August 2008 - Chimera-users - RBVI Mailing Lists

Color zone with transparency
by Tom Goddard 14 Aug '08

14 Aug '08

Daniel Wilson wrote: > Hi Tom, > > ... > > The other thing I noticed is that you lose transparency on a whole volume when you color zone one region of it? or am I making something wrong? Is it not possible to have a single volume with two different colours and transparent? > > Thanks for you advice and kind offer, > regards > Daniel > Hi Daniel, When I make a transparent surface for a volume by pressing the volume dialog color button and making opacity 0.5 and then use color zone to color part of the surface (using a PDB model), the transparent part far from the zone remains transparent. Also works if select the volume surface and use the Actions / Surface / Transparency menu then color zone. What are the exact steps you use when it fails to preserve transparency? Tom

1 1

Two transparent models
by Tom Goddard 14 Aug '08

14 Aug '08

On Aug 11, 2008, at 12:15 PM, Daniel Wilson wrote: > Dear Elaine, > > I realise that there have already been requests about fixing the bug > in Chimera for displaying two transparent maps at the same time, so I > guess I am just asking whether this is likely to be fixed anytime > soon? We are desperate to use this function for a figure for a paper :) > > THanks, > Daniel > > Dr. Daniel N. Wilson > > Gene Center Munich > Department of Chemistry and Biochemistry > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > 81377 Munich, Germany Hi Daniel, The incorrect transparency in Chimera when 2 or more models are transparent is very difficult to fix and will not be fixed any time soon. The trouble is that Chimera draws each model separately and it is not possible to correctly handle transparency without intermixing the drawing of parts of models (in depth order). If you use Chimera image saving in the POVray raytracing mode it will correctly show multiple transparent models. The trouble is that this takes a long time to render and adjusting the levels of transparency many times to get the right appearance may be tedious. It would be possible to make a script that combines the currently displayed map surfaces into a single model and hides all the original models so that multimodel transparency would appear correct on-screen. But the combined model would not update when you changed the transparency, color, ... settings of the separate maps. It would require rerunning the script that makes the single model. This would be tedious to use. But if you think it worth trying I can write the script and send it to you. It would not work for transparent molecular models (ribbons and atoms), just surfaces. Tom

1 1

Hydrogens in proteins
by Walter Novak 13 Aug '08

13 Aug '08

Hi group, So I am struggling with hydrogens in proteins. I have neutron data which shows H-atom positions. Well, Deuterons, but here are the issues. If I open a pdb in Chimera with old school hydrogen names like HG1, how can I get it to write out the new ones (like HG11) without explicitly adding the hydrogens in Chimera? I don't want the atom positions to change. Also, I notice Chimera doesn't seem to handle deuterons optimally. Writing out the pdb moved the atom name column to the left one space and changed the atom type in the last column back to H. The problem is caused by Coot, which we use to perform real space refinement of atom positions, but to quote George Sheldrick, "I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle." Unfortunately, the point of my project is to see the hydrogens!!!! Thanks for any help you can offer, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

2 2

opening CASTp results
by Walter Novak 13 Aug '08

13 Aug '08

Hi all, How can I open my own CASTp results easily? The fetch command works great, but I need to submit some modified structures, and I don't see CASTp under file type in the open window. Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

3 4

calculation of volume
by Navnit Kumar Mishra 13 Aug '08

13 Aug '08

Hello all; I am trying to compute the molecular volume of a complex. Chimera first computes solvent-excluded surface area using MSMS. I see it does not compute the surface area of ligand. I am wondering if I can add the extra parameters or atom types for my ligand in some file. I would like to calculate the molecular volume from amber trajectory. Can some one suggest me how to automate the computation of surface area and molecular volume for each snapshot. If you know, please point out the article which describes the procedure for the volume calculation. with regards, Navnit

2 1

representing 70s ribosome in ribbon
by Bong-Gyoon Han 12 Aug '08

12 Aug '08

Hi, I am tring to show the full 70S ribosome structure (PDB id: 1GIX and 1GIY) in ribbon representation with EM experimental density together. These PDB data consist of backbone atoms only (single alpha carbon for each a.a and single phosphate for each nucleotide). Ribbon option does not generate any ribbon (due to the incomplete information in the PDB?). Is there any way to show this molecule in ribbon format? I assume that backbone atoms must be enough to generate ribbons. BGHan

2 1

IMOD model reader question
by William Jeffrey Triffo 12 Aug '08

12 Aug '08

I have an IMOD model (just a bunch of contours, representing filaments) that I tried to load into Chimera, but it threw some errors. This was odd, because it was a model I had augmented (added more contours) from a previous model that did load correctly (and I re-verified after the load error). is it helpful to forward the model file in question? best, -Jeff

2 1

MatchMaker and Find Clash in nogui mode
by Ryan 11 Aug '08

11 Aug '08

Hi. I read in the archive (2004) that someone was looking to use MatchMaker in the nogui mode / command line, but that was not a possibility at the time. I am wondering if this ability has ever been implemented, and if so, how does one go about scripting this. Additionally, i would like to use the 'Find Clashes/Contacts' function in nogui mode. Is this possible? Thanks a lot, ryan

2 1

protonating the protein
by Elaine Meng 11 Aug '08

11 Aug '08

Hi Francesco, > However, if you are using charges assigned in Chimera for something > (Dock Prep with AddH, Add Charge, and write Mol2 for input to DOCK > scoring grid calculations, for example), you would need to add the > protons in Chimera before assigning charges. This could be done by > selecting the carboxylate oxygens you want to get protonated (no more > than one per carboxylate group, of course) and changing their atom > types with the command: > setattr a idatmType O3 sel > prior to running AddH and Add Charge (alone or as steps in Dock > Prep). It is not necessary to rename the residues. Add Charge will > then recognize the neutral forms of ASP and GLU and use the > corresponding partial charges. I just tested this in the Chimera > production release, 1.2540 (July 9). The above is definitely true, you do not need to rename the residues in Chimera, but further tests reveal to get the correct charge distribution on the protonated carboxylic acid, the atom names also need to match the AMBER lib files: the protonated oxygen should be named OE2 (if glutamic acid) or OD2 (if aspartic acid) and the "free" oxygen should be named OE1/OD1. This will already be true sometimes, but not always. If you need to switch the atom names around before adding charges, it can be done by text-editing the PDB file or with commands. For example, you could change the name of an atom by selecting it and then using a command like: setattr a name OE2 sel After assigning charges, you can see the values as labels, for example: labelopt info charge la :6.a Again all this was tested in the production release 1.2540. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

Volume planes tool
by Elaine Meng 08 Aug '08

08 Aug '08

Hi Jeff, Here is another idea, still not exactly what you were asking for, but perhaps worth a look. You can use the Per-Model Clipping tool (under Tools... Depiction) to show a thin slab of the data, and you can interactively rotate and translate the slab any way you want relative to the data with the mouse. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/ per-model.html Just choose which model to clip, enable clipping, turn on slab mode and adjust clipping with mouse. You may also want to adjust the contour level in Volume Viewer. I tried it on emd_1274.map in the production release (1.2540). You can use it on solid, surface, or mesh volume displays. Below I attach an image of a slab surface display together with an unclipped solid display (a second copy of the same data). There is also a command to control per-model clipping in a script, mclip. It lets you specify location/orientation in the data coordinate system or the viewing coordinate system. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mclip.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

Chimera-users August 2008