January 2016 - Chimera-users - RBVI Mailing Lists

my question
by Yanli Li 25 Jan '16

25 Jan '16

Dear sirs/madams, I am a PhD student in Universitat Autònoma de Barcelona. I am working on the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). I have got differences of cytokine profiles and phenotype regulation of antigen presenting cells by different isolates through the lab work. Now I intend to predict the structure of the whole or some parts of the viral particle with UCSF CHIMERA. However, there are only three relevant structures(nucleocapsid, nsp1, nsp4) that have been published. Is it possible to realize it? If yes, can you tell me the method in brief? Thanks a lot! Waiting for your reply. Best wishes, Yanli LI

3 2

the fastest way to convert a pdb to density map
by 李智海 22 Jan '16

22 Jan '16

Hi, Here I want to calculate a model-to-map FSC curve. If I am not wrong, firstly I am supposed to convert the pdb file to a density map. So I was just wondering in Chimera, how to use command molmap to generated a map with the same pixel size and dimensions as the corresponding map? Any help will be high appreciated. Best, Zhihai Li

2 2

Select residues with missing atoms?
by Oliver Clarke 19 Jan '16

19 Jan '16

Hello, Is there any way to select/color all protein residues with incomplete sidechains? This would be very helpful when looking at a structure and deciding whether it is necessary to run dock prep to fill them in prior to performing other calculations (e.g. sometimes I am only concerned with what is going on around a ligand binding site). Cheers, Oliver.

2 2

question
by A G Szabo 15 Jan '16

15 Jan '16

I have to admit that my understanding of the various commands to use for very specific functions in Chimera is difficult for me to find the correct command. I know how to color a specific residue using the sequence table and the color chart. So how do I color a specific atom in a residue. For example I am interested in coloring the nitrogen of the Asn amide side chain say color red. How can I do this? When I highlight a residue and visualize it as a ball and stick, then color it different from the color of the helix, the color of that part of the helix changes to the color of the ball and stick, different from the color of the rest of the helix. How can I reset the color of the helix location of that residue, leaving the ball and stick as another color. Thank you Arthur Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo Canada.

2 5

Geometric Center
by tobias.eilert＠uni-ulm.de 15 Jan '16

15 Jan '16

Hello, I want to translocate a protein such that its geometric center is the origin. Finally I want to save this new configuration in a pdb-file, so it is conserved like this. Do you have any suggestions? With kind regards Tobias Eilert

2 1

save command
by Dougherty, Matthew T 12 Jan '16

12 Jan '16

The FILE pull down menu allows for "save" and "save as". The command "save" allows for two options: with or without a session_name. Without a session_name, a dialog box is presented and effectively I am doing the "save as" in the FILE menu at that point. With a session_name, it functions as a 'save as' without the dialog box. How do I create the same effect as FILE pull down menu "save", using the save command? Looking for a generic approach for any session, not knowing the file/session name apriori, & having to type the session name everytime. I suppose there is a python method to get the session filename & path, then build the command string. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

2 1

header intact
by maozhouhe 09 Jan '16

09 Jan '16

confirm 4cb1de59074527102f482c8970f4d33506347705

1 0

Re: [Chimera-users] [chimera-dev] Volume Eraser: Recentering the eraser
by Tom Goddard 07 Jan '16

07 Jan '16

Hi Mohan, Here are a few more details about how to erase the density inside the capsid of a virus density map. The trick as you’ve seen is getting the sphere centered at the center of the virus and having the correct radius. Here’s how I do this. First I adjust the volume eraser sphere radius so it visually looks about the same radius as the outside of the virus map. Then I move the sphere with the mouse to try to center it on the virus. I rotate to look at it from different view angles and center with the mouse at each view direction. It helps if the radius of the sphere is set so that just a little bit of the density pokes through so you can visually see whether the same amount of density is poking through on all sides. Now I have the right centering and I try to get the radius I want. For this it helps to clip the map and sphere using menu Favorites / Side View and move the left vertical yellow line to the right to clip the models. I move the clip plane to cut through near the center of the virus, then adjust the sphere radius. In this view you can see the sphere size relative to the concentric layers of density. It helps here to make the sphere not transparent by clicking the color square in the Volume Eraser dialog and setting the A (opacity) channel to 1. I’ve attached a pickture. To do this in a more precise way I create a sphere and mask using it with commands shape sphere radius 240 center 0,0,0 coordinateSystem #0 color blue mask #0 #2 invert true This requires that the origin of the map is set to the center of the virus capsid. You can choose this center grid point using Volume Viewer menu Features / Coordinates setting the Origin Index. Tom > On Jan 7, 2016, at 9:38 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Mohan, > If you read the Help for Volume Eraser (press the Help button on the dialog to see it), it explains how to move and resize the eraser sphere. Or, you can see this information on our website: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleras…> > > Basically you can set which mouse button will be used to move the sphere, and then use the mouse to move it to where you want, including with Shift to move in Z (toward or away from you). There isn’t a feature to automatically put it at the center of the capsid. > > For user questions, the better address is chimera-users(a)cgl.ucsf.edu (not this address chimera-dev, which is more for programming questions). > > 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 Jan 6, 2016, at 9:01 AM, Mohan Sudabattula <mk.sudabattula(a)gmail.com> wrote: >> >> Hello, >> >> My name is Mohan Sudabattula, I am fairly new at using Chimera so please excuse my lack of understanding the program. >> >> I am currently utilizing the Volume Eraser tool and am trying to employ it erase the internal structure of a viral capsid. Upon opening the Volume Eraser it always seems to orient itself to the "frontmost face of the current display region". This is problematic because it is now only partially erasing what I am needing to be erased. >> >> Instead I am looking to have it oriented so that it is in the center of my virus. Is there any way to reorient the eraser so that this may be the case? >> >> Thank you! >> Mohan Sudabattula >> > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

1 0

Drawing shapes given coordinates
by Oliver Clarke 07 Jan '16

07 Jan '16

Dear Rebecca, I have used Elaine's suggestion before, and it works well, as in the following alias: alias ^pbond dist sel; setattr p label "" sel; setattr p drawMode 1 sel; setattr p radius 0.03 sel which places a thin black cylinder between two selected atoms. To make invisible dummy atoms at arbitrary coordinates, I would use the "mc" accelerator ("ac mc" on the command line), which places and selects a dummy atom at the center of rotation. So something like: cofr x1,y1,z1; ac mc; namesel atom1; cofr x2,y2,z2; ac mc; namesel atom2; sel atom1|atom2; pbond; vdwdefine 0.01 sel; transparency 100,a sel should work. Cheers, Oli. ------------------------------ Thank you! Theoretically if I was to create dummy atoms with coordinates at the locations where I want the cylinders to end, I could connect them with pseudobonds. I can easily shape my data that way, and if it doesn't work the BILD files will probably be fine. Thanks for the help! Cheers, Rebecca On 1/4/16, 5:20 PM, "Elaine Meng" <meng at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> wrote: >*Hi Rebecca, *>*There are two approaches for adding cylinders independent of atomsŠ but I *>*don¹t know if either will be satisfactory: *>>*(1) ³shape cylinder² is command-line and doesn¹t require using atoms as *>*endpoints, but it doesn¹t allow specifying endpoint coordinates directly. *>* A cylinder is specified by only its center, height, radius, and a *>*rotation angle. I don¹t think it is easy to figure out what angle gives *>*the desired endpoint coordinates. (We¹ve discussed the need to improve *>*this, but it may be deferred to our next-generation software in *>*development.) *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_shape.html-23cylinder&d=CwIFaQ&c=TzEZu9LIcihmW3 *>*7vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd *>*4eXf6HdP_BL9dt0gv_zz3oMdq8&s=9vZCIh2K2i-8UrGF7HkSZwZwT7CRFcS9RUZsHUsson4&e *>*= > *>>*(2) BILD-format input allows specifying endpoint coordinates of a *>*cylinder, but it is not a command. You generate a BILD text file *>*describing the objects and read it in to Chimera. BILD format is very *>*simple, however: *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_bild.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=Z2BqCMu *>*wlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_BL9dt0gv_ *>*zz3oMdq8&s=2A5wPT06BJ7QN1TDyA4kS36ILONzhA703a7xRpdnJKY&e= > *>>*The objects created with ³shape² are surface models, so you can change *>*their colors afterward. The BILD objects are not surface models and *>*cannot be recolored and do not work well with transparency. *>>*There are two approaches that depend on atoms: *>>*(1) pseudobonds can be created with the ³distance² command (or atom pairs *>*can be read in from a file with Pseudobond Reader), but pseudobonds *>*require atoms as endpoints. *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_distance.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w *>*&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP *>*_BL9dt0gv_zz3oMdq8&s=tUGhl0z5yTsTqr2tyEgexdraCTB8o2JtwjuJZTgMwvo&e= > *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_ContributedSoftware_pbreader_pbreader.html&d=CwIFaQ&c=TzEZu9LIci *>*hmW37vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH *>*6akd4eXf6HdP_BL9dt0gv_zz3oMdq8&s=nRvWQ2FPg5n33Obqd9Bee1ovSNmgCCdbaT1EH6Uc1 *>*I8&e= > *>>*(2) the ³define² command (or Axes/Planes/Centroids) tool will show *>*cylindrical axes that are best fits to specified sets of atoms. However, *>*there is currently little control over lengthŠ it is automatically *>*determined from the atomic coordinates. *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_define.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r *>*=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_B *>*L9dt0gv_zz3oMdq8&s=t9I-WC_-VvEvmTfphtU3ey2GT0sMRiFtO62hFkRj7Rk&e= > *>>*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 Jan 4, 2016, at 12:09 PM, Rebecca Swett <Rebecca_Swett at vrtx.com <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> *>>*wrote: *>>>>* Hi all, *>>* I'm trying to add some 3d shapes to a visualization. I was wondering if *>>*it would be possible to draw either a cylinder or tube given starting *>>*and ending coordinates rather than atom names/numbers or centroid? For *>>*example, if I had this coordinate pair: *>>* 6.17 1.10 -15.33 20.82 -0.70 -8.39 *>>>>* What would be the best way to go about drawing a line of some sort *>>*between those two points? I have dozens of pairs of coordinates so *>>*something command line would be ideal. *>>* Cheers, *>>* Rebecca *> This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

1 0

Suggested Improvement of Command Line
by Eric Berg 07 Jan '16

07 Jan '16

Hello, I have noticed that when giving the command line a list of residue indexes using the "select" function, the inclusion of white space will cause an error (see attachment). This is technically a pretty small quibble, but it may be beneficial in these instances to include something to filter out white space prior to parsing. Eric

2 1