October 2019 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Creating movies with alpha channel / transparent background
by Tom Goddard 28 Oct '19

28 Oct '19

Hi Martin, It is possible that some Chimera movie encode command format option will put the transparency channel into the movie -- it all depends on what ffmpeg does and what those formats support. I don't know what ffmpeg supports nor what formats support transparency -- you could try to look that up online, or you could simply try each of the Chimera formats and see if it produces a movie with transparency. Chimera simply hands the sequence of PNG images to ffmpeg (which is bundled with Chimera, ffmpeg version 2.1). From what I saw in ffmpeg docs there is not a special include transparency option -- it is simply a matter of having a transparency channel in the images and having ffmpeg support for the specific output format. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#encode-op… Tom > On Oct 28, 2019, at 2:04 PM, Martin Textor <martin_textor(a)gmx.de> wrote: > > Hi Tom, > > thank you. I'm aware that Chimera can output a series of images with a transparent background, I have done this already (using png). As this is possible, and the "movie encode" command supports, besides other formats, .avi and .mov, both of which definitely support an alpha channel, I had hoped there might be some option for "movie encode" that's just not described in the documentation which allows obtaining a video with transparent background and spares me from having to use a third-party tool. > > With regards to Elaine's reply, I want to use the video overlaid to another one, so a static background image is not an option in this specific case, but thanks for the suggestion. > > Best, > Martin > > Am Mo., 28. Okt. 2019 um 20:05 Uhr schrieb Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>: > Hi Martin, > > You can have Chimera save a series of transparent background images using the movie command, for example, > > set bgtransp > movie record dir ~/Desktop/test format png ; turn y 1 90 ; wait 90 ; movie stop > > Then you would need to encode the PNG images in ~/Desktop/test into a movie using some encoding program. I doubt the Chimera "movie encode" command supports any video format that can handle transparent background. Chimera uses ffmpeg to encode movies and apparently ffmpeg can encode some video formats with transparency, for example, as described here the motion PNG format in .mov can handle transparency > > https://stackoverflow.com/questions/644684/turn-image-sequence-into-video-w… <https://stackoverflow.com/questions/644684/turn-image-sequence-into-video-w…> > > Tom > > > > >> On Oct 28, 2019, at 10:06 AM, Martin Textor wrote: >> >> Hello, >> >> I was wondering if it is possible to create movies with a transparent background? I know that it's possible to create images with a transparent background and that the video formats supported by Chimera to encode movies include avi and mov, both of which support an alpha channel as far as I know. >> >> Kind regards, >> Martin Textor >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > > > > -- > Martin Textor > 20 Elmer Mews, > Leatherhead, Surrey, > KT22 9DN, UK > > Fon: +49(0)178 3993650 <> > Mail: martin_textor(a)gmx.de <mailto:martin_textor@gmx.de>

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Creating movies with alpha channel / transparent background
by Martin Textor 28 Oct '19

28 Oct '19

Hello, I was wondering if it is possible to create movies with a transparent background? I know that it's possible to create images with a transparent background and that the video formats supported by Chimera to encode movies include avi and mov, both of which support an alpha channel as far as I know. Kind regards, Martin Textor

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Fit list behavior query
by Oliver Clarke 28 Oct '19

28 Oct '19

Hi, I often use fitmap with the “search” flag to find the orientation of a fragment (e.g. a single domain of a larger protein) in a cryoEM map - something like “fitmap #1 #0 search 100 radius 5”. Normally, a fit list table will appear and the model will reorient to match the highest scoring entry in the fit list. One thing I have noticed is that if I run a second such command after the first (e.g. to try a different radius or number of trials), the fit list is not updated - all the entries are identical, and the model is again reoriented to match the highest entry in the first list. I find I need to first manually clear all the fits from the first trial in order for it to correctly update with the results of the second run. I wonder if it would be possible to alter this behavior such that the fits from the first run are automatically cleared if a second fitmap command is issued? Cheers Oli

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Using Chimera on IOS devices
by Lytle, Ayren 23 Oct '19

23 Oct '19

Good afternoon, I've reviewed the list of supported operating systems<http://www.rbvi.ucsf.edu/chimera/download.html> on your website and did not see IOS listed. Do you have any experience using Chimera on iPads and if so do you recommend it for College Biology students? Our instructors have referenced some Galaxy Tab A (2019) Android tablets, but we would prefer to support IOS devices over Android due to our existing central support manage systems. I've included a link below to the Andriod tablet they are considering as well. I appreciate your time. Thanks. https://www.cdwg.com/product/samsung-galaxy-tab-a-2019-tablet-android-9.0-p… Best regards, Ayren Lytle Manager, User Services College of Southern Nevada | Department of Office of Technology Services 3200 E. Cheyenne | North Las Vegas, NV. 89030 Office: (702)-651-4450<a%20href=%22tel:%20(702)-651-4450%22%3e123-456-7890%3c/a> | ayren.lytle(a)csn.edu<mailto:ayren.lytle@csn.edu> www.csn.edu/ots<https://at.csn.edu/otsservices> [ConfidentialSignatureLine]

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50 chains structure numbering errors
by Ahmad Khalifa 23 Oct '19

23 Oct '19

Hello, I'm trying to deposit a PDB with 50 chains. My PDB has a lot of HETATM records and at some point it switches from HETATM"number" to HETATM*****. The PDB throws an error regarding HETATM*****. If you any suggestions regarding the error and / or processing the .pdb to make the deposition easier, please let me know. I also wonder if I can save my file as a cif by Chimera. Regards.

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could not access chimera webpage
by Sirin Theerawatanasirikul 23 Oct '19

23 Oct '19

Dear Chimera UCSF developers I am Sirin Theerawatanasirikul from Thailand. I am working on protein structures and use chimera every day. In a couple days, I tried to access your website via safari run in Mac Os Mojave ; https://www.cgl.ucsf.edu › chimera I could not access any topic or any feature. Could you please give me a suggestion? Sincerely yours, Sirin -- Sirin Theerawatanasirikul DVM (Hon.),PhD.(Pathobiology) Assistant Professor, Department of Anatomy Faculty of Veterinary Medicine, Kasetsart University THAILAND e-mail: fvetsrth(a)ku.ac.th, sirin.t(a)ku.ac.th, numilo(a)hotmail.com office phone: +66(0)2 942 8954

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Reassign chain ID letters
by Ahmad Khalifa 21 Oct '19

21 Oct '19

Hello, I have a structure with multiple chain IDs, some of them include number chain IDs and same letter small case and capital case chain IDs. I want to reassign the chain ID's randomly so that they are letters first then numbers, capital case then small case. How can I do that?! Best regards.

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Chimera
by Arnaout, M. Amin,M.D. 18 Oct '19

18 Oct '19

I<https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…>I downloaded chimera-1.14-mac64.dmg<https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…> on my iMAC with Catalina OS but cannot open Chimera (see attached).

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Chimera on macOS Catalina (10.15)
by Tom Goddard 15 Oct '19

15 Oct '19

Apple released their next version of macOS, version 10.15, called Catalina, a week ago. I have tested the Chimera 1.13.1 and Chimera 1.14 release candidate with Catalina and they worked without obvious problems. macOS Catalina has introduced new security measures where you must give permission to each application to allow it to access Desktop, Downloads and Documents folders and external disk drives. So you will see those permission dialogs appearing in Chimera and will need to press Allow. You only need to grant permission once for each folder when you try to open data from that folder and those permissions will apply to all future Chimera uses, so it is not too annoying. Tom

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depict hydrophobicity surface in super large molecules in chimera
by Marta Perez Illana 15 Oct '19

15 Oct '19

Hi all I was trying to analyze the hydrophobic surface of two very large structures ( 3 chainsx 900 aa each so 2.700aa). As expected the default surface calculation has failed. Normally for electrostatic potential what works for me is making a mol map (molmap #3 4 gridSpacing 0.5) and then calling the pdb2pqr and apbs servers directly from chimera, which is very convenient. However I cannot find an analogous way to make it with hydrophobicity... Since the surface fails for such big molecules, the straight forward way (present-3interactive surface hydrophobicity) does fail as well... Then... is there any server than can be called from chimera, to get hydrophobicity as an attribute to be depicted? Or alternatively could you suggest any server that gives output hydrophobic column, compatible to get it after to chimera attributes? Reading a bit I found that, not as electric fields, that can be computed for structures, hydrophobicity comes just for the sequence, without taking into account the neighbours and context... P.D: I have managed to represent in other programs the hydrophobic surface, but I really want to make it in chimera, to make it more consistent and easy to organize myself... Thanks a lot! and sorry if the question goes beyond Chimera... Marta

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Chimera-users October 2019