May 2011 - Chimera-users - RBVI Mailing Lists

question about "measure rotation"
by Bobby Laird 25 May '11

25 May '11

I am using the measure rotation command in chimera to calculate the degree of rotation between two dimers, which make up a tetramer. I am using the following commands to accomplish this: mmaker #1:.A,.B #0:.A,.B pair ss write relative #0 #1 /tmp/ab-aligned.pdb close #1 open #1 /tmp/ab-aligned.pdb mmaker #1:.C,.D #0:.C,.D pair ss measure rotation #0 #1 I have noticed that when I use the "measure rotation" command that can get two different answers. I realize that the two answers are the result of an arbitrary decision made by the measure tool that result in a +/- of the same angle (i.e. 6 versus 174 degrees). Since I am looking at more several crystal structures, is there a way to force "measure rotation" to always make the same decision so that I know what relative direction the rotations are in to each other? Thanks _______________________________ Bobby W. Laird

2 1

installation of headless chimera
by bharat gupta 24 May '11

24 May '11

Hi, I am new to chimera and I am trying to install it on fedora core 6 . After followng the instructions given in installation manual nothing happens in my system. Can anybody tell me how can I install the headless version of chimera .. Thanks in advance for help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46010(a)yahoo.com

2 2

Re: [Chimera-users] Proline sidechain broken (with backbone as a ribbon)?
by Visvaldas K. 24 May '11

24 May '11

I'm very sorry, I take my question back. Actions->Atoms/bonds->Show will do the trick. Vis

2 1

Proline sidechain broken (with backbone as a ribbon)?
by Visvaldas K. 23 May '11

23 May '11

Hi, I really like the default view of a loaded PDB file, where the whole protein is shown as a ribbon, but also the sidechains next to the heterogroups are shown. Proline shows up in this representation as a sort of rhomboid (or kite) shape, which is okay. However, I cannot achieve the same effect for proline when I select proline manually. If I do Actions->Atom/bonds->sidechain/base->show, the proline sidechain appears as a broken rhomboid, which looks more like a hook, i.e. a one of the bonds is missing to close the loop. How do I obtain a "closed" proline sidechain look? Thank you, Vis

1 0

centering a volume to an atom's coordinate
by Roni Rayes 23 May '11

23 May '11

Hi, I am trying to center volumes (cylinders and spheres that I created using spider) to an atom from a pdb file. When I created the volumes I made sure that their center is in the middle of the box containing the volume. I tried to set the coordinate of the volume to the atom's coordinate (in the coordinate tab under volume viewer) but the position of the volume was not centered to the coordinates provided. Any idea on how to do that? Thank you Roni

2 1

PipesAndPlanks
by George Tzotzos 23 May '11

23 May '11

Hi everybody, I'm dealing with a dimeric hexahelical bundle. I've been trying to name the individual helices (e.g. a1, a2, etc) and colour them differently to no avail. Obviously, I'm missing something. Your guidance will be greatly appreciated. Have a good weekend George PS. Sorry if you receive this message for a second time. It was sent from a different address earlier and I'm not sure if it reached the list.

3 6

Pack molecules in Unit Cell
by Joe Osmundson 20 May '11

20 May '11

Hi everyone, I would like to transform a pdb so that it fits nicely in the unit cell, which seems to be described here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.… as "Pack molecules in unit cell". However, this is not an option when I bring up the options in the Unit Cell tool (although literally everything else that should be there IS indeed there). Is there a glitch in the most recent version? Is there an easy way to script this to essentially move the model (and its crystallographic mate) into the center of the unit cell? Thanks, Joe Osmundson Darst Lab Rockefeller University

2 3

Completely reinstall chimera
by Daniel Hitchcock 20 May '11

20 May '11

Hi, I want to completely uninstall chimera and remove all the settings from the program. I notice though if I uninstall and reinstall though, it still has all the settings and history from before. How can I completely remove Chimera from the computer so I can return to default settings? Thank you -daniel

2 1

solid-cylinder representation of helices
by Francesco Pietra 19 May '11

19 May '11

HI: Is any plan about a solid-cylinder representation of protein helices? It would be very useful to represent pathways of ligands inside a protein (in combination with centroid). Helices allow a less defined 3D perspective, especially when all is projected into a screen or paper. Thanks francesco pietra

2 1

Visualising PDB files from AMBER
by George Tzotzos 18 May '11

18 May '11

Hi everybody, I've generated a average pdb structure from an AMBER trajectory. The structure contains one water molecule (named: WAT). I fail to visualise it in Chimera despite the fact that I can select it. I'm using Chimera 1.5.2 on OSX 10.6.7 Any ideas explaining this behaviour? I'm attaching the relevant file. Thank you in advance for your help Best regards George

2 1