- ChimeraX-users - RBVI Mailing Lists

Measuring surface area of a colored portion of the map
by Y. Mutum 19 May '21

19 May '21

Hi This problem relates to surface area of a low-resolution EM map using ChimeraX I have opened the following map and the corresponding model using the following commands in ChimeraX. >>> open 4uq8; open 2676 from emdb >>> color #1 green; color zone #2 near #1 dist 4 As many parts of the map are unmodelled, I am interested 'how much of the map is unmodelled' in terms of surface area. This is mainly because the model is not accurate and I am trying to only use the raw-data (map) to estimate the surface area and avoid using the model. Is there a way to figure out how much of the map is unmodelled in terms of surface area? In this case, count the number of 'outer pixels of a map' that are colored green or gray, at a given map contour? Could you please help with a way to measure this without using the 'volume splitbyzone' command? Thanks Yaikhomba [cid:71184965-9ba5-4374-82b3-bd2b264b4b0c]

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Re: [chimerax-users] How to change the palette of hydrophobicity in ChimeraX
by Le Han 19 May '21

19 May '21

Hi Elaine, Thank you so much for your help. I managed to change it. Have a nice day! Han From: Elaine Meng<mailto:meng@cgl.ucsf.edu> Sent: Tuesday, 18 May 2021 18.12 To: Le Han<mailto:han.le@aalto.fi> Cc: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] How to change the palette of hydrophobicity in ChimeraX Hi Han, Although the icon just uses the "mlp" command with the default palette, you can use the "mlp" command with any palette that you want. The "palette" option specifies palette and "range" specifies value range. Instructions on "mlp" command and how to specify palettes: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> The hydrophobic coloring icon in the Toolbar "Molecule Display" tab uses command: mlp ...which is same as: mlp palette lipophilicity range -20,20 To use the same value range but get blue for hydrophilic and red for hydrophobic, you could use, for example, command: mlp palette blue-white-red range -20,20 Since red-white-blue is traditionally used for electrostatic coloring, however, you will have to be sure to explain the image so that people understand it is showing hydrophobicity instead. In the "mlp" instructions linked above, you can see there are several other options of the command that may interest you. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 18, 2021, at 6:55 AM, Le Han <han.le(a)aalto.fi> wrote: > > Hi, > I’d like to change the colour palette of hydrophobicity to red (most hydrophobic) – white – blue (most hydrophilic). Is it possible to do so in ChimeraX and how can I change? > Thank you in advance, > Han

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Proxy setting with user authentication
by fukamitka＠chugai-pharm.co.jp 18 May '21

18 May '21

Dear ChimeraX developers, I’m a new user of ChimeraX. How can I set username/password for HTTP/HTTPS proxy settings? Our firewall is strict and requires username/password authentication. I’d like to install ISOLDE (we purchased the license), but I can’t install it via Tools > More Tools... I downloaded the .whl file for ISOLDE from the ChimeraX Toolshed page (https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde) and tried the command below in ChimeraX windows, toolshed install /path/to/the/ChimeraX_ISOLDE-1.2.0-cp38-cp38-manylinux_2_17_x86_64.whl but failed during pip install (by SSLError, which means proxy was not set correctly). Enviroment variables http_proxy and https_proxy were set when ChimeraX executed, but not worked. Best regards, Takaaki ----- Dr. Takaaki Fukami (mailto:fukamitka@chugai-pharm.co.jp) Protein Science Dept. (Protein Science 2 Gr.) Chugai Pharmaceutical Co.,Ltd. 200 Kajiwara, Kamakura, 247-8530 Japan Tel: +81-467-47-6178

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How to change the palette of hydrophobicity in ChimeraX
by Le Han 18 May '21

18 May '21

Hi, I’d like to change the colour palette of hydrophobicity to red (most hydrophobic) – white – blue (most hydrophilic). Is it possible to do so in ChimeraX and how can I change? Thank you in advance, Han

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Pseudobond in Metalloproteins
by Rachael Coleman 17 May '21

17 May '21

Hello! I have recently switched over to using ChimeraX from PyMol and I'm really enjoying it a lot! My one question that I haven't been able to figure out is how to deal with pseudobonds in a heme-containing protein. I want ChimeraX to treat the bond between the porphyrin N atoms and the Fe atoms like a bond and not a pseudobond (so I want it to be half blue and half orange to correspond to the colors of those atoms). Is there an easy way to tell the program that a pseudobond is a bond? Best, Rachael Coleman -- *Rachael E. Coleman* PhD Candidate, Lancaster Group Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853 Pronouns: She, her, hers

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How to Color Each Atom (TAD) According to Its Gene Expression Level
by Cardiff Jiang 15 May '21

15 May '21

Dear ChimeraX Users Help, I want to color each atom, which is a TAD, according to its genes’ expression value. My code writes a Chimera marker file because it has RGB variables (shown below, the lower the gene expression, the lighter the shade of green). However, ChimeraX shows the entire model in the same color. How should I color each atom (TAD) according to its gene expression level? [image: image.png] Thank you. Best regards, Zichen “Cardiff” Jiang -- Best regards, Zichen “Cardiff” Jiang

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where is my saved image
by Kang, Yanyong 13 May '21

13 May '21

Hello, I am saving image using the command below. Do you know where the saved image is? Thanks save a.png transparentBackground true Yanyong The content of this email and of any files transmitted may contain confidential, proprietary or legally privileged information and is intended solely for the use of the person/s or entity/ies to whom it is addressed. If you have received this email in error you have no permission whatsoever to use, copy, disclose or forward all or any of its contents. Please immediately notify the sender and thereafter delete this email and any attachments.

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Release of ISOLDE 1.2
by Tristan Croll 13 May '21

13 May '21

Hi all, I'm very happy to announce the release of ISOLDE 1.2, now available for installation into the ChimeraX 1.2 release. To get it, first download and install ChimeraX 1.2 from https://www.rbvi.ucsf.edu/chimerax/download.html, then go to "Tools/More Tools..." in the menu and follow the links to install ISOLDE. Key new features include: * The ability to add residues to the ends of protein chains (see https://twitter.com/CrollTristan/status/1391747032579289089?s=20; support for nucleic acid chain extension still in development) * Lower-fidelity simulation modes for greatly improved performance on lower-end GPUs (see https://twitter.com/CrollTristan/status/1390709520876331009?s=20) * Commands to write input files for phenix.refine and phenix.real_space_refine with recommended settings for refining models from ISOLDE * Command to write a ProSMART-like restraint definition file to softly restrain the model to its current geometry in Refmac * Improvements to stability and performance of bulk solvent/scaling in crystallographic datasets * Short aliases for commonly-used commands to make life easier for power users. Please enjoy! Best regards, Tristan

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BLAST fix
by Eric Pettersen 12 May '21

12 May '21

Hi all, The RCSB switching off http access and only allowing https (which had been announced) unfortunately broke the fetching of PDB info associated with BLAST results, basically breaking the BLAST tools in both Chimera and ChimeraX. Fixes have been applied and will be available in tomorrow's daily builds. For ChimeraX, also available in the 1.2.3 release candidate -- hopefully also out tomorrow. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Generating map from structure
by Eric Pettersen 11 May '21

11 May '21

> Begin forwarded message: > > From: "Azad, Roksana" <razad(a)gc.cuny.edu> > Subject: Re: [ChimeraX] #4622: save dialog: 'SaveModelOptionWidget' object has no attribute '_name' > Date: May 11, 2021 at 9:00:00 AM PDT > To: "ChimeraX-bugs(a)cgl.ucsf.edu" <ChimeraX-bugs(a)cgl.ucsf.edu> > > Dear Eric, > Thank you so much for your reply. > > I have a model of my protein in pdb format, which I am trying to save as .mrc or any sort of volume file on chimera. However, since its a model and do not have any coordinate in the file like xtal or NMR structure, it won’t save it as .mrc or volume file and was giving me the error. > > I want to create a volume file from the model to load on cryoSPARC or relion and create 2D projections to help me pick better 2D classes from my raw data. Do you think there is an option to do something like this on chimera? > > Thank you again for your time and help in advance – very much appreciated. > > Sincerely, > Roksana > >> On May 11, 2021, at 11:50 AM, ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: >> >> #4622: save dialog: 'SaveModelOptionWidget' object has no attribute '_name' >> -----------------------------------+---------------------------- >> Reporter: razad@… | Owner: Eric Pettersen >> Type: defect | Status: closed >> Priority: normal | Milestone: >> Component: Input/Output | Version: >> Resolution: duplicate | Keywords: >> Blocked By: | Blocking: >> Notify when closed: | Platform: all >> Project: ChimeraX | >> -----------------------------------+---------------------------- >> Changes (by Eric Pettersen): >> >> * status: accepted => closed >> * resolution: => duplicate >> >> >> Comment: >> >> Hi Roksana, >> Thanks for reporting this problem. ChimeraX was trying to tell >> you that you hadn't selected anything to save in the save dialog, but >> there was an error in the code that generates that message, which is what >> you saw. So the error is easy to avoid. Nonetheless, if you want to >> always avoid it in the future you could use the current daily build or the >> 1.2.2 release candidate, both of which have this problem fixed. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> -- >> Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_tra… > >> ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chime… > >> ChimeraX Issue Tracker > >

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