May 2024 - ChimeraX-users - RBVI Mailing Lists

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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