June 2013 - Chimera-users - RBVI Mailing Lists

Chimeras limited capability to visualize correctly molecular structure
by Marek Maly 18 Jun '13

18 Jun '13

Hello all, recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene. I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success. So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file. All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694)) Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

4 5

Chimera - ball and stick - 3D printing
by Francois Richard 18 Jun '13

18 Jun '13

Hi everyone, I am trying to print a molecule from its PDB file (ID : 2BEG) using chimera and a 3D printer. I would like to print the ball and stick representation of the molecule, including the hydrogen bond. So far, (using this link : http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html) I played with molmap and volume commands and managed to print a volume but it does not include hydrogen bond. Do you have any idea how to improve the output? Thanks a lot, Francois

2 1

protein schematic representaton
by francesco oteri 13 Jun '13

13 Jun '13

Good morning to everybody, someone of you knows whether exist a program that creates schematic representation of a protein like the one in plot b and d of the figure: http://www.nature.com/nature/journal/v427/n6972/fig_tab/nature02165_F3.html Greetings, Francesco

3 3

Missing segment confuses addH
by Sam Egel 13 Jun '13

13 Jun '13

Hi, Basic Problem: I am attempting to use the addH tool on a metal containing active site I have extracted. The problem is that Chimera draws an 11 angstrom pseudo bond representing a missing segment between two residues. This bond seems to be the reason that a terminal carbon is receiving only two hydrogens rather than three. The pseudo bond runs right through the bond axis between two other carbons, both of which are protonated correctly. Can anyone please explain how to actually delete this bond (hiding through ~longbond, closing or hiding through the pseudo bond panel does not work) or provide another method to get this carbon to have three protons? I'm running v 1.6.2 of Chimera locally on Win 7 and the same problem occurs on a remote Red Hat Enterprise Linux machine running v 1.5 of Chimera. More Detail: Getting this carbon protonated in a one-stop-shop by Chimera would save me the world of time for a number of reasons, including that I need to make many files of this active site and every pdb of this enzyme has the same addH/pseudo bond problem between the same residues. The active site was extracted by writing a 10 angstrom zone around the metal to a pdb and then hand selecting the residues I cared about from there and writing them to a pdb. Workarounds: I have tried using command line ~longbond, hiding and closing out the missing segments option in the pseudo bonds panel, and deleting the bond by highlighting it and trying to delete bond under the adjust bond tab in modify structure window. If I write the pdb to an xyz (Molden) and open the xyz in Chimera, addH works just fine. However, I would really like for these files to be real pdbs that have associated residue names at the moment (residue names are, of course, deleted when converted to xyz). Thank you for your time, Sam

3 2

display of glycine atoms
by Levandoski, Mark 11 Jun '13

11 Jun '13

Hello there - I recently got a new office machine and had to reload Chimera. Although I do not recall the number of the version I had used in the past, empirically I can tell that this is some updated version. My problem is that I am trying to display various residues of a protein selectively as space-filling ("sphere") on a ribbon frame. One residue of interest is a glycine. This version of Chimera seems incapable (or I am incapable of discovering how!) of displaying the various atoms belonging to this glycine residue. All other residues seem fine. Is this a glitch? Am I doing something wrong? For comparison, I have every confidence that this should work because with my older version of the program I was able to generate just such a view. Thank you very much in advance for the help, Mark P.S. By selecting the glycine of interest I am able to color the strip of ribbon by preset color, but not by element. Mark M. Levandoski Associate Professor of Chemistry Grinnell College 641-269-4544

2 2

Selecting regions of a PDB structure
by Anindito Sen 11 Jun '13

11 Jun '13

Dear All, I have a pdb file of a large protein complex. I want to select several regions and color them differently to show the various domains. How can I do that. Thanks Andy Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

3 2

Re: [Chimera-users] movie of flying in a density map
by Tom Goddard 11 Jun '13

11 Jun '13

Hi Andy, The way to use saved positions in an animation is to save a session which includes all the saved positions. Then to make the animation you first open that session and then use the "fly" or "reset" command in a script with those named positions. This is a general method for making animations that works quite well. Setup everything in a session (which models are open, where they are placed, colors, lighting, background color, shadows, …), then just use an animation script to modify a few things. If you instead try to do all the setup in a script with no session it is much harder. I don't understand your question about clipping. Normally Chimera does not clip your maps when you zoom in. Only if you turn on clipping or make your view point move right through the map would you see clipping. Tom On Jun 11, 2013, at 1:07 AM, Anindito Sen wrote: > Hi Tom, > > In the Video tutorial about making a movie of flying through the protein complex - how can I have the positions saved (sav pos) and put it in a script. The idea is to modify a script that makes a density map rotate (which I already have) and then fly in through that. I can then alter the script accordingly to show different regions of the map (and will not need to type the whole set of commands). > > Secondly how can modify my script to zoom-in a density map without clipping the region of interest. It is obvious that a major portion of the map will be outside the view but the clipping plane will not move and clip the map (like when we zoom in manually in the Chimera window using the mouse. > > Thanks > > Andy > >> Dr. Anindito Sen (Ph.D) >> Department of Cell Biology & Anatomy >> Graduate School of Medicine >> University of Tokyo

1 0

ligating two models
by Bala subramanian 06 Jun '13

06 Jun '13

Friends, What is the best method in chimera to ligate two models. I have generated a small ligand that has to be attached attached to a protein residue. Thanks in advance, Bala -- C. Balasubramanian

2 1

Maximum volume size
by Tom Goddard 05 Jun '13

05 Jun '13

Hi Svetla, Chimera is correctly handling your 880x880x880 map. But by default Chimera displays only a single plane of very large maps, because the most common case of this is with tomograms where a single plane display is usually what you want. When it does this the Volume Viewer dialog shows a "Planes" slider in the dialog, and below that is a button "All" that will show all planes. If you want Chimera to always show the full map, use Volume Viewer menu entry Features / Data Display Options, and click off "Show plane when data larger than N Mvoxels", and then use Features / Save Default Dialog Settings so it will use that setting in all future uses of Chimera. Tom On Jun 5, 2013, at 9:54 AM, "Stoilova-McPhie, Svetla" wrote: > Dear Tom, > > Are there any limitation for the size of 3D map/volume the Volume viewer can visualize? > > We tried a 880x880x880 voxels map generated with spider and it comes out as a 2D map: 880x880x1. > WE triple checked and the volume file dimensions are indeed 880x880x880 and can be visualized as a 3D volume in the EMAN2 viewer. > > Please advise. > > Best regards, > > > Svetla Stoilova-McPhie, PhD > Assistant Professor, > Department of Neuroscience and Cell Biology > Scientist, Sealy Centre for Structural Biology > and Molecular Biophysics > University of Texas Medical Branch at Galveston > 301 University Boulevard, Galveston, Texas 77555-0620

1 0

sementation
by Jingchuan Sun 05 Jun '13

05 Jun '13

Hello, After segmentation of a 3D map into 16 subunits and assign different colors, the saved .seg map does not save the color. During the preparation of our recent paper, we had to assign the color each time we open the .seg (hundreds of times), which make me very upset, even angry sometime. If the guy writing the program allow us to save the assigned color, that would have saved us many times. Thanks! Jim

2 2