- 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

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

Saving symmetry model in pdb format
by Kailash Singh Bisht 17 May '24

17 May '24

Hello ChimeraX team I am trying to export the symmetry structure of the protomer virus protein as a pdb file but whenever I am saving that model it only saves the same protomer instead of the whole symmetry structure. Can you please help? How to export those symmetry models as PDB files -- With Regards Thanking You Kailash Singh Bisht Ph.D. Student

2 1

Displaying angles in chimera
by Prathvi Singh 16 May '24

16 May '24

Hi Elaine, Is it possible in chimera/chimeraX to display angles between two covalent bonds like in pymol? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 2

Difficulty with Ribbon Visualization in Chimera Software
by 罗舒月 15 May '24

15 May '24

Dear Chimera Software Team,     I hope this email finds you well. I am writing to seek assistance regarding a challenge I am facing while using the Chimera software. Specifically, I am experiencing difficulties in visualizing my protein structure in ribbon mode.     When I load my PDB file and choose the ribbon representation, the resulting visualization appears as linear segments rather than the desired helical structure. I am unsure whether this issue is related to my file or if there is a specific step or setting I am overlooking.    I would greatly appreciate it if you could provide me with guidance on how to achieve the desired helical ribbon model in Chimera or any insights on potential issues with my file. To assist you in troubleshooting, I have attached the PDB file in question, as well as an image showing the current ribbon visualization.    Thank you in advance for your time and support. I look forward to your prompt response.  Best regards, Shuyue Luo the result of my file the effect I want 发自我的企业微信

3 2

Difficulty with Ribbon Visualization in Chimera Software
by 罗舒月 14 May '24

14 May '24

Dear Chimera Software Team,      I hope this email finds you well. I am writing to seek assistance regarding a challenge I am facing while using the Chimera software. Specifically, I am experiencing difficulties in visualizing my protein structure in ribbon mode.      When I load my PDB file and choose the ribbon representation, the resulting visualization appears as linear segments rather than the desired helical structure. I am unsure whether this issue is related to my file or if there is a specific step or setting I am overlooking.    I would greatly appreciate it if you could provide me with guidance on how to achieve the desired helical ribbon model in Chimera or any insights on potential issues with my file. To assist you in troubleshooting, I have attached the PDB file in question, as well as an image showing the current ribbon visualization.     Thank you in advance for your time and support. I look forward to your prompt response.   Best regards, Shuyue Luo the result of my file the effect I want 发自我的企业微信

1 0

Preparing molecular structures for panel of figures
by Prathvi Singh 10 May '24

10 May '24

Hi Elaine, I want to create a panel containing 4 figures. Each figure in the panel will be a ball and sticks representation of an amino acid residue. I have tried using the "Tile Structures" feature in UCSF chimera to create the panel. Although it does ease the job a lot, I find it difficult in aligning residue labels or 2D labels. Is there a grid based feature which can display a grid on the chimera workspace so that I can use its lines as a guide to better align my labels? Thanks in advance Prathvi, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

Chimera scripting
by Flip Jansen 06 May '24

06 May '24

Hello Chimera dev team, I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? Any help is highly appreciated, I would also be happy to come by an talk in person. Best, Flip Jansen

2 1