November 2020 - Chimera-users - RBVI Mailing Lists

(no subject)
by Thirumurugan Prakasam 29 Oct '21

29 Oct '21

Hi, I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues. Looking forward to hearing from you, Many thanks, Thiru [image: image.png] -- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358

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(no subject)
by Prabuddha Bhattacharya 26 Nov '20

26 Nov '20

Dear Sir Can you help me with a step by step tutorial to find out the electrostatic potential map of a molecule on chimera? Thank you Best regards *Dr. Prabuddha Bhattacharya *

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Error message
by Kaitlyn Merrill 22 Nov '20

22 Nov '20

Hi there, I have been using Chimera and Autodock Vina through Chimera and started getting this error message whenever I attempt to use the Autodock Vina to dock a ligand. Can you please tell me how to fix this? Thanks, Kaitlyn

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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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Chimera-users November 2020