July 2023 - ChimeraX-users - RBVI Mailing Lists

Download ChimeraX
by songlu 26 Jul '23

26 Jul '23

Dear ChimeraX developers, Thank you for taking the time to read my email. I have a question about downloading ChimeraX and I hope you can help me. When I downloaded the MacOS version of the ChimeraX1.6 on the official website, I found that the download always failed. After trying to switch the browser and the network, it still doesn't work. Perhaps you can help me solve the problem or send me the installation package for the MacOs version of the ChimeraX1.6. I would greatly appreciate it. Looking forward to your reply. Sorry again for the delay in your valuable time. Wishing you a pleasant day. Yours respectfully, Songlu

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transparency for different selection
by Enrico Martinez 26 Jul '23

26 Jul '23

Dear ChimeraX users! I am dealing with the visualization of protein embedded into the plasmatic membrane (composed of water and lipids). Here is my script preset publication 1 rainbow protein palette $palette # for protein surface protein #color protein cornflower blue transparency 95 target s # for lipids surface :OL,PA,PE color :OL coral target s color :PA coral target s color :PE orangered target s hide bonds; hide atoms transparency 55 target s 1) I would like to set different values of the transparency for the surface of lipids and protein. For the moment I found only one possibility to set the transparency for the whole surface indicated above. Would it be possible to selectively apply a transparency command on the particular selection of the system ? 2) how would it be better to visualize the water in the same system in order to maintain the visibility of the protein ? Many thanks in advance Enrico

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How do you refine a structure with a new (or modified) amino acid residue in Isolde
by Trevor Sewell 25 Jul '23

25 Jul '23

Hi Everyone, I am adding residues (essentially modified cysteines ) to the polypeptide chain. e.g. HETATM 1 N2 PGR 0 1.743 -1.624 -0.731 1.00 0.00 N HETATM 2 C1 PGR 0 -0.077 -0.207 -0.018 1.00 0.00 C HETATM 3 C2 PGR 0 1.394 -0.544 0.203 1.00 0.00 C HETATM 4 C3 PGR 0 -0.485 0.927 -0.717 1.00 0.00 C HETATM 5 C4 PGR 0 -1.034 -1.073 0.503 1.00 0.00 C HETATM 6 C5 PGR 0 -1.840 1.189 -0.887 1.00 0.00 C HETATM 7 C6 PGR 0 -2.389 -0.810 0.331 1.00 0.00 C HETATM 8 C7 PGR 0 -2.794 0.323 -0.364 1.00 0.00 C HETATM 9 C8 PGR 0 2.379 0.585 -0.085 1.00 0.00 C HETATM 10 H1 PGR 0 1.529 -0.961 1.213 1.00 0.00 H HETATM 11 H2 PGR 0 0.232 1.599 -1.120 1.00 0.00 H HETATM 12 H3 PGR 0 -0.727 -1.940 1.035 1.00 0.00 H HETATM 13 H4 PGR 0 -2.145 2.053 -1.418 1.00 0.00 H HETATM 14 H5 PGR 0 -3.116 -1.477 0.733 1.00 0.00 H HETATM 15 H6 PGR 0 -3.837 0.527 -0.497 1.00 0.00 H HETATM 16 H7 PGR 0 1.655 -1.298 -1.705 1.00 0.00 H HETATM 17 H8 PGR 0 1.143 -2.449 -0.581 1.00 0.00 H HETATM 18 O18 PGR 0 3.393 0.026 -0.528 1.00 0.00 O HETATM 19 SG PGR 0 2.777 1.511 1.356 1.00 0.00 S HETATM 20 CB PGR 0 1.349 2.524 1.801 1.00 0.00 C HETATM 21 CA PGR 0 1.698 3.446 2.926 1.00 0.00 C HETATM 22 N PGR 0 0.565 4.254 3.182 1.00 0.00 N HETATM 23 C PGR 0 2.646 4.407 2.450 1.00 0.00 C HETATM 24 O24 PGR 0 2.145 5.309 1.717 1.00 0.00 O HETATM 25 O25 PGR 0 3.976 4.409 2.828 1.00 0.00 O HETATM 26 H9 PGR 0 1.980 1.252 -0.806 1.00 0.00 H HETATM 27 H11 PGR 0 1.044 3.140 0.942 1.00 0.00 H HETATM 28 H12 PGR 0 0.527 1.867 2.099 1.00 0.00 H HETATM 29 H13 PGR 0 2.043 2.881 3.803 1.00 0.00 H HETATM 30 H14 PGR 0 -0.245 3.721 3.480 1.00 0.00 H HETATM 31 H15 PGR 0 0.359 4.821 2.336 1.00 0.00 H TER My question is: How do I set up Isolde so that it can refine the structure? Many thanks, Trevor Sewell Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/report-incident

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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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