- ChimeraX-users - RBVI Mailing Lists

Access to git repository
by Tomris, I. (Ilhan) 19 Oct '20

19 Oct '20

Dear sir/madam, At the moment I am utitilizing ChimeraX to render 3D images of lightsheet data I have obtained (see attachment of 3D render). It is a pretty nice software package, although there is something I would like to implement into chimerax. A bounding box/outline box with gridpoints on it to indicate the size of the rendered volume, additionally I would also like to implement a scalebar of some sort. Hence I was wondering whether I could get access to the git repository so I could attempt to use the "Outline box" already present and put grid points on it? [cid:ab15abd2-e188-42fa-ae88-eedbeae317dd] Kind regards, Ilhan

2 1

Re: [chimerax-users] Assistance: ChimeraX save scene
by Guillaume Gaullier 19 Oct '20

19 Oct '20

Hi Priyanka, Sorry for this late reply. I am copying the chimerax-users list (if you had sent your last email to the list, somebody else would maybe have answered you earlier; also a good idea to communicate through the list because all emails are archived and that sometimes enables people to find answers to their questions directly by searching the archives). Regarding you question about colors: in ChimeraX, the command "color list" will print in the log a list of colors with their names. Color names made of more than one word are listed twice: spelled with and without a space. I just checked that if you spell color names as they are listed by this command, it works. So, in your case, try spelling it "royalblue" with no space. Regarding your second question, I think this should work, but I am not quite sure what you are trying to do: volume zone #1 nearAtoms sel range 2 newMap true minimalBounds false in which #1 is your main map (so not necessarily #1 in your session, use the correct model number for your map as seen in the model panel) and sel is a selection of the atoms of interest (in your case "/A" for chain A), "range 2" is how many angstroms away from the model atoms you want to perform the map cut-out (I put 2 arbitrarily; try different values and use what you think is best for what you are trying to do), "newMap true" tells it to generate a new object for this map cut-out (it should show up in the model panel after you run the command) and "minimalBounds false" tells it to keep the same box size as your original map (if set to true instead, it will choose the minimal box size that encloses your map cut-out; not sure which one you need, but keeping the same box size should be safe). Once you have this, you can write this map cut-out to a file with the following command: save /path/to/your/new/map.mrc models #2 (replace #2 by the correct object identifier for your new map, as reported in the model panel). I hope this helps, Guillaume > On 16 Oct 2020, at 03:31, Priyanka Abeyrathne <pabeyrat(a)gmail.com> wrote: > > Hi Guillaume, > > Thank you so much for your assistance. I am going to use it soon and if I happened to have questions I will let you know. > > I have two other questions to clarify with you. > > 1. I used the following commands to color the pdb > seq chain /A > Then I highlighted the chain A > color sel blue > > I can see the chain A color is blue. Now ChimeraX has really nice color scheme. I tried to color chain A to royal blue (#4169E1 26,41,88). When I use the above commands > seq chain /A > highlighted the chain A > color sel royal blue > Didn't change the color blue to royal blue. Cod you please assist me how to fix theis? > > 2. pdb of the protein has three chains (A, B and C). I have a cryo-EM structure of the same protein. How can I extract only chain A density from cryo-EM structure. I think I have to use a segment map command. Could you please assist me how to do this in ChimeraX. > > Thank you so much. > Kind regards, > Priyanka > > > > On Mon, Oct 12, 2020 at 3:41 AM Guillaume Gaullier <guillaume(a)gaullier.org <mailto:guillaume@gaullier.org>> wrote: > Hi Priyanka, > > If what you need is a command that can restore the camera’s position to a previously saved state after you moved it, then this should be helpful: > > 1. set the scene the way you want it > 2. run command "view name myview" ("myview" can be any name); what this does is assign a name to the current view (camera settings) > 3. rotate or translate, move around, etc. > 4. run command "view myview", which should reset the camera settings to what they were when you did step 2 above > > I believe named views are saved with the session, so you should be able to use them even after you save and close, then reopen your .cxs file. > > You will find more details in the documentation, with command "help view". Also here: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > I hope this helps, > > Guillaume > > >> On 11 Oct 2020, at 22:10, Priyanka Abeyrathne <pabeyrat(a)gmail.com <mailto:pabeyrat@gmail.com>> wrote: >> >> Hi All, >> >> Is there a save scene command in ChimeraX? >> >> Thanks, >> Priyanka >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

2 1

Set transparency on DNA stubs
by Siyu Chen 16 Oct '20

16 Oct '20

Dear chimerax developers, I am writing to ask about an issue regarding to the transparency of DNA bases. I set the double strand DNA as stubs and colored cyan, and I wanted to set it as transparent (trans 70 tar c). However, it looks like only the DNA backbones become transparent, and the bases are still bright and solid. I even tried to throw in all possible targets into the 'trans' command (acrsbpfl) and got the same looking images. I am just wondering if this is because of the style or color that makes the bases look solid? Also, do you have other suggestions to get around this issue? Thanks in advance for your time and help! Best, Siyu Chen

2 1

Chnage Chain IDs
by Kazan Ramy (M.) 13 Oct '20

13 Oct '20

Greetings to all, In UCSF Chimera tools, there's an option to change chains ID/names. Unfortunately, I can't save my model under a cif format. While in Chimera X , I can save a model under a cif format but can't change the name of my chains, or at least I'm not able to find the command for that. My main goal is to have my model under a cif format with my new naming system, any idea on how I can solve this problem? Ramy Kazan PhD Student

2 2

Assistance: ChimeraX save scene
by Priyanka Abeyrathne 12 Oct '20

12 Oct '20

Hi All, Is there a save scene command in ChimeraX? Thanks, Priyanka

3 3

Resources to get started with toolshed development
by Florian Wernert 12 Oct '20

12 Oct '20

Hi there, I'm looking forward to integrate a processing algorithm I coded into a toolshed for ChimeraX. Are there any available resources in order to get started with plugin/toolshed development for ChimeraX ? Thanks, Florian Wernert

2 1

Measure Motion / Blob Detection
by Scott, Brandon L. 09 Oct '20

09 Oct '20

Hello all, I had two questions: 1) I see there is now the option in measure area to ignore dusted objects, is it possible to have this feature in the measure motion as well? 2) For measure and mark blobs, Is there any way to use the output of the measure motion function to link the blobs since the triangle number changes in each frame, but following measure motion we know where it goes in the next frame. Thanks, Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor Nanoscience & Nanoengineering South Dakota Mines 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/> [South Dakota Mines on Facebook]<https://www.facebook.com/SouthDakotaMines/>[South Dakota Mines on Instagram]<https://www.instagram.com/southdakotamines/>[South Dakota Mines on Twitter]<https://twitter.com/sdsmt>[South Dakota Mines on Snapchat]<https://www.snapchat.com/add/sdsmt>

2 4

Option Include non-water HETATM in Modeller Comparative
by Marta Martinez 09 Oct '20

09 Oct '20

Hi all, I am running a very simple example in Modeller Comparative (a small alignment including the template structure and the target sequence to model). Since the template harbors a HEME group, I decided to select the Advanced option "Include non-water molecules HETATM residues from template". However, no one of the retrieved models contains the HEME group. Does anyone know what could be happening? Thanks in advance: MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

3 3

right mouse zone selection labels
by Sarah Piper 09 Oct '20

09 Oct '20

HI ChimeraX team, I really like the feature in ChimeraX that creates a map clipping zone in the right mouse tools - zone with automatic labelling. However, the default labels are black background and yellow text, and only the residue 3 letter code and number. Is it possible to change these labels to a white bg and customise the labels to include e.g. the one letter code and chain ID? I tried to do this with the selection - labels tool but it did not seem to change it for the zone labels. Many thanks and keep up the great work :) Sarah

2 2

Error "Cannot determine format for"
by Karjalainen, Mikael 09 Oct '20

09 Oct '20

Hi! I am trying to get transparent background in png pictures, but it is not working and I get error "Cannot determine format for". Only way to get this is by using command line? I am writing something like: save C:\Users\a\Desktop\k [ format png ] [ supersample 4 ] [ transparentBackground true ] or save C:\Users\a\Desktop\k format png supersample 4 transparentBackground true Also, I have tried different variations. Regards, Mikael

4 6