- ChimeraX-users - RBVI Mailing Lists

General developer questions
by BARRY E DEZONIA 25 Aug '23

25 Aug '23

Hello, I have been writing a plugin for ChimeraX. One feature it does now is read a PDB file, parse some info, and act on that data internally. I'd like to change it so that it can use information about a loaded PDB in ChimeraX. To this I have a couple questions: 1. Are there some basic docs on how someone could access a protein that is memory resident that was loaded from a PDB (i.e. just what data structures can I access programmatically related to a protein loaded with open(<pdbname>)). 1. How do I find the data structure(s) for the currently viewed or selected or ??? protein? I'd like someone to be viewing a protein and then launch my plugin which will use that protein and its data for the plugin's internal calculations. I'm sorry if this is noise. If there are good developer docs for these topics please feel free to point me in the right direction. Thanks.

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How to use ColorBrewer palette?
by Tianyang Liu (Staff) 25 Aug '23

25 Aug '23

Hello, I would like to colour my structure with the ColorBrewer palette using ChimeraX. But I can't seem to get it to work. I used the command: color bychain cartoons;palette Pastel1-9. The error message displayed is "Unknown command: palette Pastel1-9." Could you help me with this please? Many thanks, Tian

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Does getcrd return coordinates in pixels or in angstroms?
by Samuel Haysom 25 Aug '23

25 Aug '23

Hello, I am trying to determine the coordinates of a point on a volume for use in cryoSPARC (as described here for Chimera: Job: Local Refinement (Legacy) - CryoSPARC Guide<https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/loca…>). I was wondering if the getcrd command returns coordinates in angstroms (as it did in Chimera) or whether they are in pixels? This was not specified on the getcrd documentation page as far as I could see (Command: getcrd (ucsf.edu)<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/getcrd.html>). KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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Changing Colors and Unable to Save as pdb File
by Natalia Tegenfeldt 25 Aug '23

25 Aug '23

I have been using chimerax to visualize the proteins I'm working with, and have been highlighting sections of the sequence and changing the color to highlight those sections, but when I try to save it as a pdb, it gets rid of the colors. Is there a different way to be able to keep a section highlighted/different color when I save it as a pdb file? Thanks!

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Question on Chemistry StackExchange regarding ChimeraX Python Log.
by nikolic＠uwm.edu 24 Aug '23

24 Aug '23

Hello, I'm developing a series of commands and presets for ChimeraX and run into the following trouble in self-support: https://chemistry.stackexchange.com/q/175802/136866 Thank you! Nickolas Nikolic

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Play a volume morph
by James Kizziah 24 Aug '23

24 Aug '23

Hi, I need to record a movie of a modified volume morph focused on a small part of much larger structure. Is it possible to just play an existing morph with a command? I can generate the morph, volume zone to a reference atomic model, and make it transparent to visualize the features I'm interested in, but how can I record the movie after accomplishing these steps? Incorporating the volume morph command in a movie-making script regenerates the original morph without zoning our transparency. Thanks! James

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ViewDockX Options
by Ute Roehrig 24 Aug '23

24 Aug '23

Dear ChimeraX Developers, thank you very much for developing and providing ChimeraX! I was wondering if you could make the ViewDockX command more user friendly, especially providing the following features: 1. When opening a docking results file (format SwissDock/Dock/Vina/Glide), launch the ViewDockX tool automatically 2. In the ViewDockX table, provide the possibility to select several poses by Shift+clicking on several lines in the table (the way it was working in Chimera) 3. Let the user automatize/customize the columns he wants to see by default (provide columns as option in the command line?) Thank you very much for considering these points, Ute -- Ute Roehrig SIB | Swiss Institute of Bioinformatics Unil, Quartier Sorge, bâtiment Amphipôle, 1015 Lausanne t: +41 21 692 40 86 - f: +41 21 692 40 65 Ute.Roehrig(a)sib.swiss<mailto:Ute.Roehrig@sib.swiss> - http://www.sib.swiss

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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/

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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

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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

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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

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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]

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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

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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

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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

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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

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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 > > > >

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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

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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

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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>

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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>

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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]

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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.

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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

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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

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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>

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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

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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>

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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.

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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

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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

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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

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Fwd: how to fix this.... it is windows machine.
by Eric Pettersen 11 Aug '23

11 Aug '23

> Begin forwarded message: > > From: Krishnan Raman <RKrishnan(a)BIOCRYST.com> > Subject: how to fix this.... it is windows machine. > Date: August 11, 2023 at 12:20:16 PM PDT > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > > > Krishnan Raman > Executive Director, Structural Biology > BioCryst Pharmaceuticals > > > > > CONFIDENTIALITY NOTICE > > This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >

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Regarding Volume Morph Issue
by Chen, Shin-Fu 11 Aug '23

11 Aug '23

Hello, I hope this message finds you well. I am currently working on creating a movie using the "volume morph" command based on ten sets of mrc files. I have encountered an issue that I would appreciate your assistance with. Prior to applying the "volume morph" command, I have utilized the "color near atoms" option to assign colors to the visualization. However, after executing the "volume morph" command, the previously assigned colors are reset to a default single color. I am reaching out to seek guidance on resolving this issue. Your insights and advice would be greatly appreciated. Thank you for your attention to this matter, and I eagerly await your response. Best regards, Shin-Fu Shin-Fu Chen, Ph.D. Postdoctoral Fellow Department of Biochemistry and Molecular Biology McGovern Medical School University of Texas Health Science Center Houston 6431 Fannin St | MSB 6.326 | Houston, Texas 77030

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Re: [Chimera-users] making composite map using vop maximum command
by Elaine Meng 10 Aug '23

10 Aug '23

Hi, In ChimeraX it is documented as "volume maximum" (even though I believe that "vop maximum" like in the older program Chimera could be used). Also if you want to ask about ChimeraX specifically, there is a different email address, chimerax-users(a)cgl.ucsf.edu -- I CC'd it here so you don't need to do anything this time. Here is the ChimeraX "volume maximum" help link: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#maximum> For example, if your maps are #2 and #3, you can create a new map containing the maxima of their two values with ChimeraX command: vol max #2,3 ... but there are many additional options that could also be included in that command, so you should check the help link above to see if you want to use any of them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 7, 2023, at 2:20 PM, ytakagi--- via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi > I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? > Thanks

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Spherical mask
by Grundmann,Lorenz Emanuel 10 Aug '23

10 Aug '23

Dear chimerax-team, I am looking into a possibility to generate a spherical volume in chimerax that I can then use as a spherical mask for focused 3D classifications and signal subtractions. For my specific need, a sphere would be the ideal shape. So far I managed to generate a surface model using the ‘shape sphere’ command, to place it to the region of interest and resampling it onto the coordinate system of my protein of interest. Is there any possibility to transform the surface model into a (binarized) volume? Best, Lorenz

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Re: Advice on handling cofactor-protein electrostatic interactions
by Boaz Shaanan 08 Aug '23

08 Aug '23

Thanks Elaine, I'll do just that. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________ From: Elaine Meng <meng(a)cgl.ucsf.edu> Sent: Tuesday, August 8, 2023 11:57 AM To: �� <bshaanan(a)bgu.ac.il> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Advice on handling cofactor-protein electrostatic interactions Hi Boaz, If you use Coulombic it will automatically calculate the charges, as in my example of 1qs0 with the TPP residue. I.e. you don't have to do it in a separate step first, and in fact it may be better if you do not: if you use Add Charge first, it will also add hydrogens and make the surface a lot bumpier. If you just use Coulombic the hydrogens are added only on a temporary copy that is in memory, not on your model, and the coloring will be applied to the smoother molecular surface without hydrogens. You just need to substitute the cofactor residue name for ":tpp" in my example, if it is not TPP. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 8, 2023, at 7:09 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > Thanks a lot for the detailed reply and (as always) very helpful suggestions. I'll experiment first with the Chimerax coulombic surfaces and trick to include the cofactor. This sounds attractive, certainly for the TDP case as a starting point. As for derivatives of TDP, which are already included in the pdb, I guess I should follow the 'Add Charges' guide, right? > > Thanks again. > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Monday, August 7, 2023 10:17 PM > To: �� <bshaanan(a)bgu.ac.il> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Advice on handling cofactor-protein electrostatic interactions > > Hi Boaz, > This answer addresses coloring by electrostatic potential (ESP). Calculating the electrostatic interaction per se (energy?) is somewhat different and not something that ChimeraX does. > > ChimeraX can color some surface, which could be a molecular surface, by the values in a 3D map, which could be electrostatic potential (ESP). See "color electrostatic" > <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%…> > > The ESP map can come from a Poisson-Boltzmann calculation (APBS, DelPhi, others) or from a more simplistic Coulombic calculation which can be done directly in ChimeraX. > > Poisson-Boltzmann calculations require atomic coordinates, partial charges, and radii, but the different programs differ in how you input these values. > > If I recall correctly, APBS takes as input a pqr file (q means charge, r means radii) which would usually be generated by PDB2PQR, but you said PDB2PQR throws out the nonstandard residues like cofactors, I guess because it doesn't have charges for them. ChimeraX assigns radii and can assign atomic partial charges (via lookup table for standard residues and Antechamber calculation for nonstandard residues like cofactors). However, ChimeraX does not write pqr format. Also in ChimeraX, these partial atomic charges are for all atoms (i.e. all hydrogens explicit) and not a united-atom model (in which hydrogens on carbons are merged with those carbons so that they become implicit) which is often used for Poisson-Boltzmann calculations. So if you wanted to go the APBS route, in ChimeraX you would add hydrogens and charges, then save the cofactor radii and atomic partial charges (atom attributes "radius" and "charge") in the attribute file format, and if you were using a united-atom charge model, manually generate united atoms from CH, CH2, and CH3 groups in the cofactor by adding the hydrogen charges to those of the carbons where they are attached and figuring out the appropriate united-atom radii, then reformat the cofactor atom coordinates, radii and charge values into pqr format and then add these lines to your protein pqr file from PDB2PQR, then use the resulting combined pqr file as input to APBS to get the ESP map that includes cofactor contributions. > > Actually I don't even know if APBS would accept that pqr file or not, but that is what I imagine you would try. So let's assume the APBS calculation will run using that pqr file. > > Then you would open the APBS ESP map that includes cofactor contributions in ChimeraX and color the molecular surface. If the cofactor is covalently attached to the protein then the protein molecular surface may already include it. However, if the cofactor is not covalently attached, you would need to tell ChimeraX specifically to lump it inside of the same surface as the protein with the "include" option of "surface" when you are calculating and displaying the molecular surface. > > The "coulombic" approach wil do more of these steps for you, given the "include" trick as well as the "surfaces" option of the "coulombic" command, but calculating ESP with the relatively simplistic Coulomb's law method. For example, 1qs0 chain A includes a noncovalently bound TPP residue and I could show the surface including the TPP and colored including its potential contribution: > > open 1qs0 > surf include :tpp > coulombic surfaces #1.2 > > <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%…> > <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%…> > > See first image attached with :tpp selected (green outline surface patch) > > If you don't use the "include" and "surfaces" options in these commands, the surface will be redrawn to include only the protein part with the TPP outside of it, like other ligands and the Coulombic ESP will not include the TPP contribution. See second image attached. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > <Screen Shot 2023-08-07 at 7.08.37 PM.png><Screen Shot 2023-08-07 at 7.12.43 PM.png> > > >> On Aug 7, 2023, at 4:10 PM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hi, >> >> I would like to present effects of mutations around cofactors (TDP derivatives) on the protein - cofactors electrostatic interactions. I use APBS and chimerax to display the electrostatic surface potential of the protein, but since PDB2PQR eliminates the cofactor from the pqr file I need a tool for the cofactor surface potential. I'm wondering what tool I should use for this. Is it Antechamber+chimerax or something else? >> Is there by chance a demo for such scenario? >> I'd appreciate your advice. >> Cheers, >> >> Boaz >> >> >> Boaz Shaanan, Ph.D. >> Dept. of Life Sciences >> Ben-Gurion University of the Negev >> Beer-Sheva 84105 >> Israel >> >> E-mail: bshaanan(a)bgu.ac.il >> Phone: 972-8-647-2220 >> Fax: 972-8-647-2992 or 972-8-646-1710 >> >> >> >> >> _______________________________________________ >> 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://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%… > > _______________________________________________ > 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://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%…

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Re: [Chimera-users] Saving phi psi values to a text file
by Elaine Meng 07 Aug '23

07 Aug '23

Hi Prathvi, In Chimera there is no command to save attributes. Instead you have to use the Render by Attribute dialog's File menu as described in the bottom section of this page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.ht…> In ChimeraX, as far as I know you can only save one attribute to a file at a time with the "save" command. However, it would probably work just to use the "save" command several times and then (outside of ChimeraX) concatenate the multiple files into one file afterward. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> Another idea is that in ChimeraX you can list attribute values in the Log with the "info" command, e.g. info residues protein attribute phi So an alternative approach if you don't need the file to be in the attribute-file format is to use "info" multiple times and then save the Log contents to an HTML file with "log save" -- see help pages for those commands: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 5, 2023, at 10:14 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > Is there a command to save the phi and psi angle values of each residue of a PDB file in a text file using UCSF chimera? > > I know we can do this in chimeraX using the command: save C:\myphi.defattr attrName phi format defattr model #1 > > Also, can we use chimeraX to save the phi and psi values in a single file? > > Thanks in advance >

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Query regarding selection
by Prathvi Singh 04 Aug '23

04 Aug '23

Hi Elaine, I want to select all the atoms except the backbone oxygen and nitrogen atom of residues 100.A to 120.A . Is there a command to do this in either chimera or chimeraX? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Pseudobonds question
by Aleksei Solomonov 02 Aug '23

02 Aug '23

Dear ChimeraX Developers, I apologize for disturbing you, I have a question, how can I make pseudobonds in ChimeraX similar to Chimera? I mean when I try to create hydrogen bonds, by default, in Chimera (Tools->structure analysis->findHbonds) they appear as lines (or sticks), connected to the structure (left image). But if I export the model and import it in ChimeraX bonds become "disconnected". The same appeared if I place H-bonds directly in ChimeraX (right image). If I select pesudobond, an option of changing its length manually is unavailable. The structure is attached if needed. [cid:image002.png@01D9C590.A8D2F3A0] Thank you in advance! Best regards, Aleksei

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Missing functions for scripting
by Vincent Mallet 28 Jul '23

28 Jul '23

Hello, Thanks a lot for the awesome tool ! I have a question about how to use some commands that are not yet included in the python API : for instance "measure volume". I can run it using a cxc with : */usr/bin/chimerax --script measure.cxc --nogui --exit* Where *measure.cxc *contains looks like : *open test.mrc volume #1 level 0.42 measure volume #1* I don't understand how to do the same with a python script. Is there some way to use chimerax.tools(measure area/volume) to get this tool to work from within a python script ? My use case is that I am running this measurement for different thresholds, and I would like those thresholds to depend on the value of previous thresholds, hence I need looping. For now, I am calling subprocess on the .cxc command above from a python script, but this means that I need to load the mrc every time... Thanks in advance for your help ! Best, Vincent

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Download ChimeraX
by songlu 26 Jul '23

26 Jul '23

Dear ChimeraX developers, Thank you for taking the time to read my email. I have a question about downloading ChimeraX and I hope you can help me. When I downloaded the MacOS version of the ChimeraX1.6 on the official website, I found that the download always failed. After trying to switch the browser and the network, it still doesn't work. Perhaps you can help me solve the problem or send me the installation package for the MacOs version of the ChimeraX1.6. I would greatly appreciate it. Looking forward to your reply. Sorry again for the delay in your valuable time. Wishing you a pleasant day. Yours respectfully, Songlu

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transparency for different selection
by Enrico Martinez 26 Jul '23

26 Jul '23

Dear ChimeraX users! I am dealing with the visualization of protein embedded into the plasmatic membrane (composed of water and lipids). Here is my script preset publication 1 rainbow protein palette $palette # for protein surface protein #color protein cornflower blue transparency 95 target s # for lipids surface :OL,PA,PE color :OL coral target s color :PA coral target s color :PE orangered target s hide bonds; hide atoms transparency 55 target s 1) I would like to set different values of the transparency for the surface of lipids and protein. For the moment I found only one possibility to set the transparency for the whole surface indicated above. Would it be possible to selectively apply a transparency command on the particular selection of the system ? 2) how would it be better to visualize the water in the same system in order to maintain the visibility of the protein ? Many thanks in advance Enrico

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How do you refine a structure with a new (or modified) amino acid residue in Isolde
by Trevor Sewell 25 Jul '23

25 Jul '23

Hi Everyone, I am adding residues (essentially modified cysteines ) to the polypeptide chain. e.g. HETATM 1 N2 PGR 0 1.743 -1.624 -0.731 1.00 0.00 N HETATM 2 C1 PGR 0 -0.077 -0.207 -0.018 1.00 0.00 C HETATM 3 C2 PGR 0 1.394 -0.544 0.203 1.00 0.00 C HETATM 4 C3 PGR 0 -0.485 0.927 -0.717 1.00 0.00 C HETATM 5 C4 PGR 0 -1.034 -1.073 0.503 1.00 0.00 C HETATM 6 C5 PGR 0 -1.840 1.189 -0.887 1.00 0.00 C HETATM 7 C6 PGR 0 -2.389 -0.810 0.331 1.00 0.00 C HETATM 8 C7 PGR 0 -2.794 0.323 -0.364 1.00 0.00 C HETATM 9 C8 PGR 0 2.379 0.585 -0.085 1.00 0.00 C HETATM 10 H1 PGR 0 1.529 -0.961 1.213 1.00 0.00 H HETATM 11 H2 PGR 0 0.232 1.599 -1.120 1.00 0.00 H HETATM 12 H3 PGR 0 -0.727 -1.940 1.035 1.00 0.00 H HETATM 13 H4 PGR 0 -2.145 2.053 -1.418 1.00 0.00 H HETATM 14 H5 PGR 0 -3.116 -1.477 0.733 1.00 0.00 H HETATM 15 H6 PGR 0 -3.837 0.527 -0.497 1.00 0.00 H HETATM 16 H7 PGR 0 1.655 -1.298 -1.705 1.00 0.00 H HETATM 17 H8 PGR 0 1.143 -2.449 -0.581 1.00 0.00 H HETATM 18 O18 PGR 0 3.393 0.026 -0.528 1.00 0.00 O HETATM 19 SG PGR 0 2.777 1.511 1.356 1.00 0.00 S HETATM 20 CB PGR 0 1.349 2.524 1.801 1.00 0.00 C HETATM 21 CA PGR 0 1.698 3.446 2.926 1.00 0.00 C HETATM 22 N PGR 0 0.565 4.254 3.182 1.00 0.00 N HETATM 23 C PGR 0 2.646 4.407 2.450 1.00 0.00 C HETATM 24 O24 PGR 0 2.145 5.309 1.717 1.00 0.00 O HETATM 25 O25 PGR 0 3.976 4.409 2.828 1.00 0.00 O HETATM 26 H9 PGR 0 1.980 1.252 -0.806 1.00 0.00 H HETATM 27 H11 PGR 0 1.044 3.140 0.942 1.00 0.00 H HETATM 28 H12 PGR 0 0.527 1.867 2.099 1.00 0.00 H HETATM 29 H13 PGR 0 2.043 2.881 3.803 1.00 0.00 H HETATM 30 H14 PGR 0 -0.245 3.721 3.480 1.00 0.00 H HETATM 31 H15 PGR 0 0.359 4.821 2.336 1.00 0.00 H TER My question is: How do I set up Isolde so that it can refine the structure? Many thanks, Trevor Sewell Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/report-incident

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Regarding replacing Aspartate with Isoaspartate
by Protya, Satirtha 24 Jul '23

24 Jul '23

Hi Everyone, Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. I am facing a new issue. In one of my peptide PDB file, I need to change the Aspartate Amino Acid with Iso Aspartate Amino Acid. I have been trying to do so, but not sure how to do that. Is there any way or package that can do that? Please let me know. Hope to hear from you soon. Have a great day. -- Yours sincerely Satirtha Saha He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_med…> sahass(a)beloit.edu<mailto:sahass@beloit.edu> [Image][Image]

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Questions on Visualizing Chromatin Structure and Gene Expression in ChimeraX
by 刘致远 24 Jul '23

24 Jul '23

Dear UCSF ChimeraX Team, I am a big fan of your program and I have been greatly impressed with its capabilities. I want to express my deep appreciation for the "soft" visualization option provided in ChimeraX - the aesthetics truly appeal to me. I've been utilizing ChimeraX to visualize my chromatin structure data. While I'm aware this might not be one of the intended uses, when I simulated the 3D structure of chromatin as a protein's cif file, the result looked fantastic. Now I've encountered a challenge and I am hopeful that you might be able to provide some guidance. I am looking to represent gene expression as the size of the spheres in my chromatin structure, all in one figure. I am aware that Chimera has a method using "vdwdefine", essentially using the size of the B-factor to represent the atomic radius. Could you guide me on how to achieve this in ChimeraX? Furthermore, if I want to include multiple columns similar to the B-factor, how can I add them to the cif? Using the "defattr" command feels a bit cumbersome. It would be very convenient if I could pack a lot of dimensional information (such as the gene density of this chromatin segment, CG content, chromatin opening degree, etc.) into a single cif file. Do you have any suggestions or strategies on how to achieve these somewhat unconventional functionalities? Your assistance would be greatly appreciated. Thank you for your attention and I look forward to hearing from you soon. Best Regards, Zhiyuan Liu

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Fwd: depicting contacts
by Eric Pettersen 24 Jul '23

24 Jul '23

> Begin forwarded message: > > From: Krishnan Raman <RKrishnan(a)BIOCRYST.com> > Subject: depicting contacts > Date: July 24, 2023 at 9:50:11 AM PDT > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > Hi all, > Any ideas to depict a dramatic improvement(200 nm to femtomolar) in binding affinities before and after mutations(about seven) in chimerax? > II have tried contacts , swapaa etc. nothing seems dramatic enough for visuals > Thanks > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows > > > > > CONFIDENTIALITY NOTICE > > This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >

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Fwd: RFdiffusion in ChimeraX?
by Tom Ferrin 24 Jul '23

24 Jul '23

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Swapaa doubt
by Krishnan Raman 24 Jul '23

24 Jul '23

Hi, How do I use swapaa to do mutations on seven to ten residues in one command? Thanks Krish Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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L-D isomers
by Íñigo Izal Azcárate 21 Jul '23

21 Jul '23

Hi everyone, Is there any way of changing the isomerism of protein residues from L to D? I use ChimeraX with students and it would be great to see what happens with some features of the structure like hydrophobicity after changing isomers. Thanks so much in advance Iñigo Izal Azcárate Personal de Apoyo a la Docencia, Coordinador del programa Science and Business Departamento de Bioquímica y Genética T: 948 425600, ext 6321 inizal(a)unav.es -- *Este mensaje puede contener información confidencial. Si usted no es el destinatario o lo ha recibido por error, por favor, bórrelo de sus sistemas y comuníquelo a la mayor brevedad al remitente. Los datos personales incluidos en los correos electrónicos que intercambie con el personal de la Universidad de Navarra podrán ser almacenados en la libreta de direcciones de su interlocutor y/o en los servidores de la Universidad durante el tiempo fijado en su política interna de conservación de información. La Universidad de Navarra gestiona dichos datos con fines meramente operativos, para permitir el contacto por email entre sus trabajadores/colaboradores y terceros. Puede consultar la Política de Privacidad de la Universidad de Navarra en la dirección: **https://www.unav.edu/aviso-legal* <https://www.unav.edu/aviso-legal>**** ** ** *This email message may contain confidential information. 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. The personal information included in email messages exchanged with employees of the University of Navarra may be stored in the database of your interlocutor and/or the servers of the University for the time-period stipulated by its internal information storage policy. The University stores such data for purely administrative purposes, to facilitate e-mail contact between its employees and third parties. The University of Navarra Privacy Policy may be accessed at https://www.unav.edu/aviso-legal <https://www.unav.edu/aviso-legal> ***** ** ** _Antes de imprimir este mensaje o sus documentos anexos, asegúrese de que es necesario. Proteger el medio ambiente está en nuestras manos. Before printing this e-mail or attachments, be sure it is necessary. _It is in our hands to protect the environment.__

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