- Chimera-users - RBVI Mailing Lists

smooth backbones
by A G Szabo 17 Nov '15

17 Nov '15

I have no problems with ribbons. However I would like to show some helices as backbones only. How can I achieve the result shown on the attachment for this helix. Don't know where to start looking. Any " Actions" only gave me this. Thank you Arthur G. Szabo Professor Emeritus Wilfrid Laurier University

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isosurface and blobs
by Raffaele Raucci 13 Nov '15

13 Nov '15

Hi all, I imported in chimera a map file with .cube extension. I was able to show isosurface after setting specific isovalue. Can you tell me if it is possible, by command line, count the number of different blobs displayed as isosurface? Is it also possible determine the area and volume of each blob? Thanks in advance, Raphael

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Volume transformation based on Phenix symmetry operators
by Morris, Kyle 13 Nov '15

13 Nov '15

Dear Chimera developers and community, I have a volume and an associated symmetry operator identified by another software package for this map. I would like to transform the map according to the symmetry operator to inspect what the symmetry related map looks like, does anyone know how to do this based on the appended matrix? Thanks in advance for your help! Best wishes, Kyle ================================== >From Phenix: new_operator rota_matrix -0.0877 -0.5114 0.8549 rota_matrix 0.9251 -0.3601 -0.1206 rota_matrix 0.3695 0.7803 0.5047 tran_orth 578.6845 434.1862 -508.9168 center_orth 918.6495 790.3525 1034.0200

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ESP
by Putkey, John 13 Nov '15

13 Nov '15

I have a question about electrostatic surface potential coloring. It works fine when only one .pqr and .dx file is open. I can uncolor, recolor and adjust the ESP color scale, but odd things happen when muliple .pqr and .dx files are open. Strange color patterns are obtained even though the correct MSMS surface and .dx file are selected in the Surface Color dialog box. Its as if the program is reading two .dx files. Is it me or a bug with the system? Cheers John John A. Putkey Professor Biochemistry and Molecular Biology University of Texas Medical School 6431 Fannin Houston Texas, 77030 John.Putkey(a)uth.tmc.edu<mailto:John.Putkey@uth.tmc.edu> (713) 500-6061 Office (713) 500-6062 Laboratory (713) 500-5073 NMR Laboratory

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Chimera 2 release date
by Markus Heller 13 Nov '15

13 Nov '15

Hello, Just curious, what's the anticipated release date for Chimera 2? Couldn't find it on the homepage ... Thanks Markus

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Built-in residue specific annotations in mmCIF?
by Oliver Clarke 13 Nov '15

13 Nov '15

Hi all, As discussed on the ccp4bb (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511>), the mmCIF format incorporates an atom_sites_foornote record (http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…) which allows for the direct association of specific comments/annotations with particular atoms/residues. As part of expanding mmCIF support in Chimera2, would it be possible to consider incorporating the capacity to read, write, and display these records as labels or notes? This could be a great way of incorporating built-in-annotations in a structure pertaining to specific features that could potentially be readable by other software such as Coot and pymol. Cheers, Oliver.

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Re: [Chimera-users] compounds
by Elaine Meng 09 Nov '15

09 Nov '15

Dear Dwey, You can use “Join Models” to join any structures that are open as two separate models (from two separate input files). You just couldn’t use the “peptide” option in that tool if they are not peptides; you would have to use the “other bond” option. See the Join Models part of the Build Structure tool for details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> You are more likely to find answers to questions in the User’s Guide than in the chimera-users archive. You can search the User’s Guide with menu: Help… Search Documentation. If that doesn’t help, then emailing the forum (CC’d here) is recommended unless you are including private data. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 9, 2015, at 2:05 PM, MPI <mpi566(a)gmail.com> wrote: > > Dear Elaine > Thanks for kindly answering my questions in Chimera forum. > > I have a question related to compounds and I appreciate your > valuable oppions. > > Let's say I have compound A and compund B. Both have strucctures. > > I would like to use a moiety (part) of compound A and a moeity > (part) of compound B. I wonder if Chimera can combine the desired > moeities of compound A and compound B to generate a new compound C. > > Another simpler version. Can Cimera merge compound A and > compound B into compound D ? > > I checked Chimera list but I found that Chimera provides a > function of joining models NOT for "compounds/drugs" but rather for > "Proteins". I also see you made comments in the past. I wonder if > you can provide insights into "compounds" or some hints to allow me > working on compounds in Chimera. > Many thanks, > Dwey

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obj file origin
by Erin Cutts 08 Nov '15

08 Nov '15

I am trying to use the .obj file generated as a surface mesh. Where the chimera outputs it as a list of vertices (points in 3D), a list of nomals (which I ignore) and a list of faces defined by 3 vertex reference numbers, it is super easy to import this into any mesh handling software. The problem is it seems to reset the orgin (the 0,0,0 point) to some mysterious location. As I am trying to compare this to electrostatics stored in a grid mesh format, where the orgin is specified, it would be nice if I could find out where the .obj has translated the axis coordinates too... The problem could also be caused by Chimera loading the molecule with a translation. All this gets very hard to deal with and trace...Any ideas that doesn't lead to me getting lost in cartesian space?

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3D dashed pseudobond styles?
by Oliver Clarke 07 Nov '15

07 Nov '15

Hi all, Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful. Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds. Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues. One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do. Cheers, Oliver.

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resmap
by R.I.Koning＠lumc.nl 05 Nov '15

05 Nov '15

I want to use the colors representing resolution in Resmap to color the surface of my map. From what I understand from the documentation the script that automatically runs after Resmap is finished and “… color the surface of your input map with the results of ResMap…”. This last thing does not happen. Though this script seems to run (I see a slice depicting the remap (in 2D) moving back and forth in chimera somehow only a map with 1 slice opens in Chimera afterwards and I cannot use the resolution color coding for my surface. Should some sort of 3D file be generated that can be used to do this via Surface color or should the coloring be on the surface map by default? Both is not possible now. Best regards, Roman

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