- ChimeraX-users - RBVI Mailing Lists

Re: Help with ChimeraX and dual extruder 3D printing
by Tom Goddard 24 Aug '23

24 Aug '23

Hi Billy, ChimeraX writes out the STL files using the coordinates in the ChimeraX scene, so the STL files contain aligned coordinates. The problem is your 3D printer software is changing the alignment. Here's an example of ChimeraX commands open 1eqz surf enclose protein surf enclose nucleic save histones.stl models #1.3 save dna.stl models #1.4 If you open these two STL files in ChimeraX you will see that they are aligned. The STL files only contain x,y,z coordinates and the format does not support any positioning transformations. So the 3D printer software cannot interpret the file in a different way. So your problem is to tell the printer software not to change the alignment given in the two files. Perhaps when you specify the origin in the printer software that origin is relative to the center of the surface bounding box, so it will center the two STL files differently. Tom > On Aug 23, 2023, at 9:40 AM, Dye, Billy via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > I have been using ChimeraX to generate STL files for 3D printing models of a variety of protein structures that I use in my biology classes. I recently acquired a dual extrusion printer which should allow me to print models in two different colors. For example, I am currently trying to print a nucleosome from RCSB model 7PFX such that the DNA is printed blue from one extruder and the histones white from the second extruder. I am exporting two different STL files from ChimeraX, one with the DNA and one with the histones, and I am attempting to slice with FlashPrint 5 software for a FlashForge Creator Pro 2 printer. However, when I import the two STL files into the slicing software, they are not aligned. Even if I position both at 0,0,0 coordinates, it is obvious that the DNA and histones are not lining up properly. Is there a way to export the two STL files from ChimeraX such that they have a common reference point or origin and will thus align with one another when both are placed into the slicing software? > > Many thanks for your consideration and advice, > Billy Dye > > <PastedGraphic-2.png> > > _______________________________________________ > 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

Change default step size for volumes?
by Oliver Clarke 24 Aug '23

24 Aug '23

Hi, Is there any way in ChimeraX to change the default step size for volumes? There are volume commands (e.g. volume limitVoxelCount false) that look like they ought to do the trick but these only seem to apply to already opened volumes - is there a way to make it a persistent preference for newly opened volumes? In Chimera this was a setting in the Volume Viewer, but I can’t find an equivalent yet in ChimeraX in either the global settings or the docs for the volume command. Cheers Oli

3 5

Saving the resolution of structure to a file
by Prathvi Singh 24 Aug '23

24 Aug '23

Hi Elaine, Is there a way to save the resolution of a protein structure to a file using command line, either in chimeraX or chimera? Thanks -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

3 4

Equivalent to "ac ri" in ChimeraX?
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, In Chimera, the accelerator “ri” selects intervening residues. This is convenient because one can select two residues (let’s say at the start and end of a domain) and then select all the residues between them without having to explicitly specify a residue range (I have this bound to the alias “selbetween”) in Chimera. Is there any equivalent accelerator in ChimeraX? Cheers OIi

2 1

Help with ChimeraX and dual extruder 3D printing
by Dye, Billy 23 Aug '23

23 Aug '23

I have been using ChimeraX to generate STL files for 3D printing models of a variety of protein structures that I use in my biology classes. I recently acquired a dual extrusion printer which should allow me to print models in two different colors. For example, I am currently trying to print a nucleosome from RCSB model 7PFX such that the DNA is printed blue from one extruder and the histones white from the second extruder. I am exporting two different STL files from ChimeraX, one with the DNA and one with the histones, and I am attempting to slice with FlashPrint 5 software for a FlashForge Creator Pro 2 printer. However, when I import the two STL files into the slicing software, they are not aligned. Even if I position both at 0,0,0 coordinates, it is obvious that the DNA and histones are not lining up properly. Is there a way to export the two STL files from ChimeraX such that they have a common reference point or origin and will thus align with one another when both are placed into the slicing software? Many thanks for your consideration and advice, Billy Dye [PastedGraphic-2.png]

2 1

Trackpad modifier to translate in z?
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, In Chimera, I have shift-two-finger-drag set to translate the view in Z. This is very useful for precisely navigating around large structures without reorienting the camera, particularly when the cofr is bound to the center of view. Is there any way to replicate this behavior in ChimeraX? Cheers Oli

4 10

Add shortcuts to Model panel, log and Volume viewer to toolbar?
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, I love the ability to customize the home tab of the toolbar, but there are some other things that I would like to add there and I don’t see how. Is there any way to add shortcuts/icons for the model panel, the log and the volume viewer? The use case is that I prefer to keep all panels undocked, in order to maximize screen real estate when working on a laptop - having shortcuts to bring these up would be convenient. It would also be great to have a shortcut for either a specific alias, or a dropdown menu of aliases, for custom lighting/visualization modes defined in the startup commands. Cheers Oli

4 6

W-9 Request, Belharra Therapeutics | For Chimera
by Belharra Therapeutics Purchasing 23 Aug '23

23 Aug '23

Hello, I've recently tried to reach out regarding Chimera. All of my emails have been returned as undeliverable. Can I please get you assistance with the following information for Chimera? * A copy of your W-9 (or W-8, W-8BEN, W-8BENE for International) * Contact for your accounting department * Our account number for us to reference on our PO's, or if we are to refer to our company name. * Sales or email address to submit PO's Thank you, Heath Jarred Earle Belharra Therapeutics, Inc.. - Purchasing belharra(a)iabuyer.com<mailto:belharra@iabuyer.com> Innovative Advancement, LLC Brand & Vendor Specialist Ph: 425-686-9566 Ext. 703 www.innovativeadvancement.com<http://www.innovativeadvancement.com/> [cid:image001.gif@01D9D5BC.E5247540] <https://www.facebook.com/Innovativeadvancement/> [cid:image002.gif@01D9D5BC.E5247540] <http://twitter.com/innoadvance> [cid:image003.jpg@01D9D5BC.E5247540] CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential information and may be legally protected from disclosure. If you are not the intended recipient of this message, or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited

2 1

Regarding use of attribute assignment files and difference between ChimeraX and ChimeraX daily build
by SUHANI BHATTACHARYYA 23 Aug '23

23 Aug '23

Dear Team Chimera, I am a second-year undergraduate student at IISER, Pune. I have been using ChimeraX for some time. Earlier I have also used some older Chimera versions. They had the kdHydrophobicity under Render by Attribute for residues. However, ChimeraX does not. On reporting a problem, I was told to use attribute assignment files for kdHydrophobicity. I downloaded the file as .txt file with .defattr suffix. Then, following the instructions in the user guide, I tried to use the open command to start using the attribute file. But I was shown an error that no such file existed. I even changed the file location and checked with multiple directories, including where ChimeraX files are stored on my PC to try to open the file, but nothing has worked. Kindly provide clearer instructions on where to save and open the attribute assignment files. Thank you. Regards, Suhani Bhattacharyya

2 2

Fwd: Help with ChimeraX and 3D printing
by Elaine Meng 23 Aug '23

23 Aug '23

Dear Billy, Please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list to ask ChimeraX questions (CC'd here so you don't need to re-send) -- I am not sure of the answer, and others on the list have more expertise in this area. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: "Dye, Billy" <Billy.Dye(a)volstate.edu> > Subject: Help with ChimeraX and 3D printing > Date: August 23, 2023 at 8:31:21 AM PDT > To: "meng(a)cgl.ucsf.edu" <meng(a)cgl.ucsf.edu> > > Hello > > I hope you might give some advice on using ChimeraX with dual extrusion 3D printing. > > I have been using ChimeraX to generate STL files for 3D printing models of a variety of protein structures that I use in my biology classes. I recently acquired a dual extrusion printer which should allow me to print models in two different colors. For example, I am currently trying to print a nucleosome from RCSB model 7PFX such that the DNA is printed blue from one extruder and the histones white from the second extruder. I am exporting two different STL files from ChimeraX, one with the DNA and one with the histones, and I am attempting to slice with FlashPrint 5 software for a FlashForge Creator Pro 2 printer. However, when I import the two STL files into the slicing software, they are not aligned. Even if I position both at 0,0,0 coordinates, it is obvious that the DNA and histones are not lining up properly. Is there a way to export the two STL files from ChimeraX such that they have a common reference point or origin and will thus align with one another when both are placed into the slicing software? > > Many thanks for your consideration and advice, > Billy Dye > > > >

1 0

Regarding probeRadius
by Sakiat　Hossain 23 Aug '23

23 Aug '23

Dear Sir/Madam, Greetings. I am a nanomaterial chemist, and I would like to measure solvent accessible surface area (sasa) of my metal nanocluster using its single crystal x-ray diffraction structure. Specifically, I want to calculate H+ accessible surface area. I would appreciate it if you kindly let me know how to change probeRadius for calculating sasa in ChimeraX. I look forward to your kind help. Best, Sakia Hossain Tokyo University of Science, Japan Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

2 1

Trackpad rotation
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, The trackpad zoom/rotation settings in ChimeraX seem very different from “old” Chimera. Is there any way to replicate the behavior from Chimera? Specifically, when I pinch to zoom in ChimeraX, I often find the view rotating a lot, unless I am very careful, which does not happen in Chimera. I have tried playing around with the trackpad twist sensitivity, but so far have been unable to find settings similar to the default in Chimera. Cheers Oli

2 8

ChimeraX registration
by Rouzer, Carol A 21 Aug '23

21 Aug '23

To Anyone who can help: I recently downloaded ChimeraX after many years of using Chimera. I keep getting the following warning message: Registration file '/Users/carol/Library/Application Support/ChimeraX/registration' has expired I assume this means I should re-register, but I can’t find any mechanism to do that. Sorry for my stupidity, but I do want to be using the software legitimately. Please instruct. Thanks, Carol Carol A. Rouzer, Ph.D., M.D. Senior Editor/Writer A.B. Hancock Memorial Laboratory for Cancer Research Basic Sciences, School of Medicine Vanderbilt University Nashville, TN 37232-0146 c.rouzer(a)vanderbilt.edu<mailto:c.rouzer@vanderbilt.edu>

2 2

Installation of chimera failing
by Royan, Santana (Manufacturing, Clayton) 20 Aug '23

20 Aug '23

Hi there, I'm having trouble installing chimera on my work windows laptop for the IUCR2023 Phenix workshop. The installation keeps failing due to being unable to create the directory in the C drive (see screenshot). [cid:image003.jpg@01D9D3B7.892B9130] My organisation does restrict administrator rights on this laptop and requires me to apply for it for a limited period of time, but I have enabled these before starting the installation. I note that the installer didn't ask for admin access when installing here on this computer before the License Agreement, but it did on my personal laptop which proceeded with the installation just fine. Am I missing something with the installation package? This is happening for both the daily build executable and the 1.6.1 build. Regards, Santana Santana Royan CERC Fellow in Optimising Biodegradation of Plastics MCM Manufacturing | CSIRO santana.royan(a)csiro.au<mailto:santana.royan@csiro.au> | 03 9662 7107 Building 201 Level 2, Research Way, Clayton VIC 3128 CSIRO acknowledges the Traditional Owners of the land, sea and waters, of the area that we live and work on across Australia. We acknowledge their continuing connection to their culture and we pay our respects to their Elders past and present. CSIRO Australia's National Science Agency | csiro.au<www.csiro.au>

2 2

Difficulty docking proteins
by Weidenbach, Megan 18 Aug '23

18 Aug '23

Hi there, My name is Megan Weidenbach and I am a user of the ChimeraX software. We have been trying to dock built organic molecules to coagulant factor proteins. So far, we have had no luck with the AutoDock Vina feature. This has been tested on the mac and microsoft versions of the software. I was wondering if your team might be able to point us in the direction of some resources that could help dock the proteins and identify their binding sites? Thank you! Megan L. Weidenbach B.A. Biology & Pre-Veterinary Studies meganweidenbach(a)myunt.edu University of North Texas [cid:c8b6bc7f-58c7-4404-8b08-46a6fb60aca9]

2 1

Plugin development questions
by BARRY E DEZONIA 18 Aug '23

18 Aug '23

Hello, I have been developing a plugin in bits and pieces for a while. I am now hoping to build a bundle (or whatever) to make installation pretty seamless. My program is a bit unconventional so I have a few questions on how to proceed. My plugin templating copies one of the examples (maybe the Tool example). My plugin uses a couple of python packages/modules: * mdtraj (https://mdtraj.org/1.9.3/installation.html) * traj2nmr (https://github.com/weberdak/traj2nmr) It also will have some shell scripts I want to include and also a java program. So far we have been getting by installing things like this: * in chimerax using the command prompt entering "pip install mdtraj" or similar * from an OS terminal invoking chimerax's version of python to run traj2nmr's setup.py program so that it goes into chimerax's python's installed packages * including our shell scripts in a Runnable directory under the plugin installation directory (during development) and copying them in a similar directory under the ~/.local/share/....chimerax-path-stuf.../the-plugins-Runnable-dir. Maybe the plugin installation process does this for me already but it is often not showing the latest changes even after plenty of "dev installs" in the chimerax command prompt line. * I am just starting to want to place the java app and the shell script that launches it somewhere. Hopefully in that same Runnable directory. Right now, I am trying to learn what is the best approach to bundle this all together and have a simple installation process. Can someone advise a bit? Thanks.

4 9

Is there a python module to access ChimeraX from outside with Python?
by Jonathan David Karl Krahl 17 Aug '23

17 Aug '23

Good morning, my name is Yona and I am working at the chair of Computational BioEngineering at the Technical University in Dortmund, Germany. I was wondering, if there is a possibility to access ChimeraX from outside with Python; the module "pychimera" provides an API for Python and Chimera, but not ChimeraX, as far as I know. Do you know an alternative or a way to do it? Thanks for your help :) Yona

2 1

info retrieval
by Eduardo Mauricio Martin 17 Aug '23

17 Aug '23

To whom it may concern: According to the documentation sequences infor from a model can be retrieved by the following command: info polymers #1 saveFile "C:\Users\faits\Documents\test8.txt" Though the console keeps throwing the following error attached as image. [cid:image002.png@01D9D083.452CFE10] I just need to retrieve the residue number for each subunit to run a Python script that removes sasa values from hetatm which are not in the protein per se. If there is a work around to acquiere this inforation in a file please let me know. Kind regards, Eduardo M Martin PhD Candidate Information systems Department Autonomous University of Aguascalientes. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

2 1

re error with Movie recorder utility
by Anna Lohning 16 Aug '23

16 Aug '23

Hi I have the freeware version installed and trying to make a movie using the Tools/Utilities/Movie recorder window. At this stage, I seem to only have the command line available for commands one at a time. Anyway, under the Tools/Utilities, the only options there currently are Register Updates Be grateful for some clarification as I cant seem to find anyone having this issue. Many thanks Kind regards Anna Dr Anna Elizabeth Lohning Associate Professor - Biochemistry Faculty of Health Science & Medicine Bond University ROBINA 4229 (07) 5595 4779 alohning(a)bond.edu.au<mailto:alohning@bond.edu.au>

2 1

Getting number of residues from a PDB contain only a fragment
by huybk81＠gmail.com 16 Aug '23

16 Aug '23

Hi, I used this Python code to get the number of residues: model = run(session, 'open %s' % input_model)[0] print(model.chains[0].num_residues) It works when the input_model is a complete pdb file. However, when the input_model only contain part of the structure of the full pdb but retains the full sequence information, the code above always return the num_residues of the full structure, not the input_model only. Is there any way to get this done? Best, Huy

2 2

colouring by entity
by Manon Demulder 15 Aug '23

15 Aug '23

Hi I have a model that consists of a sheet made out of repeats of a dimer. Currently I have a .mmcif file with the monomers in each dimer being labelled either 1 or 2. I would like to give monomer 1 and 2 a different color in my sheet. Is it possible in ChimeraX to recolour the different monomers by their entity 'name'? Thanks in advance! Best Manon ------------------------------------------------------------ Manon DEMULDER PhD | Post-doctoral researcher University of Basel | Biozentrum | Ben ENGEL lab Spitalstrasse 41 | 4056 Basel | Switzerland manon.demulder(a)unibas.ch | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch>

2 1

AreaSAS Function in ChimeraX
by Andy Nguy 14 Aug '23

14 Aug '23

Hello, I was wondering if there is a AreaSAS function for ChimeraX. To my knowledge, there was such a function in Chimera under "Render by Attribute". If not, is there a way to identify all solvent-accessible residues for a protein of interest? Thanks! -- Andy.

2 1

Problem with saving files through command line
by Vorländer,Matthias Kopano 14 Aug '23

14 Aug '23

Dear Developers, I have found a strange behavior when saving files through the chimeraX command line. Essentially, file naming does not seem to be properly sensitive to capitalization. For example, when I am trying to save a file called “chain_A.pdb” and then another file called “chain_a.pdb”, “chain_A.pdb” will be overwritten with the contents of “chain_a.pdb”. It also does not matter if I am saving a pdb file or a log file. If “chain_A.pdb” does not exist, then “chain_a.pdb” will be correctly saved with as a lowercase a. Details: version 1.6.1 (2023-05-09) OS: MacOS Catalina Version 10.15.7 Would be great if this could be fixed : ) Many thanks in advance, Matthias

2 1

Library Missing in Debian v-12
by Stephen P. Molnar 14 Aug '23

14 Aug '23

I have just downloaded ucsf-chimerax_1.6.1ubuntu22.04_amd64.deb for installation on my Debian-12 platform. Unfortunately, the missing dependency libffi7 is not part of the distributiojn. Please Advise. Thanks in advance. ucsf-chimeax-- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

3 2

Opacity of atoms
by Haaris Ahsan Safdari 13 Aug '23

13 Aug '23

Hi ChimeraX team, I am working on a protein that clashes with RNA. Hence, to show those, I selected atoms of proteins (sphere representation) which are less or equal to 3.5Å from RNA and then colored them red. Through this criteria, some atoms of protein which do not clash with RNA, I keep them as lime colour. All of this works fine. Now, I wanted to show the clash more clearly since RNA segments pierces through many atoms of protein, so I wanted to make protein atoms (which is now a combination of red for clashing atoms and lime for non-clashing atoms) transparent. However, as soon as I make my protein more transparent (by changing opacity), all atoms of my protein turn red and I lose the green ones which I dont want. I just wanted to know if there is any workaround for this (to retain green while making everything more transparent) or if it is just a bug? Best regards, Haaris Ahsan Safdari

2 1