- ChimeraX-users - RBVI Mailing Lists

Regarding replacing Aspartate with Isoaspartate
by Protya, Satirtha 24 Jul '23

24 Jul '23

Hi Everyone, Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. I am facing a new issue. In one of my peptide PDB file, I need to change the Aspartate Amino Acid with Iso Aspartate Amino Acid. I have been trying to do so, but not sure how to do that. Is there any way or package that can do that? Please let me know. Hope to hear from you soon. Have a great day. -- Yours sincerely Satirtha Saha He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_med…> sahass(a)beloit.edu<mailto:sahass@beloit.edu> [Image][Image]

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Questions on Visualizing Chromatin Structure and Gene Expression in ChimeraX
by 刘致远 24 Jul '23

24 Jul '23

Dear UCSF ChimeraX Team, I am a big fan of your program and I have been greatly impressed with its capabilities. I want to express my deep appreciation for the "soft" visualization option provided in ChimeraX - the aesthetics truly appeal to me. I've been utilizing ChimeraX to visualize my chromatin structure data. While I'm aware this might not be one of the intended uses, when I simulated the 3D structure of chromatin as a protein's cif file, the result looked fantastic. Now I've encountered a challenge and I am hopeful that you might be able to provide some guidance. I am looking to represent gene expression as the size of the spheres in my chromatin structure, all in one figure. I am aware that Chimera has a method using "vdwdefine", essentially using the size of the B-factor to represent the atomic radius. Could you guide me on how to achieve this in ChimeraX? Furthermore, if I want to include multiple columns similar to the B-factor, how can I add them to the cif? Using the "defattr" command feels a bit cumbersome. It would be very convenient if I could pack a lot of dimensional information (such as the gene density of this chromatin segment, CG content, chromatin opening degree, etc.) into a single cif file. Do you have any suggestions or strategies on how to achieve these somewhat unconventional functionalities? Your assistance would be greatly appreciated. Thank you for your attention and I look forward to hearing from you soon. Best Regards, Zhiyuan Liu

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Fwd: depicting contacts
by Eric Pettersen 24 Jul '23

24 Jul '23

> Begin forwarded message: > > From: Krishnan Raman <RKrishnan(a)BIOCRYST.com> > Subject: depicting contacts > Date: July 24, 2023 at 9:50:11 AM PDT > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > Hi all, > Any ideas to depict a dramatic improvement(200 nm to femtomolar) in binding affinities before and after mutations(about seven) in chimerax? > II have tried contacts , swapaa etc. nothing seems dramatic enough for visuals > Thanks > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows > > > > > 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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Fwd: RFdiffusion in ChimeraX?
by Tom Ferrin 24 Jul '23

24 Jul '23

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Swapaa doubt
by Krishnan Raman 24 Jul '23

24 Jul '23

Hi, How do I use swapaa to do mutations on seven to ten residues in one command? Thanks Krish 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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L-D isomers
by Íñigo Izal Azcárate 21 Jul '23

21 Jul '23

Hi everyone, Is there any way of changing the isomerism of protein residues from L to D? I use ChimeraX with students and it would be great to see what happens with some features of the structure like hydrophobicity after changing isomers. Thanks so much in advance Iñigo Izal Azcárate Personal de Apoyo a la Docencia, Coordinador del programa Science and Business Departamento de Bioquímica y Genética T: 948 425600, ext 6321 inizal(a)unav.es -- *Este mensaje puede contener información confidencial. Si usted no es el destinatario o lo ha recibido por error, por favor, bórrelo de sus sistemas y comuníquelo a la mayor brevedad al remitente. Los datos personales incluidos en los correos electrónicos que intercambie con el personal de la Universidad de Navarra podrán ser almacenados en la libreta de direcciones de su interlocutor y/o en los servidores de la Universidad durante el tiempo fijado en su política interna de conservación de información. La Universidad de Navarra gestiona dichos datos con fines meramente operativos, para permitir el contacto por email entre sus trabajadores/colaboradores y terceros. Puede consultar la Política de Privacidad de la Universidad de Navarra en la dirección: **https://www.unav.edu/aviso-legal* <https://www.unav.edu/aviso-legal>**** ** ** *This email message may contain confidential information. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. The personal information included in email messages exchanged with employees of the University of Navarra may be stored in the database of your interlocutor and/or the servers of the University for the time-period stipulated by its internal information storage policy. The University stores such data for purely administrative purposes, to facilitate e-mail contact between its employees and third parties. The University of Navarra Privacy Policy may be accessed at https://www.unav.edu/aviso-legal <https://www.unav.edu/aviso-legal> ***** ** ** _Antes de imprimir este mensaje o sus documentos anexos, asegúrese de que es necesario. Proteger el medio ambiente está en nuestras manos. Before printing this e-mail or attachments, be sure it is necessary. _It is in our hands to protect the environment.__

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Re: Chimera X: Protein-Ligand Docking
by khawar siddiqui 21 Jul '23

21 Jul '23

Hi Tom,We were wondering if it is possible to include Protein-ligand docking in the next ChimeraX version. That will benefit lots of researchers also by having it within the same package. Thanks and best wishes Dr K Sohail Siddiqui,School of Biotechnology and Biomolecular Sciences (BABS),Room 420, Building D26,The University of New South Wales (UNSW),Randwick, High Street, Sydney, Australia. NSW 2052Office: +61 2 938 55193email: z3030204(a)ad.unsw.edu.au; sohailsiddiqui1995(a)yahoo.com best wishes Dr Khawar Sohail Siddiqui On Friday, 7 July 2023 at 11:25:48 am AEST, khawar siddiqui <sohailsiddiqui1995(a)yahoo.com> wrote: Hi Tom,That will be really great if the next ChimeraX version has the Animation tool so less experienced researchers who find command line difficult can prepare protein structure movies using simple clicks. Thanks a lot for considering the suggestion. Waiting eagerly for the next version with animation tool.The ChimeraX is an amazing visualization tool. Best wishesSohail Sent from Yahoo Mail for iPhone On Friday, July 7, 2023, 5:15 am, Tom Goddard <goddard(a)sonic.net> wrote: Hi Sohail, We have funding to develop a ChimeraX animation tool like the one in Chimera but better. It is part of a 4 year NIH grant that started about 9 months ago that funds a lot of the ChimeraX development. We have not started on the animation tool and it will probably take about 6 months to develop once we start on it. Tom On Jul 4, 2023, at 11:46 PM, khawar siddiqui via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: Hi Developers,ChimeraX is a great tool for protein researchers and a vast improvement on the previous Chimera. However, ChimeraX has one limitation for users who dislike command lines. Kindly incorporate the Animation movie maker facility in a New Version under Tools/utilities as was in the previous version. It was so quick and simple by using GUI. Thanks a lot Dr K Sohail Siddiqui,School of Biotechnology and Biomolecular Sciences (BABS),Room 420, Building D26,The University of New South Wales (UNSW),Randwick, High Street, Sydney, Australia. NSW 2052Office: +61 2 938 55193email: z3030204(a)ad.unsw.edu.au; sohailsiddiqui1995(a)yahoo.com Sent from Mail for Windows _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu Manage subscription:

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Regarding Usage of ChimeraX for PDB file creation
by Protya, Satirtha 21 Jul '23

21 Jul '23

Hello, Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. Currently, I am using ChimeraX for one of my research projects. I need to build structures and download the PDB files. I can do that for all L amino acid containing peptides, but I don’t know how to use ChimeraX for D amino acid containing peptides. For example, I have a sequence NWF. Now it is available in this standard L format and also in NdWF format. As ChimeraX is not case sensitive, I don’t know how I should give the command to build the structure with D amino acid containing peptide. Secondly, I have some peptides that have Amidation or NH2 at the C terminus. I don’t know how to add this to my structure. Please let me know how to solve this to issues. That will be really helpful for me. Have a great day. -- Yours sincerely Satirtha Saha He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_med…> sahass(a)beloit.edu<mailto:sahass@beloit.edu> [Image][cid:image002.png@01D9BB19.9CD8CA10]

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Matching ChimeraX color with the Adobe illustrator colors?
by Rayees Mattoo 20 Jul '23

20 Jul '23

Dear ChimeraX users, I am trying to match the colors of ChimeraX model to the Adobe illustrator drawing. I used Web safe colors to color my model in chimeraX and then used the same hex codes in the illustrator, but the colors did not match. Any thoughts or workarounds would be appreciated. Best Rayees

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Re: Opening MTZ Files
by Elaine Meng 20 Jul '23

20 Jul '23

Hi Natalie, Everything I know on this topic is written in the documentation linked below, and yes, as it says therein, you do need to have Clipper installed. Then title of the section is "Open/Save Options from Clipper": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper> I can't think of anything else to say without getting more details from you. What is the problem? Which part are you confused about? What did you try? What happened? Did you follow the instructions in the link? Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 6, 2023, at 9:14 AM, Natalie Walsh <natalie.walsh(a)slu.edu> wrote: > > Hello, I previously asked a question (sent to the wrong email, oops!) about not being able to use MTZ maps in Chimera X (I was using 1.17.1, I just installed 1.17.2 today and still have the same issues). These were the instructions previously provided: > > "The instructions of how to open MTZ files with ChimeraX are here: > > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/comman… > > > "Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc." > > I read through the like and am still confused. I have also installed the Clipper Plugin (although I am unsure if it was installed correctly) since I saw somewhere that might be needed. > > Thanks, > Natalie Walsh

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Running ChimeraX in batch mode on Mac OSX
by Enrico Martinez 20 Jul '23

20 Jul '23

Hello Greg, In addition to my previous message regarding running Chimera-X on Ubuntu, I have a similar question regarding MacOSX. In fact I have a macbook pro equipped with the Mojave (10,14.16) which I used with ChimeraX-1.3 that worked well in no-gui mode (without any additional flags like --offscreen). I've tried more recent releases of Chimera-X and found that it has not worked with Mojave. Anyway, if I do an update would it be possible to use the latest ChimeraX on Mac without gui ? Many thanks in advance Enrico

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colour palette of multiple models
by Enrico Martinez 20 Jul '23

20 Jul '23

Dear Chimera-X users ! I am performing visualisation of multi domain protein loaded in the Chimera-X as different pdbs. In the model panel each pdb coloured differently according to the model ID and everythings is OK for the first 11 models, while starting from the 12th all of them are colored in green (please see the screen-shot). Would it be possible to quickly change the auto-colouring of the multiple pdbs when I load all of them directly using chimerax workdir/*.pdb ? Many thanks in advance Enrico

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Running ChimeraX in batch mode in the Ubuntu terminal
by Enrico Martinez 20 Jul '23

20 Jul '23

Dear ChimeraX users ! I have a quick technical question. Typically I run ChimeraX with a batch script in order to perform some manipulation with input pdb and print the output image / save chimera-X session. In my Ubuntu terminal I run it using: chimerax script.cxc where the script could be something like : ### open input.pdb # do some manipulation like view, orient etc save image.png exit ## It works OK but, while running from linux terminal I have a quickly open-closed Chimera-X window which is not very practical when I put this script in loop etc. Is there any possibility to fully suppress the Chimera-X gui when I run my script in batch mode from the terminal? Many thanks in advance Enrico

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Feature request: support for MRC mode 12 (float16)
by Ricardo Righetto 20 Jul '23

20 Jul '23

Dear ChimeraX team, It seems that ChimeraX (tested version 1.6.1) does not yet support MRC data mode 12, corresponding to half-precision floating point (float16). This data mode is now supported in RELION-4 and IMOD, and is interesting to save storage in cryo-ET and subtomogram averaging workflows. Would it be possible to implement support for reading and writing this MRC data mode in ChimeraX? Thank you! Best wishes, -- Ricardo Diogo Righetto

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Q3 Score Calculation Tool ChimeraX that is similar to MapQ Plugin in Chimera
by Thu Nguyen 19 Jul '23

19 Jul '23

Good afternoon, I am calculating the Q-Scores in cryo-EM density maps and found the MapQ Plugin <https://github.com/gregdp/mapq> in Chimera that does Q3-score calculation and visualization. I wonder if we have a similar plugin in ChimeraX that does Q-score calculation? Thank you very much. Best regards, Thu

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Autodock Vina at ChimeraX
by ODA Natsuki 19 Jul '23

19 Jul '23

Dear all, Thank you for providing the license for ChimeraX. I have a question about ChimeraX for using Autodock Vina. Is it possible to use Autodock Vina at ChimeraX? I used to use Autodock Vina at Chimera before version of ChimeraX. I want to use Autodock Vina, so would you ask me the methods? Sincerely you. Natsuki ------------------------------------------------------------------ Name: Natsuki Oda Affiliation: Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University Student ID: number 1234521019 E-mail: oda.natsuki.i0(a)s.gifu-u.ac.jp ------------------------------------------------------------------

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Question about energy minimization
by Luca Massaccesi 18 Jul '23

18 Jul '23

Dear Chimera team, Can you please tell me if it’s possible to do energy minimization with Chimera X as I used to in previous Chimera? I looked for it on the Chimera X page and in many tutorials but it looks like this tool was cut out of the software. Thank you very much for your help, Luca

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view command to re-orient scene
by Enrico Martinez 17 Jul '23

17 Jul '23

Dear Chimera-X users! I would like to perform visualisation of the pre-oriented objects from a set of PDB filles. Briefly I load 20 pbs in chimera-x and the scene what I see, is depicted on the "initial.png" image attached to the mail. Then I need to orient it automatically in order that the scene would be perfectly parallel to the screen plane, as shown in the second enclosed image. What options for view command could be used to orient the object in the same way ? Many thanks in advance Enrico

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mcopy command
by Matzov Donna 17 Jul '23

17 Jul '23

Hello, I'm trying to use the mcopy command (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mcopy.html) as such: mcopy #1 toAtoms #2 settings a However, I get the following error message: Unknown command: mcopy #1 #2 settings a Am I using the wrong syntax? I am using the latest chimerax release. Thanks, Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab<https://www.weizmann.ac.il/Structural_Biology/Shalev-Benami/home>

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Slowing down a movie
by Leyre Marin Arraiza 17 Jul '23

17 Jul '23

Dear ChimeraX, I want to make a movie using ChimeraX, in which I can see the map of my protein complex rotating 360 degrees, plus a full rotation of the same map after zooming in. I managed to do so with the following command: movie record ; turn y 2 180 ; wait 180 ; zoom 1.5 ; turn y 2 180 ; wait 180 ; movie encode However, in the final .mp4 file I get, the rotation is quite fast. I would like to create the same movie, but with slower rotation. I have tried figuring it out reading through the guide and trying different commands, but I am not successful. Could you help me with this issue? Thanks in advance Best regards, Leyre Leyre Marin Arraiza PhD fellow University of Copenhagen Novo Nordisk Foundation Center for Protein Research Taylor Group Blegdamsvej 3B, Building 6, 6-1-10 2200 København N leyre.arraiza(a)cpr.ku.dk<mailto:leyre.arraiza@cpr.ku.dk> [CvwfJbQuv4S75bEAAAAASUVORK5CYII=] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

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bond: merging two models within new model
by Enrico Martinez 17 Jul '23

17 Jul '23

Dear Chimera-X users ! I need to fuse two models in the entire construction. Precisely having a water soluble domain with a linker in the first model #1 as well as transmembrane alpha helix segment in the #2 I load the both in chimera-x and then use the bond command with the aim to create a peptide bond between the last residue of the #1 and the first residue of the #2. Here is my command: # select the last residue from the core and the first residue from the TM helix; build join peptide #1:182@C #2:1@N move large The problem is that on the text step I will need to add the membrane in the TM part, but the orientation of the created construction is not optimal. How could I easily modify the mutual orientation between #1 and #2 ? I join the both initial pdbs to this message, in order that my model could be checked :-) Many thanks in advance Enrico

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Re: [Chimera-users] Chimera-X inteprhase of the AlphaFold
by Tom Goddard 17 Jul '23

17 Jul '23

Hi Enrico, The ChimeraX AlphaFold interface does not allow specifying your own structure template. But the ColabFold web server does allow this https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/Alph… using "template mode: custom" on that web page and follow instructions they list on that page for using custom templates https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/Alph… I have tried custom templates with AlphaFold in the past and it has never changed the predicted structure. AlphaFold only uses the template as a first guess at the structure then it does multiple rounds (by default 3 recycles) of creating new models. If AlphaFold is pretty confident about a different conformation than the template it simply replaces the starting structure with the conformation it prefers. Possibly if AlphaFold has low confidence in a prediction a template could bias it to get a different conformation but I've never seen that happen. This is a basic limitation of AlphaFold that it is not designed to optimize an existing structure. The input that dominates the calculation is the sequence and the deep sequence alignment that it computes, not template structures. Possibly AlphaFold could be prodded to predict different conformations by changing the deep sequence alignment to include just the sequences known to fold in the desired conformation and excluding sequences known to fold in a different conformation. Tom > On Jul 13, 2023, at 3:43 AM, Enrico Martinez via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera-X users! > > In parallel to the modeller, I am trying to use the Alpha fold > interface with the aim to full model starting from the sequence using > template. > > The problem is that I can not define manually which template I would > like to use for each prediction so the interphase takes its > automatically based on the input sequence and the final prediction is > not very precise. Would it be possible rather to specify a specific > pdb ID additionally to a given sequence ? > > Many thanks in advance > > Enrico > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ >

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ChimeraX in Debian v-12
by Stephen P. Molnar 15 Jul '23

15 Jul '23

I would lie to install ChimaeraX on my Debian v-12 desktop. However, he installer requires libffl7 which is not available. Please advise. Thais in advance -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

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Re: [Chimera-users] hiding a model slowly in ChimeraX
by Elaine Meng 14 Jul '23

14 Jul '23

Hi Andy! I added "in ChimeraX" to the subject line to make it more obvious to the Chimera users. We recommend sending ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to re-send) instead of chimera-users so that people don't get confused between the two programs - thanks! Here are some thoughts on how to do it in ChimeraX: (1) is anything in the view moving (rotation, translation, conformational change) while this model fades? If not, you can simply use "crossfade" or if you are recording a movie anyway, better to use "movie crossfade", in the script between where the model is shown and where it is hidden. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade> (2) if you want motions of the view or of individual models at the same time as the fading, then crossfade won't work. Instead you have to do something fancier. Instead of hiding the model you could try gradually changing its transparency from 0% to 100% over some number of frames. This requires combining the "transparency" command with a "perframe" command to iterate over different transparency levels, since you don't want to have to put in 100 (or more) transparency commands. For example, if the model is currently completely opaque (0% transparent) then you can make it completely transparent (100% transparent) over 240 image frames with something like roll y 0.1 perframe 'transparency #7 $1 target abcsp' range 0,100 frames 240; wait 240; ~perframe The "roll" command is only included above as an example so you can see how this fading works during motions. See the help pages for "transparency" and "perframe": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html> However, it will require experimentation with how you specify the other commands for the motion (view, turn, roll, zoom, coordset, etc.) in your command script to make this fading happen at the same time as those motions. Even experts don't get their movie scripts right on the first try; I usually have to change and re-run my script several times. I don't even add the movie-recording commands until after I get all the motions and display changes right. Carrying on from the example above, you can stop the roll and make the model opaque again with something like stop transparency #7 0 target abcsp You stay safe too! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 14, 2023, at 3:09 PM, Sen, Anindito via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera X team, > > Is there a way I can hide one of the models in a ChimeraX session slowly (like fading it off) while making a movie. > > typically I use > > hide #7 model > > Stay safe & Regards > > Anindito Sen. Ph.D > > Microscopy and Imaging Center > Texas A&M University > 301 Old Main Dr > College Station, TX 77843-2257 > > Office: ILSB Room 1133 > Tel. 979-458-9881 > fax: 979-847-8933 > http://microscopy.tamu.edu

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getting RSCC validation scores
by Das, Abhinaba 14 Jul '23

14 Jul '23

Hi ChimeraX community: I’m trying to get real space correlation coefficient value of map-model fit as done in this paper from DiMaio’s group https://elifesciences.org/articles/17219 (Table 2, RSCC validation map column). It is possible to do so in Chimera but I’m not sure how. Although the alternative might be the Map-Q & Q-score plugin in chimera (or Model-Map Q score in ChimeraX) from Greg Pintilie which “uses a real-space correlation approach to assess the resolvability of each model atom in the map” (-http://doi.org/10.1038/s41592-020-01051-w), I would like to get the RSCC values. Is it possible to obtain those values? Thanks in advance for any advice. -abhi

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