs one by one? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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Hiding Chains
by Adith Arun 04 Mar '16

04 Mar '16

Hello, I have three chains in the protein, and I want to only view one of the chains. How do I hide the other two chains, so that the only chain that is seen on the Chimera viewer is the one I want to manipulate? Thanks!

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Selection of a CASTp/Surfnet cavity from command line
by Felipe Vasquez 04 Mar '16

04 Mar '16

Hi, I was trying to automatize the selection of those residues members of a certain cavity predicted by CASTp, starting from the opening of the file to the writing of the residues list (all from command line). However, I do not know how to select a cavity with an specific ID so I have not to do it manually. There is a strategy to achieve this goal from the command line? How could I do the same for Surfnet cavities? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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closing the surface of a monomer from a dimer PDB
by Jakob Suckale 04 Mar '16

04 Mar '16

Hi all, I'm trying to generate a surface structure of tubulin A from a dimer coordinates file like 1TUB. Surfaces generated from the Action menu are cut open at the contact site between the monomers (see attachment). How can I generate a continuous surface for only one protein monomer? All the best, Jakob

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Difference mapping
by Saumya Verma 02 Mar '16

02 Mar '16

Hello everyone! I am relatively new to cryoEM and am solving my first structure. I have a question about difference mapping using Chimera, and Id like to apologize in advance if its too naïve a question for this forum. I have a cryoEM structure of a mutant virus; the x-ray structure of the wild-type virus is known. To see the differences between the two structures, I am following the following steps: - Deleting the mutated chains from the pdb (so that Ill be able to detect these in the cryoEM map) and converting the crystal structure .pdb file to .mrc, low pass filtering it to the resolution of the cryo-em refined structure and matching box size and A/pix - Fitting the two maps in Chimera and subtracting the volumes (using the command vop subtract) My question is - how do we decide the resolution to which to lowpass filter the original structure? The reason Im asking is because while my cryoEM structure is 13.3A (FSC gold standard) (Ive also checked with ResMap majority of the voxels are ~14A), it looks very less detailed when compared to the lowpass-filtered map of the original pdb. And when Im fitting the two, there are major differences in the contours, which I think is giving me false differences. Can someone please let me know what would be the best way to compare the cryoEM structure of mutant virus with the published structure of the wild-type virus. Thank you very much. Regards, Saumya PhD Student Indian Institute of Technology Delhi, India

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Re: [Chimera-users] Screen shots from coot
by Oliver Clarke 02 Mar '16

02 Mar '16

Hi John, don't know how to do exactly what you want re raster3d, but in order to avoid fiddling with the volume viewer I use a couple of aliases which make things faster, perhaps they will be useful to you too: #Usage cootmode_wire alias ^cootmode_wire ~rib; disp; color gold; color byhet; repr wire; setattr m lineWidth 2; volume # capfaces false style mesh meshlighting false squaremesh false color "#3333851effff" step 1; sop cap off; set depthCue; set dcStart 0.5; set dcEnd 0.7; background solid black; cofron; symclip 5 #Usage cootmode_wire_white alias ^cootmode_wire_white ~rib; disp; color gold; color byhet; repr wire; setattr m lineWidth 2; volume # capfaces false style mesh meshlighting false squaremesh false color "#00000000cccc" step 1; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1; background solid white; cofron; symclip 5 Also, to set maps or diffmaps to given rms level: # Sets map to x*RMS # Usage: sig #map_id rms alias ^map_sig volume $1 sdlevel $2 alias ^diffmap_sig volume $1 rmsLevel -$2 color #da1200000000 rmsLevel $2 color #0000bda00000 Or to just load map and diffmap with model from pdb, and set display settings of maps: #Load pdb and associated maps from EDS # Usage: load_pdb_and_maps pdb_id alias ^load_pdb_and_maps open 1000 $1; open 1001 edsID:$1; open 1002 edsdiffID:$1; cootmode_wire; map_sig #1001 1; diffmap_sig #1002 3 (Requires that the other aliases mentioned already exist, of course) Cheers, Oli.

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MatchMaker
by sdimicco 01 Mar '16

01 Mar '16

Dear Developer, I am using MatchMaker to compare some peptides. I would like to know if the RMSD value is referenced to the backbone atoms or to whole atom structure. Thank you in advamce. All the best.

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