November 2020 - Chimera-users - RBVI Mailing Lists

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 16 Nov '20

16 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 11 Nov '20

11 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 10 Nov '20

10 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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Chimera-users November 2020