- Chimera-users - RBVI Mailing Lists

Unable to dock
by Panapakam, Jyotheeswaran 20 Jul '23

20 Jul '23

[cid:9962344b-5095-47ba-a1c2-1c6fef113ef2] Dear Official, I was unable to move the green grid, thus, I am unable to dock a compound on the protein target. Could you please help me with this? Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas.

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How do I colour all my hydrogen atoms grey?
by Mazin Nasralla 17 Jul '23

17 Jul '23

Hello, I imported an x,y,z model of water molecules into Chimera. I want to create an image of my water structure so I am setting the background to grey. That works. But I would prefer to set the hydrogen atom colour to light grey. I can't work out how to do that. I can select each individual atom, and then colour edit it but that will take ages. Is there a simple command line solution? Thanks Mazin

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hiding a model slowly
by Sen, Anindito 14 Jul '23

14 Jul '23

Dear Chimera X team, Is there a way I can hide one of the models in a ChimeraX session slowly (like fading it off) while making a movie. typically I use hide #7 model Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

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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 04 Jul '23

04 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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