- Chimera-users - RBVI Mailing Lists

Stereo in ChimeraX
by Engelhardt, Peter 01 Jul '24

01 Jul '24

Hi chimera team, We can’t get any stereo to work in ChimeraX though several trials. In the earlier Chimera all worked perfectly. We are especially interested in red-cyan stereo as it’s most suitable for a large public and easy to use even with colors. Could you please let us know how to install e.g. red-cyan stereo for ChimeraX. We thank you in advance Cheers Peter __________________________ Peter Engelhardt PhD., Docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography and Nanoscopy Nanomicroscopy Center (NMC), Otanano Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil Phone: +358 400193342 Email: Peter.Engelhardt(a)Helsinki.Fi<https://webmail.helsinki.fi/horde/imp/dynamic.php?page=message&buid=2535&ma…> Email: Peter.Engelhardt(a)Aalto.Fi<mailto:Peter.Engelhardt@Aalto.Fi> Sent from my iPhone

2 1

script for comparing surfaces bits
by chiarini＠takisbiotech.it 24 Jun '24

24 Jun '24

Dear all, I'm trying to come up with some method to compare surfaces of the same protein area over some trajectory. A simple RMSF doesn't cover the analysis as a roto-traslation of some parts might retain the surface form and shape, whereas a residue might have a complete rearrangement of its surrounding without undergoing large RMSF changes. Some software based on Masif are available, tough they do not confront between trj frames. Are there any turnarounds in chimera to do this? A function similar to RMSD but for surfaces that maybe could be emplyed in this specific case? Thank you all, Valerio Chiarini -- Dr. Valerio Chiarini _Senior Scientist_ Proteins & Monoclona Antibodies Department b Takis Biotech c/o Tecnopolo Via di Castel Romano, 100 00128 Rome, Italy Tel.: +39 06-50576077 Fax: +39 06-50576710 Email: chiarini(a)takisbiotech.it Web: http://www.takisbiotech.it 196/03_ _Le informazioni contenute in questa comunicazione e gli eventuali documenti allegati hanno carattere confidenziale, sono tutelate dal segreto professionale e sono ad uso esclusivo del destinatario. Nel caso questa comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua diffusione e riproduzione C( contraria alla legge e preghiamo di darci prontamente avviso e di cancellare quanto ricevuto. __Grazie._ _This e-mail message and any files transmitted with it are subject to attorney-client privilege and contain confidential information intended only for the person(s) to whom it is addressed. If you are not the intended recipient, you are hereby notified that any use or distribution of this e-mail is strictly prohibited: please notify the sender and delete the original message. __Thank you._

2 1

(no subject)
by furkan calapoğlu 20 Jun '24

20 Jun '24

How can i do organometalic ligand and protein docking ?

2 1

Score decimals question
by VALERIA MARIA CARRILLO RAMIREZ 19 Jun '24

19 Jun '24

Hi, I'm doing a work for college and my professor is asking for an analysis via Autodock Vina. However I have to calculate scores and the program is giving them with only one decimal and I need to report the values with 3 decimals. How can I change that? Thanks a lot :)

2 1

Aligning small molecules in Chimera
by Prathvi Singh 19 Jun '24

19 Jun '24

Hi Elaine, Is it possible to superimpose/align small molecules in chimera/chimeraX? I have isolated a very small part of a polypeptide chain from a PDB file (it contains a CO and NH group engaged in peptide bond formation and both the groups are flanked by C-alpha atoms such that the structure's formula becomes CH3-CO-NH-CH3). I have 10 such PDB files. I want to extract this fragment from each PDB file and superimpose them to know the differences. Thank you Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

RBVI downtime
by Eric Pettersen 13 Jun '24

13 Jun '24

Hi all, The RBVI compute cluster will be down for scheduled maintenance Monday and Tuesday of next week (June 17/18) which means that the Chimera and ChimeraX web sites (including the ChimeraX toolshed) and mailing lists will be down during that time. This also means that web services from Chimera/ChimeraX that access our compute cluster will not work (Blast Protein, Modeller tools, sequence realignment). We are sorry for any inconvenience. --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

ChimeraX_InfoRequest
by Altan KARA (MAM-GMBE) 10 Jun '24

10 Jun '24

To whom it may concern, How we can create high resolution images with ChimeraX? No matter what I tried still the outputted images are not in high resolution. Thanks Dr. Altan KARA Kd. Uzman Araştırmacı TÜBİTAK MAM Gen Mühendisliği ve Biyoteknoloji Enstitüsü Barış Mah. Dr. Zeki Acar Cad. No.1 P.K. 21 41470 GEBZE / KOCAELİ T +90 262 677 3371 F +90 262 641 2309 www.mam.gov.tr altan.kara(a)tubitak.gov.tr

2 2

Converting a carbonyl group to carboxylic acid group
by Prathvi Singh 06 Jun '24

06 Jun '24

Hi Elaine, I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 3

Help saving models as .pdb file
by Jacek Jagodzinski 03 Jun '24

03 Jun '24

I have constructed model of pentameric protein by exchanging one of the chains with a very closely related chain from other variant of such pentameric protein. Chimera recognizes that my model consists of parts of two proteins. I would like to save it as a single protein file. When I attempt to save model as a single file (option in save dialog) a PDB file is produced. However, when I open this file in other application (such as Cresset Flare) to explore molecular dynamics or docking in this newly constructed hybrid system - it opens as two different proteins. Is it possible to “merge” the parts to become a single pentameric protein, that would behave as single entity during docking or MD computations? Jacek Jagodzinski PS. I am not computational chemist, I am medicinal chemist by training and long career.

2 2

Using Chimera/AutoDock Vina for oligomers
by Ballanah Torbett 24 May '24

24 May '24

Hello, I hope this email finds you well! I had a question about using the Chimera and its AutoDock Vina interface, as I'm relatively new to using these programs. I've been able to dock substrate onto one binding site of my protein of interest, but I'd like to apply it to the other three binding sites of the tetramer as well. I wouldn't be able to work with the monomer since the active sites are formed from the interactions between the N and C termini. I have also tried saving the session as a new PDB file and docking a new substrate, but it bound to the already-occupied site. Is there a way to dock substrate onto the other sites while "ignoring" the occupied site? Thank you! Sincerely, Ballanah Torbett 3rd Year PhD Student Gaucher Group Georgia State University

2 1