- Chimera-users - RBVI Mailing Lists

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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