June 2007 - Chimera-users - RBVI Mailing Lists

rmsd and display queries
by bala 09 Jun '07

09 Jun '07

Hello, 1) Basically i hav three conformations (only 3 pdb) of the same molecule picked up from three different regions of a simulated trajectory. I hv to calculte rmsd and superimpose structure. I tried the emsemble match but it seems that it can work on only two conformation. Kindly suggest me how i can overcome this. 2) Is it possible to create a substructure (subset) of a molecule and do rmsd calcutn and superimposing only on the substructures for the conformations i have.

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New to the board
by Campbell, Patrick 08 Jun '07

08 Jun '07

Hello, I am a grad student and have only been recently been introduced to Chimera. I have a quick question which I hope, someone will be able to assist me with. I am looking at a pdb protein, 2NEF which is composed of 40 NMR structures. I was able to isolate one of the chains and was wondering if a. It is possible to change part of the sequence on the chain (from AAAA to EEEE for instance). b. Is it possible to then use the changed sequence (B) to morph it against the original 3d sequence (A) c. Is it possible to align the changed fragment of B with the original A d. Could the changed sequence (B) be saved for future use or does one have to go through the process of creating it each time it is used on CHIMERA? thanks much pat

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Re: [Chimera-users] rmsd and display queries
by Elaine Meng 08 Jun '07

08 Jun '07

On Jun 8, 2007, at 12:06 AM, bala wrote: > Hi Elaine, > Thank you for your inputs. I think i didnt mention my second query > reg. substructure creation clearly, > I hve a 20 mer duplex RNA, i want to visualize only a few base > pairs at the middle. Is there any way that i can select, display > and do actions only the portion of interest and undisplay other > portion > Bala Hi Bala, Of course. The general procedure is to (1) select what you are interested in (2) invert the selection so now it contains only what you are *not* interested in (3) hide or delete the selection (if you're confident you won't want the other parts, deleting will make later steps simpler) (4) if you only hid rather than deleting, now select the parts of interest again, and use the Actions menu to work with those parts There are many different ways to do each step, too many to describe in this mail. Below, I'll just give an example using commands, but be aware that selection can also be done with Ctrl-click and arrow key operations, or with the Select menu, or using the Sequence tool: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html Commands example: open 6bna sel :4-8.a,5-9.b sel invert delete sel Then carry on with what is left, using commands or the menu as you prefer. I hope this helps, 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

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Re: [Chimera-users] IMOD mesh/surface colors
by Elaine Meng 07 Jun '07

07 Jun '07

Hi Jeff, There are two general reasons why the *displayed* marker radius and link radius might not equal the values shown in Volume Path Tracer. In the following explanation, atom = marker and bond = link. (1) The atom or marker is in the "ball" representation rather than "sphere." displayed ball radius = (ball scale)(atom radius) where the default ball scale is 0.25. You could - change the atom to the "sphere" representation, which uses the full radius. "Actions... Atoms/Bonds... sphere" or the command "repr sphere sel" will change the selected atoms to the sphere representation. or - stay in the "ball" representation but change the "ball scale" factor to 1.0 (I'll describe how to get to this parameter below) (2) Similar to the markers, displayed bond or link radius = (stick scale)(bond radius) You could make sure that the "stick scale" factor is 1.0. It probably already is, since that's the default. Of course, the bond or link should also be the stick representation, not wire. Volume Path Tracer automatically makes them sticks when the radius is >0, however. In the Model Panel, if you click the IMOD contours model (or any molecule model) on the left and "attributes..." on the right (or just double-click the model on the left), that opens the molecule model attributes panel. In there you can see and change the ball scale and stick scale values. In your example file trial2.mod, I selected a few markers and links and set all their radii to 20. After I changed the marker to sphere, it did match up in size with the connected link. The more I zoomed in, the better it looked. It may be a level of detail issue if they don't look matched up when zoomed out. You can increase the number of subdivisions used to draw the spheres/cylinders with subdivision quality in Effects (under Tools... Viewing Controls). The parallel links did not quite touch, however, but since you said the contours were approximately 40 A apart, I think it is working correctly! If you still have trouble, though, let me know. I hope this helps, 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 On Jun 7, 2007, at 12:12 PM, William Jeffrey Triffo wrote: > thanks Elaine, > > another thing I noticed, when I change the marker (atom?) radius in > Volume Path Tracer, it does not appear to change quite right. For > instance, if I set the 'Link' radius to something like '20', and > likewise the Marker radius to '20', they will not be the same size. > > In general when making marker sets, this is not the case, and the > radius acts the same between the two settings. For these markers, > the contours were place approx. 40 A apart, so a marker (or link) > radius of '20' should make the contours 'kiss' when viewed as a > marker set, correct? > > thanks for your prompt response, it would make sense that I would > miss the color setting instructions on the actual page for the tool... > > -Jeff

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Saving images with the povray option
by jean-francois menetret 07 Jun '07

07 Jun '07

I am trying to save images with the povray option using chimera2416, but the camera viewpoint is lower than the center of the scene, so that I just see the bottom of the scene. Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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IMOD scaling and alignment
by Tom Goddard 05 Jun '07

05 Jun '07

Points placed in IMOD may not have proper scale and alignment when opened in Chimera together with the original MRC map. There are some IMOD settings that can fix this. Jeff wrote: > great, > > I don't know if I replied earlier or not, but if the issue comes up > with anyone else, setting the magnitude of the IMOD model (which a > user would typically do in the IMOD tool 3dmod) to be equal in > magnitude to the pixel size listed in the MRC header of the > desired/corresponding volume map is enough to ensure the proper > scaling; the default for units in 3dmod appears to be nm, while in MRC > files it is generally Angstroms. Applying a translation equal to the > origin offset that chimera uses in the MRC header is then sufficient > to co-register the two. > > -J

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Little help to write a python script
by Eduardo Sanz Garcia 05 Jun '07

05 Jun '07

I have previously written command scripts for chimera. Now, I need to do something more complicated that, I believe, is not possible to do from the command line. This is the task: I have a list of 100 electron density maps. 1- I want to display each map, one by one. 2- Change the default threshold. 3- Save an image of the current volume. 4- Close the current volume and open the next model. Has anyone done this before? An example of a python script that can do this or something similar could help me a lot. Thanks in advance.

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Volume segmentation question
by Toby Starborg 05 Jun '07

05 Jun '07

Dear Chimera users. I am new to using chimera, so this question may seem a bit simplistic. I'm trying to use Chimera to examine EM tomographs of fairly busy data sets. I'd like to be able to divide the data into separate features so that I can better understand which parts are noise and which are structural (segmentation). So far I have found the "Pick Surface Pieces" tool is very useful for colouring the surface of features of interest. I have also found it useful to colour some surfaces with 0 opacity to remove items that are in the way, but I would prefer to do this in a more permanent fashion sot that I can return to a data set and quickly compare structures. I have also tried using "Volume Path Tracker" with "Color Zone" and "Split Map by Color" (after adjusting the voxel size to angstroms rather than nm to give a reasonable volume segmentation). My question is would it be possible to alter "Pick Surface Pieces" so that it colours (or tags in some way) all of the voxels within the chosen mesh, so that it would then be possible to split the map into separate compartments that could be saved and examined separately? This would also offer the ability to use different threshold levels to examine different features. I realise that this is more of a wish list than a trouble shooting question, but I'd also appreciate any input from more experienced Chimera/tomography users. Thank you for your help. Toby S -- Dr T Starborg FLS, University of Manchester Michael Smith Building, Rumford Street, Manchester,M13 9PL. UK tel:+44(0)161 275 1557 fax +44(0)161 275 1505

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(no subject)
by Газизов А.С. 04 Jun '07

04 Jun '07

Hello everybody. Is there Fe2+ ion in Chimera? I'm trying to add charges to hem molecule and it always appears to be Fe3+ (and Add Charge tool reports "There is odd number of electrons..." and fails).Assigning odd overall charge helps (i.e. +1, +3, etc), but I need +2...

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problem with chimera-->followup
by Vinay Kumar 04 Jun '07

04 Jun '07

Hello all, Firstly. Greg, Thank you. Though, i have been using the linux OS for quite sometime, i still have a few doubts about upgrading and these sort of things. I have actually gone to mesa3d, OpenGL, and DRI websites. but they contain terms which i am not acquainted with. I have downloaded, MesaLib 6.4.2 and tried installing it as per their instructions, only to find the installation stopping with some error. ( i shall post the error in the next email.) I would like to know, if the installation went well, would i have upgraded X11?? With regards, Vinay. ps- MesaLib 6.5.3 was available, but 6.4.2 was stated to be a stable release hence opted that.

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Chimera-users June 2007