- Chimera-users - RBVI Mailing Lists

Chimera-X inteprhase of the AlphaFold
by Enrico Martinez 13 Jul '23

13 Jul '23

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

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Modeler interphase in Chimera
by Enrico Martinez 13 Jul '23

13 Jul '23

Dear Chimera Users! I would like to try MODELLER interphase implemented in the Chimera for prediction of the segments missed in input PDB structure having as the input: the pdb structure with missed N and C terminal fragments (everything in one chain), as well as the full sequence of the protein in FASTA. Could you please provide me with a link to the tutorial (or just explain a very basic workflow here .. ), which simply explains how I could predict the model based on the data and save the predicted solutions in pdb format ? Many thanks in advance Cheers Enrico

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Remove me from mailing list
by Saima Sam 10 Jul '23

10 Jul '23

Hi, I am no longer a user of Chimera so please opt me out of these emails. I would truly appreciate it.

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Placing of a hame-ion centre into an AlfaFold structure
by George Tzotzos 10 Jul '23

10 Jul '23

I’d be grateful for any suggestions regarding the following problem/question. Problem Placing of the haem-iron centre in mosquito P450 structure(s) obtained by means of AlfaFold. This is required for follow up docking simulations. There no insect P450 structures deposited in PDB. However, there are numerous mammalian P450 crystal structures some of which are homologous to the mosquito structures I’m dealing with. A distinctive feature of these structures is a haem-iron centre tethered to the protein via a cysteine thiolate ligand. Six regions have been designated as substrate recognition sites (SRS 1-6) based on comparative sequence analysis methods. These SRS are conserved and are thought to participate in the formation of the substrate access channel, and form part of the catalytic site surrounding the haem iron center. My initial approach would be to use Chimera to align the AlfaFold structure against its mammalian homologue PDB structure and assume that the haem-iron centre would be located in the same place. Is there a better way to achieve the same objective?. Your help will be greatly appreciated. Best regards George

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Chimera?
by Emma 05 Jul '23

05 Jul '23

Chimera, this is me again

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Opening MTZ files on Mac OS
by Natalie Walsh 03 Jul '23

03 Jul '23

Hello, I am having troubles opening MTZ maps from PDB on ChimeraX 17.1. on Mac OS. I read somewhere that you need to download the Clipper plug-in. I went ahead and installed that (although I am not sure that I was successful) and am still struggling to open these files. Thank you, Natalie Walsh

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Removing lonbond links from pipes-and-planks representation
by philip.robinson＠bbk.ac.uk 02 Jul '23

02 Jul '23

Hi, I'm trying to generate a pipes-and-planks representation of an atomic model that contains gaps. Before generating the pipes-and-planks representation I hid the long bonds to remove the links in the gap regions. However, the gaps are connected again in the pipes-and-planks representation and I cannot find the command to hide them. Any help would be appreciated. Phil

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ChimeraX Question
by Bani Kaur 30 Jun '23

30 Jun '23

Hi, I hope you are doing well! My name is Bani Kaur and I am an active user of ChimeraX for a research project concerning protein modeling, specifically with the CFTR protein. I have been running into issues with showing atoms on my residue, specifically after I change the romater. I am not sure what to do about this as I have downloaded the latest version of ChimeraX. Additionally, I am not able to see clashes for some very reason and am only able to see it when limit by selection is unchecked, but for my research project, we require that it is checked in the clashes settings. Thank you so much for your help! Best, Bani Kaur

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Questions regarding reply log
by Prathvi Singh 28 Jun '23

28 Jun '23

Hi Elaine, Is there a way to clear the Reply Log using the command line? Is there a way to write the contents of the Reply log to a text file? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Supoort for automating superimposition process of multiple pairs of structures using command line
by Vaibhav Anand 27 Jun '23

27 Jun '23

Hello Chimera team, I am seeking your assistance in automating the process of superimposing multiple pairs of structures using the command line. I've performed the MD simulation of the UBA domain (PDB ID - 1OQY), and for analyzing the structural changes, I've extracted the 11 structures from the trajectory at 500ns to 1000ns with steps of 50ns. In total, I've 12 structures [1 reference structure (em.gro - energy minimized structure) and 11 extracted structures]. Now I want to superimpose each extracted structure w.r.t. em.gro and save the image of superimposition with the image name to be (time + rmsd_value). For the RMSD value, I'll have to save the reply log file (or the last 10-15 lines of the reply log) and then copy the rmsd value and save my image file with it. Could you please give me an outline or references on how I can do this task? Thank you for your attention Regards, Vaibhav

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