June 2024 - Chimera-users - RBVI Mailing Lists

ChimeraX_InfoRequest
by Altan KARA (MAM-GMBE) 09 Jun '24

09 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