October 2024 - ChimeraX-users - RBVI Mailing Lists

Sequence alignment and Extraction
by Mamadou Sangare 25 Oct '24

25 Oct '24

Dear, I would like to align two protein structures A and B, select and extract the parts of the B sequence that match A in a fasta file. Thank you for your support.

2 1

Visualisation of water near protein
by Enrico Martinez 25 Oct '24

25 Oct '24

Dear Chimera X users ! I have a question about the visualization of water around the protein. When I open the pdb + trajectory of the whale system, ChimeraX masks most of the water box, only showing some selected water molecules (probably involved in the interactions with the protein). Then, viewing the MD system, I can observe an exchange of this water, which is great ! Would it be possible via some command to modify the number of the displayed water in the beginning of simulation e.g. showing more water observed in the proximity to protein (..but still not the whole water box !) ? Many thanks in advance Enrico

2 4

Coloring by attribute
by Murugesh Narayanappa 24 Oct '24

24 Oct '24

Hi, I am Murugesh, a postdoctoral fellow in Dr. Rajat Rohatgi’s lab at Stanford University. I created an attribute file using z-scores and mapped these scores onto a structure, applying a gradient color scheme. However, I would like to know if there's a way to use discrete colors instead. Specifically, I want to apply a single color with uniform intensity for a selected range of z-scores (e.g., from 3 to 10) rather than using a gradient. I haven’t been able to figure this out. Is there an option or command I can try? I would appreciate any guidance. Thank you, Murugesh

2 2

Re: Inquiry About Translating ChimeraX GUI Language
by Zach Pearson 24 Oct '24

24 Oct '24

I think that was meant for Tom, I barely said anything, but thank you on his behalf and good luck with your translation project! We’re excited to see it. — Zach > On 24 Oct 2024, at 00:14, 刘俊骅 <273667986(a)qq.com> wrote: > > Dear Zach, > Thank you very much for your detailed and clear response. The direction you provided has been extremely helpful and will enable me to delve deeper into understanding these projects. I am excited to explore the code and see how I can customize the GUI interface to better suit my needs. > Your guidance has given me a great starting point, and I appreciate the time and effort you have invested in helping me. Your support is greatly appreciated, and it reinforces my enthusiasm for working with ChimeraX. > Once again, thank you for your assistance and for developing such an outstanding tool. Your work is truly making a significant impact on the scientific community. > Best regards, > Junhua Liu > > ------------------ 原始邮件 ------------------ > 发件人: "Zach Pearson" <zjp(a)cgl.ucsf.edu>; > 发送时间: 2024年10月23日(星期三) 凌晨2:35 > 收件人: "刘俊骅"<273667986(a)qq.com>; > 抄送: "ChimeraX Users Help"<chimerax-users(a)cgl.ucsf.edu>; > 主题: Re: [chimerax-users] Inquiry About Translating ChimeraX GUI Language > > A very cursory googling for ‘PyQt multilanguage’ brings up this repo: https://github.com/yjg30737/pyqt-multi-language-example but it is for PyQt5. > > Feel free to fork the ChimeraX repository and make pull requests. We would be eager to learn how to do this and turn it into a community-driven project. > > — Zach > > > On 22 Oct 2024, at 11:14, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hi Junhua, > > > > That would be great to add some Chinese language support in ChimeraX. We haven't looked into supporting languages other than English, but there are many Chinese speaking ChimeraX users. ChimeraX uses the Qt window toolkit which has "internationalization" support. Specifically ChimeraX uses the Python interface to Qt, called PyQt. If you figured out how to customize the ChimeraX GUI text we'd be interested in including that in ChimeraX. Your ChiimeraX distribution includes all the Python code which creates the user interface, so you could experiment with just changing the Python code in your distribution. The ChimeraX code is also on Github here > > > > https://github.com/RBVI/ChimeraX > > > > Here is the place in the code where the top level File, Edit, Select, Actions, Tools, ... menus are created. > > > > https://github.com/RBVI/ChimeraX/blob/1f1a0512d53424163992b53eadeffd2d9e39d… > > > > I guess the individual menu entries are added in many places in the code. For instance the File / Open... entry is here > > > > https://github.com/RBVI/ChimeraX/blob/1f1a0512d53424163992b53eadeffd2d9e39d… > > > > and it uses the add_menu_entry() function which probably is used to add all the menu entries > > > > https://github.com/RBVI/ChimeraX/blob/1f1a0512d53424163992b53eadeffd2d9e39d… > > > > Let us know what you figure out. > > > > Tom > > > > > >> On Oct 22, 2024, at 9:36 AM, 刘俊骅 via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > >> > >> Dear UCSF ChimeraX Developers, > >> I hope this email finds you well. > >> Firstly, I would like to express my sincere gratitude for developing such a powerful and versatile software as UCSF ChimeraX. It has been an invaluable tool for my research and visualization needs. > >> I have a question regarding the translation of the GUI interface language. I am interested in translating the interface into another language. Since I noticed that UCSF ChimeraX is based on Python, I was wondering if it is possible to modify certain .json, .py, or .xml files to change the displayed language. My intention is purely for personal use, and I have no plans to distribute or profit from any modifications. > >> Could you please provide any guidance or resources on how to achieve this? Any pointers or documentation would be greatly appreciated. > >> Thank you very much for your time and consideration. > >> Best regards! > >> Junhua Liu 273667986(a)qq.com > >> _______________________________________________ > >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ > > > > _______________________________________________ > > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

1 0

Inquiry About Translating ChimeraX GUI Language
by 刘俊骅 24 Oct '24

24 Oct '24

Dear UCSF ChimeraX Developers, I hope this email finds you well. Firstly, I would like to express my sincere gratitude for developing such a powerful and versatile software as UCSF ChimeraX. It has been an invaluable tool for my research and visualization needs. I have a question regarding the translation of the GUI interface language. I am interested in translating the interface into another language. Since I noticed that UCSF ChimeraX is based on Python, I was wondering if it is possible to modify certain .json, .py, or .xml files to change the displayed language. My intention is purely for personal use, and I have no plans to distribute or profit from any modifications. Could you please provide any guidance or resources on how to achieve this? Any pointers or documentation would be greatly appreciated. Thank you very much for your time and consideration. Best regards! Junhua Liu 273667986(a)qq.com

5 6

Running_chimera_in_R
by Eric Pettersen 23 Oct '24

23 Oct '24

> From: Bipasa Show <bipasa.show22ug(a)apu.edu.in> > Subject: Running_chimera_in_R > Date: October 21, 2024 at 10:48:18 PM PDT > To: chimerax-users(a)cgl.ucsf.edu > > > Dear Team Chimera X, > Hope this email finds you well. I am reaching out in order to know if there is a way I can use R to automate specific processes in Chimera and Chimera X like structure-based sequence alignment, finding SASA for multiple residues etc. . It would be nice if you could let me know if automation in these softwares are possible using R. > Thanks and regards, > Bipasa

2 2

Problem with the coulombic protein
by svle＠tiscali.it 23 Oct '24

23 Oct '24

Hi, I have six representative frames, in pdb format , of six clusters evaluated with cpptraj of a trajectory . For three representative frames the command "coulombic protein" the surface is produced without any problem whereas for the remaining three I receive errors similar to the following text: coulombic protein Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue CYM (net charge -1) with am1-bcc method Running ANTECHAMBER command: /usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmp76d1_frw/ante.in.mol2 -fi mol2 -o /tmp/tmp76d1_frw/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n (CYM) (CYM) Welcome to antechamber 20.0: molecular input file processor. (CYM) (CYM) Info: Finished reading file (/tmp/tmp76d1_frw/ante.in.mol2); atoms read (22), bonds read (21). (CYM) Info: Determining atomic numbers from atomic symbols which are case sensitive. (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (CYM) (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (CYM) Info: Total number of electrons: 94; net charge: -1 (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1 (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC (CYM) Charges for residue CYM determined Assigning partial charges to residue CYM (net charge -1) with am1-bcc method CYM: number of electrons (92) + formal charge (-1) is odd; cannot compute charges for radical species using AM1-BCC method Any suggestions to solve this problem? Thanks. Saverio

2 4

Re: Mercator projection of MRC voluem coloured by attribute
by Tom Goddard 23 Oct '24

23 Oct '24

Hi Pranav, The image in my last email was created useing the 5 commands I listed in that email. The main drawback is it gives a 360 view from a point at the middle of the map looking out. So it can be used to see what the inside of a virus capsid looks like, but not the outside. My other suggestion about combining strips of a thousand images during a rotation is what would allow getting an outside 360 degree view. Tom > On Oct 23, 2024, at 10:40 AM, Pranav Shah <pranav.shah(a)strubi.ox.ac.uk> wrote: > > Love it! Thanks Tom, this might just work. WOuld you be happy to share the script you used to generate that stretched out view? > > > Best, > Pranav > -- > Pranav Shah > Post-doctoral Research Associate (PDRA) > Division of Structural Biology (STRUBI) > University of Oxford. > Center for Human Genetics, > Roosevelt Drive, > Oxford, OX3 7BN, UK > > ________________________________________ > From: Tom Goddard <goddard(a)sonic.net> > Sent: 22 October 2024 20:19 > To: Pranav Shah > Cc: ChimeraX-bugs(a)cgl.ucsf.edu > Subject: Re: [chimerax-users] Mercator projection of MRC voluem coloured by attribute > > Hi Pranav, > > I guess you mean you want to save a 360 degree projection image of your colored map? There is nothing quite like that in ChimeraX. If you want a 360 view from the center of the map you can get that with "camera 360" after positioning the view point in the middle of the map. For example > > open 1080 from emdb > color cylindrical #1 palette redblue > move z 350 > turn x 90 center #1 > camera 360 > > There is also command volume unroll that can unroll a cylindrical map. But it does not preserve coloring. And there was a flatten icosahedron capability that worked with atomic models in Chimera that is not in ChimeraX. > > https://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.… > > For what you want you could spin the model around 360 degrees recording images each 0.2 degree, then have a script take the center column of pixels from each image and lay those columns side-by-side in a single image 1800 pixels wide. > > Tom > > Example of camera 360 giving view inside map EMDB 1080. > [emd1080.png][emd1080_360.png] > > On Oct 22, 2024, at 10:51 AM, Pranav Shah via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > hi Team, > This is potentially a left-of-center question, but is there a way I > could generate a mercator projection of an MRC volume that I have > colored by zone? I am happy to code this up in the chimerax python > environment, but I am not sure how I could access the voxel colour > information before projecting the volume. > > Best, > Pranav > -- > Pranav Shah > Postdoctoral Research Fellow. > > Division of Structural Biology, > Wellcome Trust Centre for Human Genetics, > University of Oxford, > Roosevelt Drive, Oxford OX3 7BN, > UK > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ > >

1 0

Installing plugins not working
by Oliver Clarke 23 Oct '24

23 Oct '24

Hi, Since the website came back, I can't get installing external tools (e.g. Clipper, ISOLDE) to work - is it just me or down for others also? It says it is downloading the bundle when I click install, but nothing happens after that. Cheers Oli

3 2

Mercator projection of MRC voluem coloured by attribute
by Pranav Shah 22 Oct '24

22 Oct '24

hi Team, This is potentially a left-of-center question, but is there a way I could generate a mercator projection of an MRC volume that I have colored by zone? I am happy to code this up in the chimerax python environment, but I am not sure how I could access the voxel colour information before projecting the volume. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 1