- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [chimera-dev] Problem with Matchmaker tool
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Tiglath, (1) 1av1 is not a dimer. It is a tetramer, 4 copies of the same peptide, chains A,B,C,D. See: <https://www.rcsb.org/structure/1AV1> (2) Matchmaker is working correctly, but you have to choose "Specific chain of reference structure" (not "Best-aligning") and then specify exactly which chain of 1av1 you want as the Reference. You have to use it twice, so that you can match #0 to one reference chain and #1 to a DIFFERENT reference chain. Otherwise they will both go to exactly the same place because they will match the same chain, which I guess is what happened to you before. Actually, maybe you need to use it four times with four copies of your model if you expect to get something that looks similar to 1av1. The chimera-users(a)cgl.ucsf.edu address is recommended for "how to use" questions, so I'm CC-ing it here. The chimera-dev list is more for programming questions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 20, 2020, at 5:17 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > > Hi > For some reason I'm not able to use the matchmaker tool to build a dimer model of the protein I'm studying. Here are the steps that I use: > > • I open twice the monomer model > • Then I open the dimer template, then click on the Matchmaker tool. > <image.png> > 3. In the Reference structure panel I click on the dimer template (1AV1) > 4. In the Structure(s) to match panel I click on monomer#0 (Human Monomeric Apo A-I, the protein I'm studying) then click OK > 5. Then I click on monomer #1 followed by OK > > But when I close the dimer template I get back the monomer not the dimer model of the protein. I'm not sure what I'm doing right. > Thanks > Tiglath

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Question on aligning one molecule to two other molecules
by Doc Deldou 18 Nov '20

18 Nov '20

Dear Chimera team, I am trying to perform a "manual" docking of a DNA molecule in a protein structure using homology with proteins structures resolved with DNA. I know that the first part of my protein (the recognition domain) is similar to one structure and the other part (the cleavage domain) is similar to another one. So I built a dsDNA with the recognition sequence of my target protein and I first aligned it with the DNA of the similar recognition structure using the phoshore groups, then I matched aligned my protein structure to the protein part of the similar recognition structure. After that I matched aligned my protein to the similar protein cleavage domain bringing the DNA molecule with it. And now ideally I would like to align the DNA part with the DNA of the similar cleavage domain but keep the first recognition part of my DNA more or less at the same position. So I tried to align another copy of my DNA to both DNA molecules but I don't think it is possible. Do you have a trick or a command I could use to reach my goal? I'm using Chimera X. Below is what I obtained, in green my target protein, in purple the DNA I first aligned relatively to the DNA of my similar recognition structure, in "pink" the DNA strand of the similar cleavage structure with the bond to be cleaved in yellow, and the dsDNA with all the colored nucleotides is the one I am trying to position in between the two site with also the bond to be cleaved in yellow. I tried to rotate it and translate it manually to have something in between but some DNA parts are clashing with the protein part and I would like to have something the more accurate possible. [image: manualdocking.jpg] Best regards, -- Adèle Dramé-Maigné @Docdeldou Docteur en Biochimie et Instagrammeuse Blog: http://bit.ly/2zkiPWI LinkedIn: http://bit.ly/2afmtEq

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Saving representives from ensemble cluster
by James Lloyd 18 Nov '20

18 Nov '20

Hi, I have a few Gromacs trajectories (just protein in solvent) which I have clustered using the ensemble cluster tool. I want to save each representive model from each cluster. However I am unsure whether these representive models need to be saved relative to another model (this option was ready ticked). Since I want to use each file separately with VinaDock, would unticking this option be wise? Thanks This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

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Re: [Chimera-users] Saving Image of row stereo
by Tom Goddard 17 Nov '20

17 Nov '20

Hi Divita, I see. If you want to depict that a molecule can be in various positions a better approach is to actually open 2 to 4 copies of it positioned slightly differently, maybe showing the copies as transparent. Another approach is to save 5 copies of the image where you move the variable molecule a bit for each, then blend the images in Photoshop or Gimp. Tom > On Nov 17, 2020, at 10:14 AM, Divita Mathur <dmathur4(a)gmu.edu> wrote: > > Thanks for your response, Tom. I guess I should tell you what I am trying to achieve. > > The row stereo image is interesting to me as it can be interpreted as a “vibrating” or “shaky” molecule (check attached). I want to represent that the green dye (and perhaps the underlying pink scaffold) is shaking and it is not constrained enough. Is there a camera setting that you can recommend? > > The screenshot has these horizontal lines which I suspect have something to do with the quality of my computer screen. > > Best, > > -- > Divita Mathur, PhD > Research Assistant Professor > George Mason University & > Center for Bio/Molecular Science and Engineering > Naval Research Laboratory > (202) 767-0687 (Office) > From: Tom Goddard <goddard(a)sonic.net> > Date: Tuesday, November 17, 2020 at 12:58 PM > To: Divita Mathur <dmathur4(a)gmu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Saving Image of row stereo > > Hi Divita, <> > > I don't think Chimera can save the row interleaved image. Such an image is not very useful since it would have to be positioned on a row interleaved stereo display (e.g. Zalman) with no scaling to appear 3d since even rows give one eye image and odd rows the other eye image. Your best bet would be to try a screen capture program. > > Tom > > > >> On Nov 16, 2020, at 6:23 PM, Divita Mathur <dmathur4(a)gmu.edu <mailto:dmathur4@gmu.edu>> wrote: >> >> Hi all, >> >> I am trying to save a rendering created using the Camera setting – row stereo. The rendering appears dark and without the row stereo settings when the image is saved (tried many formats). How can I save the actual rendering as an image? >> >> Regards, >> Divita Mathur >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://secure-web.cisco.com/1xK9pP0Vy3veE9y4SgXHuL5DpartYSf6j9ncrP3zwdNXWs…> > > <Screen Shot 2020-11-16 at 9.30.16 PM.png>

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POV-Ray surface color
by Greg Williams 17 Nov '20

17 Nov '20

I am rendering a two-submit protein, split, with different colored mesh surfaces on the subunits. If I render to an image with Chimera, the surfaces appear in the colors assigned. If I render with POV-Ray, both mesh surfaces render as black. I assigned the colors using MSMS surface attributes with color sources as "atoms", using the color well in the Component Atom Attributes panel. Where in the literature should I read to sort this out? Thanks!

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Color marker and bonds
by karine.gouriet 17 Nov '20

17 Nov '20

Dear all we want to correspond the marker color with the bond color. here the bond color is the angle of the scalar product of the bond line and another vector. It is possible to change the marker color by the bond color and not the inverse ? Thanks a lot for your help. PS: I joint the file.py corresponding to the modification of rgba function we want. -- -------------------------------------- Karine GOURIET Maître de Conférences tel : 03.20.43.43.98. Unité Matériaux et Transformation CNRS UMR 8207 - Université de Lille 1 Bat C6, Bureau 213 59655 Villeneuve D'ascq http://umet.univ-lille1.fr/ --------------------------------------

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Saving Image of row stereo
by Divita Mathur 17 Nov '20

17 Nov '20

Hi all, I am trying to save a rendering created using the Camera setting – row stereo. The rendering appears dark and without the row stereo settings when the image is saved (tried many formats). How can I save the actual rendering as an image? Regards, Divita Mathur

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icosahedral annulus
by Pranav Shah 17 Nov '20

17 Nov '20

Hi Elaine, i was wondering if there was an "easy" way to create an icosahedral ring-mask using chimera's shape and mask commands. At the moment, I am creating two icosahedral shapes of big and small radii and them subtracting the small one from the big one, but this results in inconsistent results i.e the mask does not enclose the volume I wish to cover. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Chimera morph map multiple volumes
by Ahmad Khalifa 15 Nov '20

15 Nov '20

Is there a way to morph multiple volumes into a single movie? I tried morphing two maps first with the hope that I can do another morph between the resulting morph and a third map, but it didn't work. Any suggestions or easy alternatives to join the morphs together? Thanks.

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solvent exposed surface area
by Jordan Alexis Gewing-Mullins 15 Nov '20

15 Nov '20

Hi there! I hope you're doing well. I am trying to calculate the solvent exposed surface area for each amino acid in a protein, and from the tutorial it says that once I create a surface it should automatically generate a text file with the areaSAS information, but I have no clue where to find that file. Where does it get saved? Thanks, Jordan

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zone & segname
by Francesco Pietra 15 Nov '20

15 Nov '20

Hello Working with charmm36, therefore with the great aid of segname for my homotrimer, when commanding sel :27.M z<3 I get also a water molecule, with O-atom Tip3 3687.W OH2 Is there any way to extend the above command in order to have the segname associated with this water residue? This is because there are eight 3687.W residues with different segnames. I tried to solve indirectly the problem with sel :3687.W@/pdbSegment=WT# where # ranges from 1 to 8 (i.e., the same residue name for segname WT1 to WT8). Contrary to my expectations, it does not work The same with sel :3687@/pdbSegment=WT# Thanks for advice francesco pietra

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help
by Rayna L. DeChance 13 Nov '20

13 Nov '20

Hi, I was wondering if you knew how to cut out (clip) a part of the protein and save the remaining part as a PDB file. I attached the file I was working with that has the two proteins that are aligned together and we want only a certain part of this alignment to be clip. Thank you

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distance with homotrimer
by Francesco Pietra 12 Nov '20

12 Nov '20

Hello I am trying to measure (from command line) the distance between atom NH1 in residue 27, chain M atom OG1 in residue 215, chain A command distance :27@NH1 :215@OG1 error: 6 atoms were selected. The error message is correct because the system is a homotrimer. My question: any way to specify the chains? Any of my attempts failed. Thanks for advice (getting distances from the command line would be quicker that graphically as I have a large number of disnces to measure)

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I tasser models
by Sitbon, Yoel 10 Nov '20

10 Nov '20

Hello, I hope you are doing well. I obtained prediction models from I tasser and would like to visualize them on chimera. I was able to open them but i cannot open the sequence of amino acids. Do you perhaps know how to look at them? Thank you Yoel Get Outlook for Android<https://aka.ms/ghei36>

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Fw: Chimera can't open files
by Cain, Cheryl A 09 Nov '20

09 Nov '20

Please see the question below. Thanks, Cheryl Cheryl Cain cheryl.cain(a)ucsf.edu Operations Coordinator, Department of Pharmaceutical Chemistry Accreditation Project Coordinator, School of Pharmacy UCSF ________________________________ From: Jie Yang <jieyang(a)scripps.edu> Sent: Monday, November 9, 2020 4:12 PM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Subject: Chimera can't open files Hi there, I have a problem that my Chimera can’t open/fetch .PDB files in my Mac(see attached). I believe the problem was because I accidentally denied access of Chimera to the Users/jieyang/Downloads. Could you let me know how should I reverse this? Thank you very much! Best Jie Yang [cid:8ef2ed16-18af-4541-aeab-3a4697900cb5]

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reset all models to the same center of rotation
by C.J. 06 Nov '20

06 Nov '20

Hi Chimera community, I have several models, both maps and pdbs, aligned. But the common center for rotation is far away from the model when I use "Volume Eraser". How can I reset the center for all models in command-line way? Thank you! Jianhao

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Re: [Chimera-users] PDB fetch broken
by Tom Goddard 05 Nov '20

05 Nov '20

Hi John, Try using the "Ignore any cached data" in the Chimera menu File / Fetch... panel. I suspect Chimera cached a bad file when the fetch was broken. If you use this ignore cached data option it will fetch a new copy of the file. Unfortunately when RCSB disabled their legacy web fetch the last couple days they made it so when you tried to fetch it returned an html page saying "PDB has discontinued this fetch" with an http "success" code (200). Since Chimera got the success code it assumed that html text was actually the PDB file and it cached it in ~/Downloads/Chimera/PDB Then when you try to open that same PDB file it is getting that cached html page instead of the cached PDB file. I asked RCSB to return an error code (404) on fetch so that does not happen, but they did even better and temporarily have reenabled the old fetch URLs to help Chimera users. They will still turn off the old fetch in a month or so. Tom > On Nov 5, 2020, at 6:26 AM, John Rose <rose(a)bcl4.bmb.uga.edu> wrote: > > Hi, > > Downloaded the Chimera 1.15 build but the problem still persists. > > Thanks, > > John Rose > > > John Rose Ph.D. > Associate Professor > SER-CAT Associate Director for Program > Rm. B204B > Department of Biochemistry and Molecular Biology > Davison Life Sciences Complex > 120 Green Street > University of Georgia > Athens, GA 30602-7229 > =============================== > Phone: 706-542-1750 > Fax: 706-542-3077 > > > > >> On Nov 4, 2020, at 1:28 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Chimera PDB fetch is broken starting November 3 and a command like "open 1a0m" produces an empty model with no error. >> >> We will be putting a new version (release candidate) of Chimera on the download page today or tomorrow that fixes this. >> >> What happened is that the RCSB has shutdown the URL Chimera uses to fetch PDB files (e.g. https://www.rcsb.org/pdb/files/1a0m.pdb <https://www.rcsb.org/pdb/files/1a0m.pdb>). Although RCSB announced this long ago the Chimera development team missed that this URL was going away. >> >> Tom >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

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PDB fetch broken
by Tom Goddard 04 Nov '20

04 Nov '20

Chimera PDB fetch is broken starting November 3 and a command like "open 1a0m" produces an empty model with no error. We will be putting a new version (release candidate) of Chimera on the download page today or tomorrow that fixes this. What happened is that the RCSB has shutdown the URL Chimera uses to fetch PDB files (e.g. https://www.rcsb.org/pdb/files/1a0m.pdb <https://www.rcsb.org/pdb/files/1a0m.pdb>). Although RCSB announced this long ago the Chimera development team missed that this URL was going away. Tom

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Fwd: How to setup Nvidia 3D Vision on Ubuntu
by Tom Goddard 03 Nov '20

03 Nov '20

Here's a picture from Kenneth of the DIN and USB cables needed to use the 3D Vision emitter on Linux. > Begin forwarded message: > > From: Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> > Subject: Re: [Chimera-users] How to setup Nvidia 3D Vision on Ubuntu > Date: November 3, 2020 at 11:17:18 AM PST > To: Tom Goddard <goddard(a)sonic.net> > > Actually, the pic does not have the cable in it, only the extra on-board cable that connects to the GPU and serves up the 3pin female. Here is a pic of both the din and usb cable connected to the emitter. The DIN is a must for linux. the special cable is on the left and the usb is on the right. > > kas > > > Kenneth A. Satyshur, M.S., Ph.D. > Senior Scientist, > College of Ag and Life Sciences: Department of Bacteriology; > School of Medicine and Public Health: > Departments of Biomolecular Chemistry, > Neuroscience, Oncology, and Carbone Cancer Center > (Small Molecule Screening Facility) > University of Wisconsin-Madison > Madison, Wisconsin, 53706 > 608-215-5207 >

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How to setup Nvidia 3D Vision on Ubuntu
by Tom Goddard 03 Nov '20

03 Nov '20

Hi Wei, I'd suggest using Ubuntu 20.04, the latest Ubuntu, the current Chimera 1.14 or daily build will work fine on that. I am not certain that Quadro FX 4800 graphics drivers will be available for Ubuntu 20, probably they will be, but you might want to look for that online before proceeding. That graphics cards is very old, from 2008. The other thing to know is that Nvidia discontinued support for Nvidia 3D Vision stereo glasses in 2019 https://nvidia.custhelp.com/app/answers/detail/a_id/4845 meaning those glasses and emitter will no longer work using just the current Nvidia graphics driver. But they claim that there is a separate driver for the USB emitter that allows it to work. https://www.nvidia.com/en-us/drivers/nv3dvisionusb/390_41/nv3dvisionusb-dri… <https://www.nvidia.com/en-us/drivers/nv3dvisionusb/390_41/nv3dvisionusb-dri…> I have not tried it. If you get it to work I'd be interested in hearing about it since we have an old Nvidia 3D Vision system. Tom > On Oct 29, 2020, at 6:41 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: > > Hi Tom, > > Hope everything is well. > > One university's computer lab recently retired some workstations that were used for 3D visualization before. I managed to get a couple workstations with the 3D glasses and emitters. But I need to reinstall the operating system on those machines. > > The graphic card of the workstation is Nvidia Quadro FX4800. > The emitter is NVIDIA P854. > The glasses are NVIDIA-P854 and ViewSonic-PGD250. > > I plan to install Ubuntu. I am wondering which version of Ubuntu is suitable for using UCSF Chimera. Do we need to install cuda to make it work? Do we need to install an older version of Chimera? > > Sorry I just sent the message to you to follow the previous chain of conversation. Shall I email the chimera-user in the future with such questions? > > Thank you, > > Wei >

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Capping in VRML
by Greg Williams 02 Nov '20

02 Nov '20

When I export a vrml file to process in my Cinema 4D application, the ends of the helices, coils and sheets are capped at the ends with a material that is different then the material I use to color the secondary structure features. In Cinema 4D, I have to change every capped end individually. Where do I change the vrml export settings so that the individual objects are capped with the right material? Thanks!

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Accessible surface area calculation
by Martino Benvenuti 02 Nov '20

02 Nov '20

Good morning, I would like to know if it is possible to calculate with Chimera the accessible surface area for a selected amminoacid of a protein. May you help me to figure it out? Thank you for having developed such a great program! Have a nice day, Martino Benvenuti. -- Martino BENVENUTI Ph.D. in chemistry. <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Screenshots for publication?
by Gustaf Olsson 02 Nov '20

02 Nov '20

Would it be acceptable to include screenshots of the Chimera GUI in publications as long as chimera is being cited as suggested? Best regards // Gustaf

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Select multiple files and open in the same instance
by Ahmad Khalifa 30 Oct '20

30 Oct '20

I used to have Chimera configured to select multiple files, click open, and have them all open in the same instance. After I reinstalled it, now it opens an instance for every file, how can I change it back? Regards.

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Chimera: Per-model clipping and contour level
by Selenschik, Philipp 30 Oct '20

30 Oct '20

Hello, I really enjoy working with Chimera (version 1.14), however I encounter two problems: I fitted the X-ray based crystal structure of apoferritin to my cryo-EM density map, determined the symmetry and based on that the algorithm fits 24 subunits to the map. Really nice. Now I would like to show a "sliced" image of both map and structure. I tried doing so by "Side view", enabling "clip". That works, but I would like to rotate the clipped object. Then I tried per-model-clipping. Here I can clip the map and structures separately. However, I have to choose all fitted (e.g. 12 out of 24) substructures and the clipping works only partially. What am I doing wrong? Also, I tried to figure out the best contour level setting. It seems there is no guide as to which is ideal? Based on a tutorial, I assumed 1 A³/Da for a globular protein, which turns out to be around 620*10³ A³ for my protein. The problem here is: If I slide beyond approx.. 550*10³ A³ all that remains is a square. What's wrong? I hope you can help me out :) Kind regards Philipp

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Help with something really simple
by M. Elizabeth Stroupe 29 Oct '20

29 Oct '20

Hi ChimeraX team, I need to measure a simple angle between three atoms, two within one model and the third in another model to describe a domain motion. In Chimera I could do this from the Structure Analysis tab but now it seems you can only measure distances. I tried the following command(s) and they both gave me an error. I also tried including commas between the angles. What am I doing wrong? angle #1/A:602@C7m,:222@CB,#17/A:602@C7M measure angle #1/A:602@C7m #1/A:222@CB #17/A:602@C7M Thank you! Beth

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MD Simulation on Chimera
by Samiha I Amer 27 Oct '20

27 Oct '20

Please may I know the ideal system specification to run a successful molecular Dynamics simulation on Chimera? Thank you Sent from Yahoo Mail on Android

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REGARDING CHIMERA SESSION FILE
by ASIF JAHAN SHUVRO 26 Oct '20

26 Oct '20

Dear concern, this is Asif from BRAC University, Biotechnology program. I hope you're in good health. I need a little help from you. Recently, I have joined two peptide fragments by forming a peptide bond between them using your standalone UCSF Chimera software. The file has been saved as a Chimera session fle. However, I'm not finding any clue on how to convert it into an entire pdb file. I'm not being able to do any other modification to it since a pdb file is required for this purpose. Could you please help me out on this regard? kindly let me know how can I generate a pdb file from that session file format. I wish to hear your reply. Thanks in advance! Regards, Asif Jahan Shuvro Biotechnology Program Department of Mathematics & Natural Sciences BRAC University

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Morphing PDB
by Reza Khayat 26 Oct '20

26 Oct '20

Hi, Is it possible to morph multiple chains serially? I have a trimer in two different conformations, I would like to morph Chain A in conformation 1 to Chain A in conformation 2. Then, I'd like to do this with chain B and finally chain C. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Running Chimera on X server
by Ahmad Khalifa 26 Oct '20

26 Oct '20

The refresh rate of Chimera running on a linux server is very slow. I'm connected to the server with an ssh client with X server. I wonder if it's because Chimera is not configured properly or possibly the X server. I also tried to make some movies but they are always blank (black screen). Any suggestions?

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Query on selecting one water molecule
by Izzati Mokthar 26 Oct '20

26 Oct '20

Hi, I am Izzati. I would like to ask how to select only one water molecule in chimera? Thank you

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(no subject)
by Yasser Almeida 22 Oct '20

22 Oct '20

Dear Anabel, As others pointed out, you can just represent the beads as balls, points, or wire, and remove all the pseudbonds. On the other hand, how did you obtained your pdb? If you used GNOM in the ATSAS package (GUI version), it writes pdbs with a bigger bead size, which Chimera fails to represent by default. But if you use GNOM in the command line, it writes pdbs with a smaller bead size, which are more compact, smoother, and better for representation in Chimera, and others. Best, Yasser Dear Chimera team, > I am a user from your software and I would like to have a > superimposition of some crystallographic structures in a recent saxs > pdb model I obtained. However, I cannot visualize the saxs pdb file > with Chimera. Would you have any tips or inputs how can I do this? > Thank you very much in advance for all your help, > Kind regards, > Anabel

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Broken links, system requirements
by Calvin Dodge 21 Oct '20

21 Oct '20

Hello, I have been trying to find out what the hardware requirements are for Chimera. For example, how can it be run in a cluster environment with CUDA cards, but no Nvidia graphics cards? My search for information has been hampered by an apparent failure or reorganization of the main site -https://www.cgl.ucsf.edu/chimera/ Every internal link from that page (like to Downloads) is broken. Will the broken links be fixed? Is another page the preferred one for Chimera? Do I need the OSMesa version to run without graphics cards? Thanks, Calvin Dodge Calvin Dodge Systems Analyst Office: 832-271-7148 Email : cdodge(a)x-iss.com<mailto:ellorente@x-iss.com> http://www.x-iss.com<https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> [cid:image001.png@01D5DB72.2E9C2F40]<http://www.x-iss.com/> Smart Management and Analytics for Clusters

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Re: [Chimera-users] Broken links, system requirements
by Greg Couch 21 Oct '20

21 Oct '20

Your university might want the regular version of Chimera to remotely display data. In that case, you should set up VirtualGL as well. And a RDP solution, like x2go. It doesn't perform as well as Chimera running locally on the desktop, but it might be sufficient. -- Greg On 10/21/2020 11:21 AM, Calvin Dodge wrote: > > Greg, > > Thanks for your reply _/I/_ don’t want to run Chimera in a cluster > environment, but the university I’m doing the install for does. I’ll > install the headless version. > > Sincerely, > > Calvin Dodge > > */Calvin Dodge/*/ > Systems Analyst/ > > /Office: 832-271-7148/ > > / > /Email : cdodge(a)x-iss.com <mailto:ellorente@x-iss.com> > > http://www.x-iss.com > <https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> > > <http://www.x-iss.com/> > > Smart Management and Analytics for Clusters > > *From: *Greg Couch <mailto:gregc@cgl.ucsf.edu> > *Sent: *Wednesday, October 21, 2020 12:24 PM > *To: *Calvin Dodge <mailto:cdodge@x-iss.com>; > chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > *Subject: *Re: [Chimera-users] Broken links, system requirements > > (We're working on the web site issues.) > > So the real question is why do you want to run Chimera in a cluster > environment? > > Chimera is not designed to run in a cluster environment, it is > designed to run a user's desktop computer using 3D graphics. Chimera > does not use CUDA. That said, there is a headless version for Linux > that uses a software implementation of OpenGL to create images that > you could use in a cluster, so no graphics card is needed. > > ChimeraX, our successor to Chimera, can take advantage of CUDA in some > circumstances, but it is not required. ChimeraX also only works > headless on Linux, with a software implementation of OpenGL. The > headless operation is included in every Linux version. So no graphics > card is needed there either. We are investigating ways to take > advantage of the graphic card's performance when running headless, but > we're not there yet. > > HTH, > > Greg > > On 10/21/2020 9:24 AM, Calvin Dodge wrote: > > Hello, > > I have been trying to find out what the hardware requirements are > for Chimera. For example, how can it be run in a cluster > environment with CUDA cards, but no Nvidia graphics cards? > > My search for information has been hampered by an apparent failure > or reorganization of the main site -https://www.cgl.ucsf.edu/chimera/ > > Every internal link from that page (like to Downloads) is broken. > > Will the broken links be fixed? Is another page the preferred one > for Chimera? Do I need the OSMesa version to run without graphics > cards? > > Thanks, > > Calvin Dodge > > */Calvin Dodge/*/ > Systems Analyst/ > > /Office: 832-271-7148/ > > / > /Email : cdodge(a)x-iss.com <mailto:ellorente@x-iss.com> > > http://www.x-iss.com > <https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> > > <http://www.x-iss.com/> > > Smart Management and Analytics for Clusters > > > > _______________________________________________ > > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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issues with visualization of saxs models in chimera
by Anabel Pacios Michelena 20 Oct '20

20 Oct '20

Dear Chimera team, I am a user from your software and I would like to have a superimposition of some crystallographic structures in a recent saxs pdb model I obtained. However, I cannot visualize the saxs pdb file with Chimera. Would you have any tips or inputs how can I do this? Thank you very much in advance for all your help, Kind regards, Anabel

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Writing residues coordinates and COMs
by Yasser Almeida 20 Oct '20

20 Oct '20

Hello, I am writing a python script to iterate through all the residues of my model and write the residue coordinates and its correspondent center of mass. I tried with 'runCommand' with the command 'write' but it only accepts a model to be written, not a specific residue. Any thoughts? Thanks in advance. Yasser

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Query about energy minimisation
by Izzati Mokthar 19 Oct '20

19 Oct '20

Hi, I am Izzati. I have a few queries on UCSF Chimera. I need your guide to use the tools. I have two questions. Below are the questions: 1.I would like to do energy minimisation for protein structure with PDB ID: 2J9F. I click Structure editing > Minimize Structure. To be honest, I don't know how to set the settings. I used the default setting and a warning pops up as the attached picture. Do you have any suggestion of reference that I can refer to, to do the energy minimisation? [image: 5.png] 2. I need to also do molecular dynamics for my research. May I know whether I can use chimera to run molecular dynamics as well. If yes, where can I refer to the tutorials? Thank you in advance for your response. Regards, Izzati.

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atom ID
by Francesco Pietra 18 Oct '20

18 Oct '20

Dear all Which is the quickest way to identify the atom ID? As visualized in the context of a multimer, where three identical subunits, distinct by chain name, bind the same peptide, also distinct by chain name. Atom IDs are needed to build a QM-MM simulation. thanks francesco pietra

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PyChimera addCharge
by Matas Tiskus 16 Oct '20

16 Oct '20

Hello, I was looking for ways to add charges to protein structures in a python script and write a .mol2 file. I believe it is possible to do with importing pychimera into the script, but i can't seem to make it work. How would the code for this purpose look like? Matas

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Re: [Chimera-users] [chimera-dev] Building a dimeric protein model
by Elaine Meng 15 Oct '20

15 Oct '20

On Oct 15, 2020, at 1:41 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > Hi > I've built a monomeric model using Chimera's MODELLER interface. I was wondering whether it's possible to use this model in Chimera to create a dimer. The dimer of the protein that I'm studying is composed of two antiparallel symmetric monomers. > Thank you > Tiglath > Hi Tiglath, Sure, but you would need to know the proper positioning of the two monomers in the dimer. There is nothing in Chimera to figure that out automatically. If there is a known dimer structure of a related protein and you think your modeled protein forms a similar dimer, you can simply (1) save your new monomer model as a PDB file (2) start a new Chimera, open that new PDB file two times so that you have two copies open (3) open the known dimer structure of the related protein, let's say it has chains A and B (4) superimpose one copy of your monomer model onto chain A of the known dimer structure, and superimpose the other copy of your monomer model onto chain B of the known dimer structure. Different methods of superimposing structures are discussed in the link below. Probably the easiest is to use the Matchmaker tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (4) close the known dimer structure, and what you have left is the approximate dimer with two copies of your model, which can be saved as a session, or combined into a single model (see "combine" command) and then saved as a PDB file. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Alternatively if you have a dimeric template structure you can use Modeller to make a dimeric comparative model directly, but to do that you would have to use the Modeller interface in our newer program ChimeraX. The one in Chimera only allows modeling monomers. Modeller interface in ChimeraX: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> This chimera-dev e-mail address is mostly for programming questions. For general user questions like this (for future reference) a better address to use is chimera-users(a)cgl.ucsf.edu CC'd here, and there is also a similar address for ChimeraX: chimerax-users(a)cgl.ucsf.edu I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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kill graphics windows after crash
by Dieter Blaas 15 Oct '20

15 Oct '20

Hi, please forgive me when this question is not directly related to Chimera: Sometimes Chimera becomes unresponsive because of a slow network connection. When I then try exiting it or killing it with <ctrl> c from the terminal I used to start it or killing the chimera-related process as shown with ps -ealf|grep UCSF or grep chimera the chimera windows remain and I cannot remove them. Any way of doing so? Thanks for hints, best, Dieter ----------------------------------------------------------------------- Dieter Blaas, Max Perutz Labortories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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how to get specific view
by Shuo 15 Oct '20

15 Oct '20

Dear sir or madam, I wonder how to get specific view parameter in Chimera, just like command get_view in Pymol. So that next time I can easily adjust the view in Chimera. Best Shuo

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Modelling missing residues in a protein
by Edmund Marinelli 14 Oct '20

14 Oct '20

Hello: I see that Chimera uses Modeller for modeling missing residues . Does Chimera have access to any other web based services that would perform similar function? Thanks, Edmund R Marinelli, PhD

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MOLE 2.5 plugin
by Reza Khayat 13 Oct '20

13 Oct '20

Hi, I'm receiving the following error when launching the MOLE 2.5 plugin from Chimera. The plugin was installed as suggested by the developers: Favorites -> Preferences -> Add -> Select directory The plugin's icon appears in my tool bar. However, launching it generates the following error in the Reply Log. Traceback (most recent call last): File "C:\Program Files\Chimera 1.13.1rc\share\chimera\toolbar.py", line 26, in _guard func() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 954, in <lambda> icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 76, in display dialog = find(name, create=1) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 61, in find return d() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' Error in toolbar callback: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: See reply log for Python traceback.? Any help is appreciated. Best wishes, Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Help on using Modeller interface
by Moradkhan, Tiglath A 09 Oct '20

09 Oct '20

Hi I'm currently trying to use the Modeller interface but I'm having difficulties. I am trying to model a monomeric protein but one of the templates is a homotetramer containing chains A, B, C and D. I only need to use chain A to model the protein but I'm not sure how to do it. Whenever I use the Modeller interface, it uses all of the chains which is not what I want. Unfortunately, this is the only template that I can use since the others are either structures that have since been refuted or don't really correspond to the protein I'm studying. I would be very grateful for your help. Thanks Tiglath

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Help for Chimera please
by EMILIE MONTELLIER 09 Oct '20

09 Oct '20

Hello, I have just downloaded your Chimera software. It looks great! I would like to map a list a specific amino acid on p53 protein and I struggle to find a way to do it. I have downloaded the PDB file of 1TUP TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA (at [ https://www.rcsb.org/ | https://www.rcsb.org ] ). For exemple what would be the command to hightlight amino acid 175 + 248 + 273 + 282 on p53 protein? Thanks by advance for your help, Regards, Emilie Emilie Montellier, PhD Postdoctoral Researcher Institute for Advanced Biosciences Team Tumor Molecular Pathology & Biomarkers Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier(a)univ-grenoble-alpes.fr

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Latest nightly broken on Mac (10.15.7)
by Oliver Clarke 09 Oct '20

09 Oct '20

Hi, In the notes for the latest nightly Chimera build, it states "Many user-interface problems on Mac fixed by upgrading the Tk windowing toolkit to version 8.6.10" - this sounds great, but it seems to have broken basic functionality, at least on my system. See screen recording here: https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0 <https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0> Many UI elements are not responsive any more (including the "Report a Bug" dialog, hence why I am reporting here). This is using Mac OS X 10.15.7 on a macbook pro 16", using the trackpad. Cheers Oli

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AutoDOCK plugin for UCSF Chimera
by James Starlight 08 Oct '20

08 Oct '20

Dear Chimera users! Having already used AUTODOCK plugin of UCSF Chimera (for simple docking of 1 receptor with the ligand and structural examination of binding pocket) I wonder to know whether there is some tool built-in CHIMERA (or ChimeraX) suitable for the manipulating with DLG filles produced by Autodock? Particularly I would be interested to combine several DLG filles with their further reclasterization (in the same manner like it could be found in Autodock-Tools) and examination of particular clusters. I would be helpful for any suggestions! Kind regards Gleb

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matchmaker and MSA
by arrafzaher＠campus.technion.ac.il 06 Oct '20

06 Oct '20

Hi, Suppose I have 3 structures #0 #1 and #2. If I impose structure alignment of both #1 and #2 to #0. I receive two MSA alignment. Is there a way to view one MSA of the 3 structures and not 2 MSA of them. Thanks, Zaher

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Volume eraser accelerator not working properly
by Ahmad Khalifa 01 Oct '20

01 Oct '20

As I keep clicking "es", the shadows / lighting keep changing, but after clicking 10 times or so, it finally erases. Is this something I'm doing? How can I change to a more easier accelerator?

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