- Chimera-users - RBVI Mailing Lists

error code -1073741819
by Beni Sued 09 Mar '21

09 Mar '21

Hey there I've been using UCSF chimera for some time with no problems but it is having trouble starting up, this is the error message: *Cannot execute 'gzip': no automatic decompression of .Z filesinitializing general preferencesloading Tixinitializing graphicsReturn code: -1073741819Press return or enter to to exit* precisely like this gentleman: https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html and this https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html my dxdiag info is attached, nothing wrong jumps to me. What I've tried: - uninstalling and reinstalling Chimera - manually installing GZIP for windows ( https://sourceforge.net/projects/gzip-for-windows/ ) - updating drivers (graphics drivers and chipset drivers) - getting the alpha version of the program - going to and fro compute mode in the the graphical settings I'm using Chimera 1.15 and this is my hardware chipset b550m ryzen 5600x RX 590 in trying to fix it I learned about ChimeraX, I'm learning to use it, but I would still like to keep chimera until i can properly stop and change my workflow thanks so much, let me know if I missed any info

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renseignements
by Camelia Hamadouche 09 Mar '21

09 Mar '21

je n'arrive pas a télecharger votre logiciel meme si je clique sur accepter on me dirige vers une fenetre disant quelle partie vous ne voulez pas accepter? alors que j'ai bien cliqué sur accepter

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each rotation of the molecule in chimera will unexpectedly add an extra "c" at command line
by xiaoyu liu 03 Mar '21

03 Mar '21

Hello, I'm Xiaoyu Liu, a chimera user. Thank you for developing and sharing this powerful software. I have a problem now and bothered me for a while when using chimera. I'm wondering if you know how to solve it. I downloaded chimera-1.15-mac64.dmg <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…> from "https://www.cgl.ucsf.edu/chimera/download.html" for my Mac OS Catalina(10.15.5). When I rotate the molecule with left mouse button, an extra character "c" will be automatically added in command line. Each rotation will result in adding one "c". Here I have some screen shot to show more clearly. [image: image.png] [image: image.png] [image: image.png] I tried to restart my computer. It is helpful within the first 10 minutes after the restart, but later it has the problem again. Please let me know if you know how to solve it. Many thanks! Best, Xiaoyu

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problem with pdb file saved from chimera-autodock vina analysis
by Amol Ghodke 03 Mar '21

03 Mar '21

Hi, First of all thank you so much for making such a wonderful tool and sharing it freely with scientific community. I have been using chimera for sometime now and performed docking analysis using autodock vina. I recently come across a problem. After exporting pdb file with desired docking pose, I tried to run protein ligand interaction analysis on PLIP<https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index> server. But ligand in my file does not get recognised for analysis. I opened pdb file in a text editor and upon looking care fully I see chimera saves receptor and ligand as separate model like this ATOM 7453 HD2 PRO A 462 15.986 11.983 20.450 1.00 0.00 H ATOM 7454 HD3 PRO A 462 16.532 10.334 20.885 1.00 0.00 H ENDMDL MODEL 2 HETATM 1 S1 CGT A 1 9.051 5.106 43.099 1.00 0.00 S HETATM 2 C6 CGT A 1 8.150 3.680 42.370 1.00 0.00 C After comparing it with the pdb file from pbd database I removed “ENDMDL” and “MODEL 2” and re-ran the PLIP analysis. This time it works but PLIP also mentions that – [cid:image001.png@01D7103D.5D0AB030] Analysis went well but the .pse file that I get from PLIP server does not allow me to show ligand in stick format in Pymol software. I suspect this is due to the original pdb file format. I also noticed that pdb file when opened in pymol shows ligand and receptor as different states which is not correct (if I am right). I have attached both original pdb file that I saved from Chimera-autodock vina and pse file from PLIP analysis. May I request to help me resolve this issue? Please let me know if you need any further information or clarification. Thanks for your time and support Amol --------------------------------------------------------------------------------------------------------------------------------------------------------- Dr Amol Bharat Ghodke | Post-Doctoral Research Fellow Queensland Alliance for Agriculture and Food Innovation Level 3, Queensland Bioscience Precinct [#80] Room 3.318, 306 Carmody Rd, St Lucia The University of Queensland St Lucia, Brisbane Qld 4072, AU E. a.ghodke(a)uq.edu.au<mailto:a.ghodke@uq.edu.au>

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active/non active
by Ana Andreea ARTENI 03 Mar '21

03 Mar '21

Dear all, I want to fit a pdb structure into a cryoem map. Accordingly to the youtube tutorials I open both, place the correct pixel size, centre, and then I want to zoom only on the pdb file, but inactivating the cryoem map doesn't work: both maps zoom together. What am I doing wrong? Best regards, -- Ana Andreea ARTENI, PhD ******************************** UMR 9198 Institut de Biologie Intégrative de la Cellule Platforme de cryo-microscopie électronique Bâtiment 14B (RDC. pièce 111) 1 avenue de la Terrasse 91198 Gif-sur-Yvette Cedex, FRANCE Phone: + 33 (0)1 69 82 38 56 Fax: +33 (0)1 69 82 43 08 E-mail : ana-andreea.arteni(a)i2bc.paris-saclay.fr Site web: http://www.i2bc.paris-saclay.fr/spip.php?article277

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editing session file
by Olivier Bignucolo 02 Mar '21

02 Mar '21

Dear Chimera-users, I am new to Chimera. I saved a session.py file that manages the appearance of, say, folder1/proteinA.pdb. I would like to apply exactly the same formats, colors, etc... to proteinB.pdb located in folder2. I edited session.py but was unable to find out how to do it. It seems that the python script does not contain any line like: "open("filename","r") or anything similar. How can I reuse session.py for a new pdb file? Thanks Olivier

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Hydrophobicity extensions
by Sam Hopgood 26 Feb '21

26 Feb '21

Hello, I'm currently studying at Imperial to complete my final year project for my MSci in Chemistry, but due to remote working I have to take on more of a computational project rather than something lab based and I'm not too experienced in the area and neither is my group. I have been told to use chimera to model the hydrophobic surface of proteins and determine a value for the surface hydrophobicity that can be later linked to data collected from HIC studies. I've been told to use chimera to model this but even basic visualisation of the hydrophobic surface does not work for proteins as large as rubisco. I know this is a big ask and an open ended question but are you aware of any extensions available to use to mitigate this issue? Or are you aware of any techniques I could use utilising the software to calculate an actual value for the surface hydrophobicity? I hope you are all keeping safe and well, and thank you for any insight! Best, Sam

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Re: [Chimera-users] Chimera-users Digest, Vol 214, Issue 8
by Khurram Shahzad 26 Feb '21

26 Feb '21

My username and password incorrect plese help me On Thu, Feb 25, 2021, 7:11 PM <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: (no subject) (Thomas Cheatham) > 2. MD analysis of ion position (Elaine Meng) > 3. Re: Chimera Visualization Tool (Ela Ka) > 4. Chimera help submission (David Leeming) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 24 Feb 2021 21:06:55 +0000 > From: Thomas Cheatham <tec3(a)utah.edu> > To: K Jan <10dunajkr(a)gmail.com>, "chimera-users(a)cgl.ucsf.edu" > <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] (no subject) > Message-ID: <6bbb12c3268847adbbf93577d9f4313a(a)utah.edu> > Content-Type: text/plain; charset="us-ascii" > > > The program CPPTRAJ can bin ion densities on a grid which can be > visualized with chimera... > > See: > https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-s… > > CPPTRAJ is available in AmberTools or via GitHub - > https://github.com/Amber-MD/ > > Also AmberHub may have a tutorial related - > https://amberhub.chpc.utah.edu/making-a-3d-histogram/ > > --tec3 > > ________________________________________ > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of K > Jan <10dunajkr(a)gmail.com> > Sent: Wednesday, February 24, 2021 1:53:36 PM > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] (no subject) > > Hello, > > I`ve just finished a simulation on DNA with K+ ions and I would like to > get images of the average ion location at different points in the > simulation. > > I was wondering how I could find the average location of K+ ions ( because > right now they`re scattered around the DNA) at different points of the > simulation.? > > Thanks > > > > ------------------------------ > > Message: 2 > Date: Wed, 24 Feb 2021 13:22:02 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: K Jan <10dunajkr(a)gmail.com> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] MD analysis of ion position > Message-ID: <870D7C13-E4ED-49DB-8AA0-5E503A94DCA9(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Thanks, I agree that CPPTRAJ is a great solution for analyzing > trajectories. Looks like it can read several formats: > <https://amberhub.chpc.utah.edu/cpptraj/trajectory-file-commands/> > > Alternatively: > In Chimera, if you can view your trajectory in the MD Movie tool, you can > also use that tool to calculate and display an occupancy map. I think > that's essentially the same thing that Tom mentioned, a density map on a > grid that can be viewed as isosurfaces. > > MD Movie help, click "Occupancy Analysis" in the left hand links: > < > https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie… > > > > Occupancy analysis is also covered in the last section of this Chimera > tutorial: > < > https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html… > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 24, 2021, at 1:06 PM, Thomas Cheatham <tec3(a)utah.edu> wrote: > > > > > > The program CPPTRAJ can bin ion densities on a grid which can be > visualized with chimera... > > > > See: > https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-s… > > > > CPPTRAJ is available in AmberTools or via GitHub - > https://github.com/Amber-MD/ > > > > Also AmberHub may have a tutorial related - > https://amberhub.chpc.utah.edu/making-a-3d-histogram/ > > > > --tec3 > > > > ________________________________________ > > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of K > Jan <10dunajkr(a)gmail.com> > > Sent: Wednesday, February 24, 2021 1:53:36 PM > > To: chimera-users(a)cgl.ucsf.edu > > Subject: [Chimera-users] (no subject) > > > > Hello, > > > > I`ve just finished a simulation on DNA with K+ ions and I would like to > get images of the average ion location at different points in the > simulation. > > > > I was wondering how I could find the average location of K+ ions ( > because right now they`re scattered around the DNA) at different points of > the simulation.? > > > > Thanks > > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 24 Feb 2021 22:18:45 +0330 > From: Ela Ka <e.kashani.a(a)gmail.com> > To: Chimera User Help <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Chimera Visualization Tool > Message-ID: > < > CAFiNxG3Ca3WthCUCR3Oad2bt+i6mmMSTsCAkOTvG3oez7s1dzQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Elaine, > > Thank you very much. I appreciate your consideration. Sure, we'll take care > of the credit and other considerations. > > Best Regards > Elaheh Kashani-Amin > > On Wed, Feb 24, 2021, 10:13 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > Dear Elaheh Kashani-Amin, > > Thanks for asking. Yes, it would be acceptable to use Chimera (free > > version) to create images for your slides, providing that Chimera is > > credited for the images in these materials. > > > > However, if you were going to use Chimera interactively as part of the > > paid educational sessions, your group would need to license the software > as > > described here: > > <https://www.rbvi.ucsf.edu/chimera/commercial_license.html> > > > > Best regards, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 24, 2021, at 2:40 AM, Ela Ka <e.kashani.a(a)gmail.com> wrote: > > > > > > Dear Madam/Sir, > > > > > > We are a group of researchers who try to prepare educational contents > in > > different aspects of protein molecular modeling for the students. Access > to > > these educational content is not free. We need to prepare some pictures > of > > proteins, ligand-receptor interaction, etc. for the slides. Can we use > the > > Chimera software (free version) to prepare some pictures for the slides? > > Though, we won't use the tool, itself, for those educational sessions. > > > > > > Thank you for your consideration > > > > > > Best Regards > > > Elaheh Kashani-Amin > > > PhD, Bioscience > > > > >

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Chimera help submission
by David Leeming 25 Feb '21

25 Feb '21

Dear Chimera users, I'm attempting to write a chimera script to automate the process of calculating the relative exposure of residues as per this tutorial: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html The script I have is as follows: rc('surface') # defines areaSES of residues rc('defattr C:/Users/Admin/Downloads/areaSESgxg.txt log 0') # define attribute using areaSESgxg.txt for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for r in m.residues: r.relSESA = r.areaSES/ r.areaSESgxg However, when I run this script, I am receiving this error: [cid:39cc50d4-a627-494c-b0f5-411a7785a9a2] When I run the process using the UI I can successfully calculate relSESA By using the command: "surface" Then using the assign attribute function to assign areaSESgxg.txt Followed by using the calculate attribute function to calculate per residue: residue.areaSES/ residue.areaSESgxg Could you advise on any methods I could use to fix this script to produce the output I am receiving from the UI. Kind regards, David

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(no subject)
by K Jan 24 Feb '21

24 Feb '21

Hello, I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation. I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.? Thanks

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