October 2024 - ChimeraX-users - RBVI Mailing Lists

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

placing a model at points defined in a CMM file
by Pranav Shah 22 Oct '24

22 Oct '24

hi Team, In addition to my previous question, is there a chimeraX function I could leverage to translate a pdb model to a point defined in a CMM file? 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

Viewing ccp4 volume data - Hiding outline box volume outside surface
by Stylianos Iliadis 22 Oct '24

22 Oct '24

Hello, I want to visualise a surface (isosurface) loaded from a ccp4 file on top of a protein binding site. When I load the volume and adjust the level properly, I can see the “correct” surface (visualised usually on Pymol), but this is only possible when I view slices of the volume=cube box. If I don’t use the sliced view, I only see a cube. Essentially, my question is how can someone hide the “negative” volume inside the cube box that is not part of the depicted isosurface? Thanks, Best, Stel Iliadis

2 1

Named selection problem
by Patrick Moynihan 22 Oct '24

22 Oct '24

Hi, I was hoping someone could help me with a persistent problem I am having. I am running ChimeraX version 1.8 (2024-06-10) on OSX. This problem has persisted for quite a while through several versions. If I work in ChimeraX and save a group of atoms as a named selection, it generally works as expected for the first group. After that, if I use the command “name XXXX” or define a selection via the GUI, it seems to take the input and reserve the name. However, when I return and select that named selection, the entire protein gets selected. I cannot for the life of me figure out why. I’ve tried low numbers of atoms and high, short names and long, the problem persists. Any advice would be appreciated. Thanks, Patrick

2 1

Set transparency of multiple models
by Ioannis Skalidis 22 Oct '24

22 Oct '24

Dear ChimeraX mailing list, I was wondering if there is a command to set the alpha (transparency) of multiple models (not maps). So far, I know that this is possible for maps through the transparency command, but the only way I know of to make a model transparent is to set each model alpha value individually in its color panel. Thanks for your help! Cheers, Dr. Ioannis Skalidis | Structural Biochemist | Twitter: @imjohnskal <https://twitter.com/imjohnskal> | johnskalidis(a)gmail.com

2 1

Query regarding Chimerax capablities
by Joseph Clifford 21 Oct '24

21 Oct '24

Hi Team, I hope this email reaches you well. I am a R&D scientist at Randox Laboratories and was wondering if possible could you model the nicked free form of PSA with the additional 7 amino acids at the N-term. I am exploring the capabilities of chimerax and want to put a business case together to my manager regarding this software application. [cid:54b7fcba-418a-438f-a6b0-5358e796c896] Many thanks in advance, Joseph Clifford This e-mail and any attachments are confidential and intended solely for the addressee and may also be privileged or exempt from disclosure under applicable law. If you are not the addressee, or have received this e-mail in error, please notify the sender immediately, delete it from your system and do not copy, disclose or otherwise act upon any part of this e-mail or its attachments. E-mail communications are not guaranteed to be secure or virus-free. Therefore Randox does not accept responsibility for any loss arising from unauthorised access to, or interference with, any e-mail communications by any third party, or from the transmission of any viruses. Randox does not accept liability for any errors or omissions in the contents of this message which arise as a result of e-mail transmission. Replies to this e-mail may be monitored by Randox for business and operational purposes. Any opinion or other information in this e-mail or its attachments that does not relate to the business of Randox is personal to the sender and is not given or endorsed by Randox.

2 1