April 2015 - Chimera-users - RBVI Mailing Lists

Delete Bug?
by Korbin West 27 Apr '15

27 Apr '15

Hi all, I'm running some code on Chimera to select only certain chains and nearby aspects, but when I try to delete the extraneous information, Chimera freezes up. I'll detail the commands I use below, and for reference I'm interested in the H chain of 1CT1, but it doesn't seem to work with any of its chains. open 1CT1 zonesel :.h 3.5 extend true select invert del sel It then freezes on del sel. I've tried this with other pdb files and it works fine, but for some reason it stops on this one. For example, it works fine on 1PZ3 for its A and B chains. Is this some kind of bug or is there a work-around to this issue? We looked at the residues and couldn't find anything out of place, so we are not sure what is happening. Much thanks in advance. Best, Korbin West? Wabash College

3 3

Making a composite residue
by Repic Matej 23 Apr '15

23 Apr '15

Hello, I wonder if it is possible to construct a composite residue from two existing residues in Chimera? What I would like to do is concatenate residues ALA100 (mid chain) and GLY200 (end of chain) to make a composite residue AGL100. Chimera won't let me set the same residue number via the "resrenumber" command. Preferably, the composite residue would have all the atoms listed where ALA100 was in the original pdb. While I realize there are trivial text editor-based workarounds I would like to know if there is a native way. Thank you all, ---------------------------------------- Matej Repic Ecole Polytechnique Fédérale de Lausanne SB - ISIC - LCBC BCH 4108 CH - 1015 Lausanne ----------------------------------------

2 1

about volume viewer
by 张雷 21 Apr '15

21 Apr '15

Hi, the experts of Chimera, I am a new user of Chimera and have a question to consult you. When I display a 3D model in the volume viewer, I found that there was an original value of the level, as the attached figure shown. If I increased and decreased the values of level, the densities of 3D models were different. Therefore, how to deternime the right value of level for a protein. It is known that the average density of proteins is 1.35 g/cm3; If a protein has a molecular weight of 1350 kDa, and 1 Da = 1.66054E-27 kg; therefore, the protein volume is 1661 nm3.If I want to display the volume of 1661 nm3 in chimera, how can I decide the value of level? In another words, how can I calculate the value of level from the actual volume of a protein? Thank you! Best wishes! Lei Zhang Peking University, Beijing, China

3 3

Re: [Chimera-users] coloring individual segments of a protein
by Greg Couch 21 Apr '15

21 Apr '15

To get a different resolution than 72 dpi, you need to turn on the "Use print units" option in the Save Image dialog, and set the "Print resolution" and pick the image width and height. Or you can use a program like Adobe PhotoShop or GIMP to edit the DPI if you already have an image that you like. HTH, Greg On 04/21/2015 03:01 PM, A G Szabo wrote: > Greg > > Thanks for your reply > > > I had just sent Elaine another question that perhaps you might be able to > answer. > > I am currently writing a book and the editor would like the protein > structure images saved with at 300 dpi. When I saved an image of > Ribonuclease, PDB 5RSA, both as a png file and a Jpeg file the editor > indicated that the resolution was not sufficient and was only 72 dpi. > > Suggestions? > > Thanks > > ags

1 0

Residue Numbers vs. Residue Codes
by Korbin West 21 Apr '15

21 Apr '15

Hi all, I'm trying to determine uncommon ligands in pdb files using a python code, but have run into an odd dilemma. In my code, I open a pdb in Chimera, select the ligand, and write out the residue list. However, the formatting of this list changes depending on how I run the program. If I run the program through xterm, it will print out only residue numbers. If I run the program though Chimera's Idle, however, I will get the residue codes and the residue numbers. For example, I ran this with 3VKG, you can see the results in the attached files, where I show a sample code of what I'm using, the xterm results and the Chimera results. I want to do this for a large number of pdbs, so I'd like to do this --nogui through xterm, but I need the residue codes. Has anyone else ran into this problem or know of a work-around? Thanks in advance. Best, Korbin West Wabash College

2 1

coloring individual segments of a protein
by A G Szabo 21 Apr '15

21 Apr '15

How do I use Chimera to color a protein in the following way: for example: Helix 1 - red Helix 2 - yellow Helix 3 - magenta Strand 1 - dark blue Strand 2 - cyan Etc. A G Szabo

3 7

keyboard accelerators
by Dougherty, Matthew T 20 Apr '15

20 Apr '15

Hi, had a few questions about the documentation. A click in the graphics window may be required. Sometimes it is necessary to click in the graphics window to take back focus from some other dialog so that accelerator or command keystrokes will register. >> is there a way to send accelerators through the Viewing-Side View? I have been dedicating one monitor for the 3D graphics and the other for control, menus, etc. using various USB devices sending accelerators. Would prefer not put to the focus/mouse cursor on the 3D graphics. Accelerators could be shown on menu entries. The keyboard shortcuts could be shown on the corresponding menu entries to make them easier to learn.? >> How? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

3 3

Help in MD movie
by Ankit Agrawal 18 Apr '15

18 Apr '15

Hi I have trajectory file from gromacs and opened in chimera. Now I am doing inertia calculation. I wrote a python script to show the ellipsoid. But this script is showing only the ellipsoid. I want ellipsoid as well as the molecular structure of that frame, i.e. both ellipsoid and the molecule. so that I can show the how molecule is changing its position. This is like a structure overlay but I want it with ellipsoid. thanks regards Ankit Agrawal

2 1

Reducing the map to a cubic box
by Sushree Tripathy 17 Apr '15

17 Apr '15

Hi, I went through the chimera user's guide and as per the syntax used "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map. Please help. Thanks Sushree. Sushree Tripathy Graduate Student Department of Physics University at Buffalo

2 1

Generating a map from atomic molecule
by Tom Goddard 17 Apr '15

17 Apr '15

Hi Zhihai, The reason your map surface shows the triangulation is because the grid spacing is large. You made the map with molmap with 30A resolution. By default molmap sets the grid spacing to 1/3 of the requested resolution, so 10 Angstroms in this case. Apparently this is too coarse for your needs. So spedify a finer grid spacing in the molmap command. For instance molmap #0 30 gridSpacing 3 to produce 30 A resolution with 3 A grid spacing. Here is the molmap documentation http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html> Tom > On Apr 16, 2015, at 8:45 PM, 李智海 wrote: > > Hi Tom, > It seems that the low-resolution (about 30A) map generated from atomic model by “molmap" has many artifacts on its surface (see first attached figure), and I can see many rectangle signatures of it in Fourier space (see 2nd attached figure) so that I can not use it as the start map for further reconstruction. > Please tell me how can I get rid of this. Thank you! > > Best wishes! > > > Zhihai Li > > <molmap_30A.png><FFT.png> > > Zhihai Li > > Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics. > School of Life Sciences, Xiamen University. > Xiang'an Road(South), Xiang'an District, Xiamen City, > Fujian Province, China. > >> On Apr 15, 2015, at 1:28 AM, Tom Goddard wrote: >> >> Hi Zhihai, >> >> If you want the map computed from an atomic model but on a grid that matches a reference map then you should compute the map with molmap and then resample it on the reference map grid. If #0 is the atomic model and #1 the reference map. >> >> molmap #0 8 edgePadding 50 >> vop resample #0 onGrid #1 >> >> Here the 8 is the resolution for the computed map and 50 Angstroms controls how far beyond the molecule bounding to compute the map. >> >> Tom >> >> >> >>> On Apr 13, 2015, at 9:00 PM, 李智海 wrote: >>> >>> hi, >>> here I want to generate a density map from a atomic model in Chimera, then convert the generating map into .pif file to do as the initial map performing in Auto3dem. >>> I have met some questions to successfully finish these work. >>> >>> 1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size. >>> >>> 2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. >>> >>> >>> Thanks in advanced! >>> >>> Best wishes! >>> >>> Zhihai Li >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> >

1 0

Chimera-users April 2015