- ChimeraX-users - RBVI Mailing Lists

Question Regarding rangecolor kdHydrophobic command
by Knotts, Garrett 29 May '24

29 May '24

Good morning, I am in the process of switching over from Chimera to ChimeraX. I have found ChimeraX to be incredibly more user friendly and well-designed. I wanted to reach out regarding the rangecolor kdHydrophobic command. I often use this command in chimera to color protein surfaces based on hydrophobic character. However, we have a color scheme which our lab has consistently used. In the switch from Chimera to ChimeraX, I have not found a way to color by hydrophobicity with our color scheme using this or other commands, but I have found a way to color hydrophobic regions onto surfaces, without the ability to change the colors. Is there a way to do this in ChimeraX? Thanks for the help! Best, _______________________________ Garrett Knotts Undergraduate Lab Assistant (Johnson Lab) Legislative Director of the Mississippi State University Student Association Vice President of Honors Ambassadors Sigma Phi Epsilon Learning Community Coordinator [cid:8783bc97-b3f7-4f42-85c5-130c16ad956f]

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Behavior of "cd" when executed through a script
by Vorländer,Matthias Kopano 29 May '24

29 May '24

Dear ChimeraX team, I have a series of scripts that contain a “cd” statement to set the working directory. I execute the scripts (which opens a model and map and colors the map). I then manually adjust the orientation and threshold and want to save a picture with “save map.png” (I want this png tp be saved in the folder that I set with the script). I have noticed that in this scenario ChimeraX has “forgotten” the cd statement from the script file and has fallen back to default working directory (or the last working directory manually set in the session before I exectuted my script). At least for me it would be more convenient and logical if the working directory can be set and maintained after habing executed a script. Note: if I don’t execute the script by double clicking but by copy/paste, the working directory is correctly maintained. Would be great if the behavior could be adjusted 😊 Many thanks and best wishes, Matthias

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Command not found from cxc file v1.7.1 on M2 Mac
by Hong Glenn Meng ZHAN 29 May '24

29 May '24

Evening all, I was trying to color code my imod models based on their volume (see attached). It worked ok for me just one model file opened in ChimeraX. When I was doing anther model file, I can passed the individual command in the command line to change color: color #1.1 #ceecc8 However, when I generate a cxc file and open it from command line or click on Open, it showed Unknown command: color #1.1 #ceecc8 Any input where I was not doing correctly? Thanks for helping! -Hong [Screenshot 2024-05-28 at 11.22.11 PM.png][image2.png]

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Python scripting for Dipole moment calculation
by andreumormaldon＠outlook.com 28 May '24

28 May '24

Hi all! I am trying to calculate the dipole moment of different proteins at different pH values. The .pdb and .dx files are generated with pdb2pqr and apbs software. I have found a script that is written for chimera, but it seems that the modules are not translated to ChimeraX, or at least I am not able to make it work. So I have decided to try to write my own script. So far I am able to obtain the center of mass of the protein as well as the charges of all the atoms in the molecule, but I cannot find a way to build a vector to where calculate the dipole (as it is done in the chimera script). Can anyone give me some insights? Does ChimeraX have as well the class Vector and Point? Thank you very much for your help! Best, Andreu

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Is it possible to set attribute on chain via Python script?
by Artie Kushner 27 May '24

27 May '24

I apologize in advance if this is off topic. I heard that people use chimerax mailing list to share tips and ask for help and saw some archives online that came in handy. I'm wondering if it's possible to set an attribute on the whole atomic chain (for future byattribute coloring) the way it is done in the example with Atom/Residue ? ( https://rbvi.github.io/chimerax-recipes/helixmlp/helixmlp.html) I'm trying something similar in my script: ``` from chimerax.core.commands import run from chimerax.atomic import Residue, Atom, Chain # the regular Cmd setup.. c:Chain polyclass:str = ... input from external spruce c.polymer_class = polyclass Chain.register_attr(session, 'polymer_class', 'Polymer Class', attr_type = str) ``` But when i run `color byattribute polymer_class /6 palette lipophilicity` it's not getting picked up: `No known/registered numeric attribute polymer_class`. Maybe it's not possible to color by string attributes? Thanks a lot for your advice Artem

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Morph Trajectory to smooth motion
by Alexander Hung Lee 26 May '24

26 May '24

I've morphed between a series of models/submodels to create a smooth trajectory but is it possible to morph a loaded trajectory that's topology and trajectory file (.nc)? Or is there another way to smooth the motion of it if morph is just to create a trajectory between models? Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Surface caps not drawn in script
by Daniel Asarnow 24 May '24

24 May '24

Hi Tom/Elaine, I have a series of models with SES surfaces and per-model clipping, and I am trying to create figures for each in a script with several blocks like the following: hide target m show #1 target ms save fig1.png If I run the commands myself, the figures are as expected, but when I run the script / copy and paste several of these blocks, the surface caps aren't drawn. Am I missing something? Or can I trigger the caps somehow? Thanks! Best, -da

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Re: Reg. alphafold contacts maxPae parsing
by Greg Couch 24 May '24

24 May '24

HI Anthony, Please send all ChimeraX question to the chimerax-users mailing list, so the appropriate person can answer you. While in general I am not involved with the alphafold support, in this particular case, I believe the answer is to use the current ChimeraX release candidate or daily build. Alphafold 3 changed the PAE format, so new code had to be written. And that has been mentioned on the mailing list, so if you are not already a member, I recommend joining. -- Greg On 5/24/2024 6:24 AM, Antony Merlin Jose wrote: > Dear Greg, > I have been using the alphafold contacts to parse the .pkl files to > show the pseudobonds in ChimeraX (e.g., alphafold contacts #1/A to > #1/B maxPae 5 distance 6). The .pkl files were generated from a > locally installed Alphafold 2.3. Now that there is an AlphaFold 3 > server, (https://golgi.sandbox.google.com/) I ran some complexes on > there and downloaded the results. The results include .json files that > have the PAE information. Would using the same commands with this file > also result in the correct parsing of the PAE values? How can I see > the python code that corresponds to each command on ChimeraX? > Thank you > Best, > Antony >

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Zn fingers
by Dyda, Frederick (NIH/NIDDK) [E] 24 May '24

24 May '24

I have a structure with some Zn fingers. How can I describe the Zn2+ tetrahedral environment for Isolde? Cryo EM density is less than spectacular... Thanks. Fred ******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 NIDDK Bldg. 5. Room 338 e-mail: Fred.Dyda(a)nih.gov Bethesda, MD 20892-0560 URGENT message: 2022476710(a)msg.fi.google.com Google map: 39.001168, -77.102048 http://www-mslmb.niddk.nih.gov/dyda/dydalab.html *******************************************************************************

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Fwd: some more clarifications on this?
by Eric Pettersen 23 May '24

23 May '24

> Begin forwarded message: > > From: Krishnan Raman <RKrishnan(a)BIOCRYST.com> > Subject: some more clarifications on this? > Date: May 23, 2024 at 8:22:08 AM PDT > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > Aligning two VR headsets in one room. Two Vive or Vive Pro VR headsets can be used in the same room, each connected to its own computer. Each headset uses the same pair of base stations. A problem sometimes arises that the two headsets do not see the ChimeraX structures displayed at the same location in the room. Specifically, one headset may see the structure positions as if the room is rotated 180° relative to the other headset. This happens because the SteamVR room setup is run separately on each computer and produces a different coordinate system. For structures to have the same room position in both headsets, the room boundaries traced using SteamVR room setup should be the same for both computers. The first step of SteamVR room setup in which users are asked to point the hand controller at the screen and click is the key to avoiding 180° misorientation. At that step, it is important to point along the short axis of the rectangle defining the room bounds (that will be traced in a later step). SteamVR chooses between two coordinate system orientations rotated 180° from each other based on the direction of pointing. If pointing is along the long axis of the rectangle bounds, a slight tilt toward the left or right of the long axis produces opposite coordinate system orientations. Pointing along the short axis instead is a reliable way to make both computers use the same orientation. (The computer screen position is irrelevant.) > > https://www.cgl.ucsf.edu/chimerax/docs/user/commands/meeting.html#:~:text=T… <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/meeting.html#:~:text=T…>. > > I was successful in doing a hybrid meeting with one 2d monitor and one VR headset (quest pro) -air linked. I do see that my images in the VR are rotated by 180 deg. With respect to the 2d monitor. Do I still have to run steam vr on both computers to bring them into same coordinate system? > > > > Krishnan Raman > Executive Director, Structural Biology > BioCryst Pharmaceuticals > > > > > CONFIDENTIALITY NOTICE > > This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >

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Re: Replies from mailing list not send to inbox
by Alexander Hung Lee 23 May '24

23 May '24

In reply to Elaine Meng, I went to this link but it already confirmed "Member already subscribed." I also didn't get a direct email from you even though you included my individual email address. Currently replying by going to the mail archive and clicking the reply button in the thread. https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimerax-users.cgl.ucsf.ed… Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Re: Match atoms
by Alexander Hung Lee 23 May '24

23 May '24

Thanks Elaine! Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Replies from mailing list not send to inbox
by Alexander Hung Lee 23 May '24

23 May '24

Hi everyone, Earlier I had sent a help request "Match Atoms." After looking in the online mail archive, I found that I received replies to my problem, but didn't get an email. How do I fix this? I accidentally sent the email again thinking it wasn't received... Sorry, Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Match atoms
by Alexander Hung Lee 22 May '24

22 May '24

Hi everyone, I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix" tl;dr. Trying to align ring atoms of a ligand instead of protein chain Chimerax mask 1 = #1:203@C19,C20,C21,C16,C17,O18 mask 2 = #2:125@C2,C3,C4,C5,C6,O6 matchmaker: No matrix compatible with both reference structure and all match structures match: Same as above. In reply log, match is extended to matchmaker Chimera mask 1 = #0:203@C19,C20,C21,C16,C17,O18 mask 2 = #1:125@C2,C3,C4,C5,C6,O6 matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix match: Gives me RMSD ** I need this atom match functionality in ChimeraX Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Fwd: Uncaught bounce notification
by Eric Pettersen 22 May '24

22 May '24

> Begin forwarded message: > From: Allen Place <place(a)umces.edu> > Subject: Re: Your message to chimerax-users(a)cgl.ucsf.edu awaits moderator approval > Date: May 16, 2024 at 5:11:31 AM PDT > To: chimerax-users-bounces(a)cgl.ucsf.edu > > > Help with commands. I know how to Select regions in my protein sequence, but How do I select different colors for those selections? These are various modules that I have assigned prior to the prediction based on homology. > Al > > >> On May 15, 2024, at 9:45 AM, chimerax-users-bounces(a)cgl.ucsf.edu wrote: >> >> Your mail to 'chimerax-users(a)cgl.ucsf.edu' with the subject >> >> Alphafold3 models >> >> Is being held until the list moderator can review it for approval. >> >> The message is being held because: >> >> The message is not from a list member >> >> Either the message will get posted to the list, or you will receive >> notification of the moderator's decision. > > Allen R. Place(he/him/his) > Professor, Associate Director of Research, > Director of BASLab, Director of HAB-CTI > Institute of Marine and Environmental Technology > University of Maryland Center for Environmental Sciences > The Rita Rossi Colwell Center > 701 East Pratt Street > Baltimore, MD 21202 > 410-234-8828 > place(a)umces.edu > > ALAN, ALLAN, ALLEN > From the Gaelic word for “cheerful” > > He is smart, makes friends easily, and never loses his sense of humour. > > He thrives on a challenge > > > Sign up to receive our quarterly newsletter, Inside IMET! > > >

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Improvement suggestion
by Lionel Carlo Clarens 22 May '24

22 May '24

Dear User List, I am a frequent user of ChimeraX. Currently, the only way to create animations is via the command line. In contrast, the older Chimera version has an intuitive, user-friendly interface for making simple and effective animations. It would be an excellent and straightforward improvement to migrate this functionality from Chimera to ChimeraX, as I currently need to use both software. Best regards, Lionel C.

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question about using ChimeraX
by 天剑流痕 21 May '24

21 May '24

This chimerax software is very useful. Could you please tell me how to connect two amino acid residues or atoms in the protein 3d diagram 天剑流痕 475514296(a)qq.com  

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Sign up for the user group's email list
by Md Saiful Islam - MRC LMB 20 May '24

20 May '24

Hi Is it possible please to add me to the Chimera X user group's email list. Cheers Saif

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Doubt
by GOTZONE BARANDIKA 19 May '24

19 May '24

Dear developers, I am a new user of ChimeraX. I need to create dimers in order to analyse adsorbate-adsorbant interactions for DFT calculation. I am able to create the image on the screen, but I don´t know how to save the atomic coordinates of the dimer in a single file. If I save a .pdb file in order to produce a .xyz file, just the information of one of the entities is kept. Can you please help me? [cid:image003.jpg@01DAA921.4F8EE270] Best regards, [Diapositiva1]

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How to copy fitted monomer in a symmetric map?
by Noha Elhosseiny 18 May '24

18 May '24

Hi, I have a map with C15 symmetry in which I already refined the fitting of a single monomer (asymmetric unit) in the map using coot. I now want to generate the complete 15-mer atomic model. I watched your tutorial : ( https://youtu.be/v3jI43YJQMg?si=WeQg2ef2MPOw2J7H) and I tried to use the command "sym #2 (my model) C15 to do that, but instead of getting the monomers fitted around the axis of symmetry, I could see that 15 versions were visible but in a circular circumference around my map, away from the center, and the monomers are widely spaced from one another. I kind of expected this because I did not specify any coordinates to do this copying, so how can I fix this? Another question: when I use the command "measure symmetry" I get "C3, center 270 270 244". So I do not understand why it's detecting a C3 when it's clearly a C15. I think the above coordinates of the center can be used to solve my fitting problem but I am not exactly sure how. Finally I understood that even if the monomers appear properly fitted, given I manage to do it, that these are just graphical copies. So how can I then make real copies of the graphical representation of the 15-mer? Thanks Noha -- *Noha M. Elhosseiny, PhD* Department of Microbiology & Immunology Faculty of Pharmacy, Cairo University. Kasr El-Ainy St, Cairo, Egypt, 11562- Lab C-407 Website: https://eg.linkedin.com/in/nohaelhosseiny <https://eg.linkedin.com/in/nohaelhosseiny>

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Re: Displaying surface model of blob clostest to a centroid
by Tom Goddard 17 May '24

17 May '24

Hi Yoseph, So you have a volume and you have markers shown in ChimeraX and you wanted to show only the connected surface piece from the volume contour surface that is closest to a specific marker? Do I have that right? You show in your image a lot of markers, but you only want to find the surface piece close to one of them? And you just want to show it and hide all the other parts of the surface? What if the closest surface piece is far away? Or what if a tiny spec of surface is close, but a bigger surface piece is nearby? I think that would require writing some Python code. There is nothing in ChimeraX that I can think of that computes connected surface pieces that are close to a marker. Did you consider just showing a zone of the surface around the marker out to a certain specified distance? The ChimeraX surface zone command does that, described here https://www.cgl.ucsf.edu/chimerax/docs/user/commands/surface.html#zone Tom > On May 17, 2024, at 4:05 PM, Yoseph Loyd <yoseph.loyd(a)mines.sdsmt.edu> wrote: > > Hi Tom, > > Sorry I was having a difficult time uploading an example image to the form. I'll attach it below, I'm displaying tracked centroids as small spheres. I was hoping that there existed a way to display the nearest yellow blob to the tracks I care about. The yellow blobs signal wise are full binary objects. Thank you for helping me with this. > > Best, > Yoseph > > On Fri, May 17, 2024 at 4:43 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Yoseph, >> >> I don't know what you mean "objects that fit to a centroid that I've tracked". What kind of object? The centroid of what? And why isn't it displayed currently? You'll have to explain better. >> >> Tom >> >> > On May 17, 2024, at 2:07 PM, Yoseph Loyd via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Hi, >> > >> > My name is Yoseph, I was wondering if there is a way to display objects that fit to a centroid that I've tracked and imported into chimera. Thank you for taking the time to read this and have a nice day. >> > >> > >> > Best, >> > Yoseph >> > _______________________________________________ >> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> > >>

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Displaying surface model of blob clostest to a centroid
by yoseph.loyd＠mines.sdsmt.edu 17 May '24

17 May '24

Hi, My name is Yoseph, I was wondering if there is a way to display objects that fit to a centroid that I've tracked and imported into chimera. Thank you for taking the time to read this and have a nice day. Best, Yoseph

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Re: [Chimera-users] Saving symmetry model in pdb format
by Elaine Meng 17 May '24

17 May '24

Hi Kailash Singh Bisht, You sent the message to chimera-users which is for Chimera questions. However, you said "ChimeraX team" so I am guessing that you are actually using ChimeraX, and I CC'd the chimerax-users address above -- please use that one for ChimeraX questions. You didn't say how you created the symmetry structure. I am guessing that when you create the symmetry structure with the "sym" command, you need to include the option "copies true" so that you get real atomic copies instead of just graphical clones. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On May 17, 2024, at 12:27 AM, Kailash Singh Bisht via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello ChimeraX team > > I am trying to export the symmetry structure of the protomer virus protein as a pdb file but whenever I am saving that model it only saves the same protomer instead of the whole symmetry structure. Can you please help? How to export those symmetry models as PDB files > > -- > With Regards > Thanking You > > Kailash Singh Bisht > Ph.D. Student

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prediction of 5mC modification and transcription factor interaction through AlphaFold 3
by Kaan Okay - HI 17 May '24

17 May '24

Hi, I use Alphafold through UCSF ChimeraX. It is a very nice tool, I believe its developers have done a good job. As you know, AlphaFold 3 is a new model that allows us to predict DNA modification and protein interactions (https://www.nature.com/articles/s41586-024-07487-w) What I wonder is when this model will be transferred to UCSF ChimeraX and whether we can predict protein interactions and DNA modifications (e.g., 5mC modification on cytosine bases in DNA). I'm looking forward to hearing from you. All the best.

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Cinematographic effects in MD movie recording
by Enrico Martinez 17 May '24

17 May '24

Dear Chimera-X users ! I would like to add some cinematographic effects such as changing the camera angle back and forth during a short recording time of MD movies. Could you suggest some scripting tricks that I could add to the following coordset routine: # start recording movie record size 3840,2160 supersample 1 ## play movie from beginning to the end coordset #1 1,1000,1 wait 1000 etc Would it be possible to bend the camera automatically e.g. during the first 250 steps of recording ? Any other possibilities ? Yours with thanks Enrico

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