- ChimeraX-users - RBVI Mailing Lists

Sequential model display controls bound to buttonpanel button?
by Oliver Clarke 19 Jan '24

19 Jan '24

Hi all, I really like the new sequential model display controls in the daily build - thank you so much for implementing these! Would it be possible to add them as a command, e.g. nextmodel and prevmodel? This way I could add them to my box of buttons, and have them in the main GUI window, without needing to switch over to the model panel. Cheers Oli

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Re: Increase cofactor size
by Tristan Croll 19 Jan '24

19 Jan '24

(disclaimer: you should probably follow Elaine’s much more extensive advice) “atomspec” just refers to any selection string - e.g. “#1/A:50”, “:LIG”, “sel” etc. On Fri, 19 Jan 2024 at 18:52, Cameron Larson <cllarson(a)ucdavis.edu> wrote: > Thank you for your help. > A silly question, but what is might 'atomspec' be? a range of atoms? > > Thank you, Tristan > > On Fri, Jan 19, 2024 at 11:51 AM Tristan Croll <tcroll(a)altoslabs.com> > wrote: > >> Try "setattr {atomspec} bonds radius {value in Angstroms}". >> >> Best, >> Tristan >> >> On Fri, Jan 19, 2024 at 4:28 PM Cameron Larson via ChimeraX-users < >> chimerax-users(a)cgl.ucsf.edu> wrote: >> >>> Hello, >>> >>> I am using chimeraX to visualize a ligand. I am familiar with the >>> commands to increase protein thickness ('cartoon style protein thickness') >>> but how can I do this for a ligand or other molecule? >>> >>> Really appreciate the help, >>> >>> -Cameron Larson >>> _______________________________________________ >>> 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/ >>> >> >> Altos Labs UK Limited | England | Company reg 13484917 >> Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, >> United Kingdom, WA14 2DT >> <https://www.google.com/maps/search/1+Ashley+Road,+Altrincham,+Cheshire,+Uni…> >> > -- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

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Increase cofactor size
by Cameron Larson 19 Jan '24

19 Jan '24

Hello, I am using chimeraX to visualize a ligand. I am familiar with the commands to increase protein thickness ('cartoon style protein thickness') but how can I do this for a ligand or other molecule? Really appreciate the help, -Cameron Larson

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Question about Cylinder Representation
by Elaine Meng 18 Jan '24

18 Jan '24

Hi Maxine, Somehow I missed your earlier question about how to make cartoon helix tubes straight instead of curved: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu…> The short answer is that sorry, ChimeraX currently does not have an option to make them straight. This feature request is in our database as ticket #1242: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/1242> There are some possible workarounds mentioned in the comments on that ticket, namely: ---------------- (1) you could try "define axis" with "perHelix true" and some padding value to show straight cylinders for helices, and then hide the ribbon. The main problem with this workaround is that the other parts of the ribbon do not connect well to the straight cylinders in some places. Example: open 2gbp hide atoms define axis perhelix true padding 2.0 hide helix ribbon Also if you only care about one specific helix, you can hide all of the other straight cylinders and only hide the ribbon for the specific residues in that helix. (2) If you want to modify the Python code in your ChimeraX distribution you can change one line and it will always produce straight helix tubes. The line is 154 in file ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax/atomic/sse.py [** NOTE this is an old comment so the python version is higher now, I believe python3.11 instead of 3.9, and the line number is also different, I believe it's line 166 instead of 154 **] ...on Mac (different location on Windows and Linux, ask if you can't find it) change MIN_CURVE_LENGTH = 13 to MIN_CURVE_LENGTH = 1300 ---------------- I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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check waters to a csv file?
by Francisco Murphy Pérez 18 Jan '24

18 Jan '24

In chimerax ... tools -> structure analysis -> check waters Can we get the information from this analysis into a csv file? Can we add also the bfactor? Thanks

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Plotting Difference Map of Electron Density
by Gourav Das 16 Jan '24

16 Jan '24

Greetings everyone! I am trying to plot difference map of electron density using ChimeraX. I have created the cube file using Multiwfn. I want to show red and blue isosurfaces (+0.0012 and -0.0012 a.u., respectively) to represent the regions in which electron density is increased and decreased respectively. Please help me regarding this issue. With regards, Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

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Different ways to crop out a map region
by Thu Nguyen 16 Jan '24

16 Jan '24

Good afternoon, I am looking for several methods to crop out a map region from a larger density map. So far I know the command "volume region" but to use the command I need to know in advance the grid indices of the region I want to crop. Are there any more convenient methods to crop out a map region (maybe using mouse to directly drag a region from the volume map)? Thank you very much. Best regards, Thu

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Hide arrows/axes
by Lluís Eixerés Ros 16 Jan '24

16 Jan '24

Dear ChimeraX developer, I’m Lluís Eixerés, a PhD student at the Biomedicine Institute of Valencia, Spain. I’m using ChimeraX and after opening a mtz file, these arrows/axes (see figure attached) appeared at the centre of the screen. I have tried to hide them (they also appear after snapshotting) but I can’t. Could you explain me how to do it, please? Thank you. Regards, LL

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Help in Extracting pLDDT confidence Scores in CSV Format from ChimeraX AlphaFold
by Amit Singh 14 Jan '24

14 Jan '24

Dear ChimeraX Developer, I hope this message finds you well. I am reaching out as a newcomer to ChimeraX and Alphafold, seeking guidance on extracting the pLDDT score in CSV format from the best model obtained through ChimeraX AlphaFold. Specifically, I am interested in obtaining information such as Binding Protein, Bond Type, Protein Residue, Peptide Residue, Distance (Å), and the "pLDDT Range Score." Despite my attempts with the B-factor, I have encountered challenges in extracting the pLDDT range confidence score. I would greatly appreciate any assistance or guidance you can provide on this matter. Thank you for your time and consideration. Kind regards, Amit

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Re: Question regarding gaussian filtering
by Tom Goddard 13 Jan '24

13 Jan '24

Hi Dennis, You need to be clearer about what you are trying to achieve "So I guess my question is whether there is a good way to mimick/visualize a lower resolution experimental map using a higher resolution experimental map without considering a sophisticated noise model." If you wanted to mimic a low resolution map for purposes of testing an algorithm (e.g. fitting, segmentation, ...) then the signal to noise at various frequencies would be important. If you just want it to look like a low resolution map to the human eye (why?), well I don't know how much having very different signal-to-noise as a function of frequency will visually alter the appearance. The effects of Gaussian smoothing or simply truncating beyond a certain frequency will create a map that has much higher signal-to-noise then a real low resolution map. You won't see the low resolution noise characteristic of an actual low resolution map. I don't know if that would be visually apparent. Tom > On Jan 10, 2024, at 12:40 AM, Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se> wrote: > > Hi Dennis, > > A low-pass filter is what you want then: this doesn't dampen signal and noise, simply discards everything past a certain spatial frequency you choose. Just like the low-pass filter applied on-the-fly when using a map as a reference for a 3D refinement or classification job. > I don't know how this can be done in ChimeraX though. > > Guillaume > > From: Dennis Dannecker via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> > Sent: Wednesday, January 10, 2024 7:15:09 AM > To: Tom Goddard > Cc: chimerax-users(a)cgl.ucsf.edu > Subject: [chimerax-users] Re: Question regarding gaussian filtering > > Hi Tom, > > thank you vey rmuch for the fast and elaborate response. > > I believe I understand it much better now and see why the resolution > per se is not what I am after. > > My intention is to visualize/model the appearance of a lower > resolution map using a higher resolution map. While this should in > principal be possible (the other way around not) but would then > require an appropriate noise model. > > So the gaussian filtering only dampens the amplitudes of the > frequencies in Fourier space. The dampening can be controlled by the > standard deviation of the used gaussian function. The dampening > affects signal and noise equally. > > Does this correspond to a gaussian lowpass filter? Because I was > thinking about removing the high frequencies and setting the cutoff at > different frequencies then corresponding to different "resolutions". > While the resulting map probably has a higher signal-to-noise ratio at > lower frequencies (lower than the cutoff) than an experimental map of > a resolution that this map tries to depict it may still be a good > visual approximation. > > So I guess my question is whether there is a good way to > mimick/visualize a lower resolution experimental map using a higher > resolution experimental map without considering a sophisticated noise > model. > > Thanks again for your help. > > Best > Dennis > > > > Quoting Tom Goddard <goddard(a)sonic.net>: > > > Hi Dennis, > > > > I don't know the answer to your question, but here are some > > thoughts about it. The Gaussian convolution filter just scales the > > Fourier space coefficients by a Gaussian making the higher > > frequencies have lower amplitudes. That is reversible, the high > > frequencies can be scaled back up. So although the real-space > > smoothed map looks lower resolution, it still has the same high > > resolution content. The noise and the signal have both been scaled > > down at high resolutions so the signal-to-noise is just as good at > > those high resolutions. If you did this smoothing on two half-maps > > used to compute the resolution by Fourier shell correlation it would > > still give 2 Angstroms, the smoothing did not change the FSC > > resolution! If you were for example testing a fitting method it > > could easily extract that high resolution information and use it. > > In order to really lower the resolution you would need to add noise > > at high frequencies so the high-frequency signal is lost. > > > > That said you could ask if the noise at high frequencies was not > > scaled down, only the signal, then what would the reduced resolution > > be. We know at the FSC resolution the signal-to-noise ratio is some > > specific value that gives the cutoff correlation. But you would > > need a model of the noise amplitude at other lower frequencies to > > know how attenuating just the signal but not the noise would change > > the resolution. Maybe there is a pretty reliable noise model for > > these cryoEM maps, I'm not sure. > > > > Tom > > > > > >> On Jan 9, 2024, at 2:41 PM, Dennis Dannecker via ChimeraX-users > >> <chimerax-users(a)cgl.ucsf.edu> wrote: > >> > >> > >> Hello, > >> > >> I would like to ask a question regarding the gaussian filtering. > >> > >> I filtered a given map (downloaded from the emdb with the "open" > >> command from chimerax) in chimerax using the following command: > >> > >> vop gaussian #1 sDev X > >> > >> with X taking different values ranging from 0.25 to 20 with different steps. > >> > >> Now I would like to know the resolutions these maps actually > >> correspond to after this gaussian filtering. The originally loaded > >> map is stated to have nominal resolution of 2 Angstroms (GSFSC). > >> sDev defines the standard deviation in Angstrom of the 3D Gaussian > >> function that is used for the filtering. How can one now calculate > >> the resolution these filtered maps correspond to? Is it possible to > >> calculate or state a resolution for these maps that is related to > >> the resolution given for the original map (here 2 Angstroms). > >> > >> Thank you very much. > >> > >> Kind regards > >> > >> Dennis > >> > >> > >> > >> > >> Dennis Dannecker > >> Master Student of Biochemistry > >> Department of Chemistry > >> Faculty of Mathematics and Natural Sciences > >> University of Cologne > >> Albertus-Magnus-Platz > >> 50923 Cologne, Germany > >> _______________________________________________ > >> 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/ > > > -- > Dennis Dannecker > Master Student of Biochemistry > Department of Chemistry > Faculty of Mathematics and Natural Sciences > University of Cologne > Albertus-Magnus-Platz > 50923 Cologne, Germany > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ > > VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. > CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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