November 2022 - ChimeraX-users - RBVI Mailing Lists

create chain as a new model from exiting PDB model
by tim smith 15 Nov '22

15 Nov '22

Hi All, I would like to create chain A as a separate model from the existing model. Could you please help me. Thank you. Best regards Tim

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Question about pad parameter
by Thu Nguyen 15 Nov '22

15 Nov '22

Hello, I am using the volume cover command to crop the chain from the protein map. Here is what I did: > open 12554 from emdb > open 7ns0 > volume cover #1 atomBox #2/A1 pad 1.0 Suppose I want to add extra 17 voxels on each size of the chain, what value of pad should I add? Also, could you tell me the unit of pad in this command? Thank you very much. Best regards, Thu

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Re: [chimerax-users] Google colab sign in inquiry
by Tom Goddard 15 Nov '22

15 Nov '22

Hi Alejandro, On Windows the QtWebEngine Google Colab authentication info is in C:\Users\<username>\AppData\Roaming\ChimeraX\QtWebEngine\AlphaFold You can delete that directory and try using ChimeraX AlphaFold prediction again. Tom > On Nov 14, 2022, at 5:38 PM, Abraham, Alejandro <alejandro.abraham(a)icahn.mssm.edu> wrote: > > Hi Tom, > > Thank you for your email. I cannot see the login page anymore, and uninstalling ChimeraX to later reinstall it does not work. > Is there a folder where sign in is saved like in Macs ? I am using a Windows 10 PC. > Thanks again. > > Best, > > Alejandro > > > On Mon, Nov 14, 2022 at 12:59 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Alejandro, > > ChimeraX remembers your Google Colab sign-in. I don't understand why it would not let you sign in. A screenshot showing what you see would help understand the problem. > > If you signed in and ran AlphaFold previously but you want to change the account you sign in with, that should also be possible by clicking the image in the upper right corner of the AlphaFold Run panel which is just a web browser -- that button which shows the icon for your Google account will pull down a menu and let you sign out. And then you can also use it to sign in to another account. > > If somehow the ChimeraX remembered Google sign-in is causing problems you can delete that remembered sign-in info. On Mac you would delete the directory > > ~/Library/Caches?/UCSF ChimeraX/QtWebEngine/AlphaFold > > This is described further in this ChimeraX bug report > > https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7654#comment:2 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7654#comment:2> > > Tom > > >> On Nov 14, 2022, at 7:36 AM, Abraham, Alejandro via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Dear ChimeraX Support Team, >> >> Before all, congratulations on such awesome software. >> On another note I wanted to contact you because I am not able to connect to Google sign in when trying to predict with alpha fold. Is there a way to reset login ? >> >> Thanks again. >> >> Best, >> >> Alejandro >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

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stretching protein?
by Noriega, Heather 14 Nov '22

14 Nov '22

Hello, I hope this email finds everyone well. I was wondering if ChimeraX had a function specific to "stretching" the protein. I am going to attach a picture, for reference. Is it possible to stretch the monomer to build a larger capsid? Thanks in advance. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883 [image: image.png]

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Export PAE plot
by Clara Jegousse (TSL) 14 Nov '22

14 Nov '22

Dear ChimeraX team, After watching the YouTube tutorial on “how to show AlphaFold error estimates with ChimeraX”, I was wondering how to export the plot as an image (pdf, png?). Kind regards, Clara

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Google colab sign in inquiry
by Abraham, Alejandro 14 Nov '22

14 Nov '22

Dear ChimeraX Support Team, Before all, congratulations on such awesome software. On another note I wanted to contact you because I am not able to connect to Google sign in when trying to predict with alpha fold. Is there a way to reset login ? Thanks again. Best, Alejandro

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ChimeraX 1.5rc running on Nvidia RTX Titan [ubuntu 22.04]
by HONG ZHAN 11 Nov '22

11 Nov '22

Dear, I recently installed a Nvidia RTX Titan GPU card, and ChimeraX 1.5rc, it is a bit wired. I can open the window using intergrated GPU but if I just clicked on Chimerax or try to open it in terminal, it failed to open the program... Is ChimeraX only working on integrated GPU? Also, I cannot install the chimerax using apt install as in the website description, but dpkg -i works... is this the right way to install? many thanks! Hong

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.pdb from Protein Data Bank has more chains than expected
by McClean, Phillip 10 Nov '22

10 Nov '22

Hi Everyone, I downloaded the 7FDL .pdb from the Protein Data Bank. I was expecting just two chains (it is a heteromeric complex), but I found 12 chains in the file (A-L). I was expecting two chains because the manuscript suggested they were just modeling protein fragments of the two protein. It appears that chains that A,C,E,G,I,K are multiple models of one fragment, while chains B,D,F,H,J,L are multiple models of the second fragment. Two questions. Why are multiple structures reported, and how to I visualize just two fragments at the same time, for example A and B. I have attached the .pdb file. Thanks for any advise. Phil McClean

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Density extraction
by Dmitry Semchonok 09 Nov '22

09 Nov '22

Dear colleagues, I have a 3D map of the helix. 1. Do you know how can I extract 1 subunit? 2. Also, if there is no x-ray structure available. Thanks in advance. Kind regards, Dmitry

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Fast Archive Search
by Kazan Ramy 09 Nov '22

09 Nov '22

Greetings to all, How can one search the archive with given keywords? Like for example, Ctrl + F search. I can only find the manual search by subject, thread ... and limited by month. Cheers, Ramy

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ChimeraX-users November 2022