- Chimera-users - RBVI Mailing Lists

Double chain IDs
by Albert WEIXLBAUMER 08 Aug '19

08 Aug '19

Dear Chimera developers, My apologies if this question has been asked before but I was not able to find an answer so far. I am dealing with PDB files that contain too many individual chains and as such need two-character chain IDs. Ideally I do not want to split the PDB-files (to be able and work with single-character chain IDs). In addition, the PDB-file also contains more than 100,000 atoms and thus uses alphanumeric atom numbers. It seems Chimera is not aware of the two-character chain IDs because selecting a certain chain in the GUI shows only single character chain IDs and it leads to the selection of the two distinct chains (e.g. chain AA and chain BA are both treated as chain A). Is there a workaround? I’ve also noticed that saving such a PDB-file in Chimera changes all ATOM records to HETATM - I don’t know if this is related to the double-character chain IDs or alphanumeric atom numbers but this causes problems downstream because it’s very difficult to change this back to ATOM records without also affecting true HETATM entries. Thank you for your help! Best regards, Albert -- Albert Weixlbaumer Centre for Integrative Biology Department of Integrated Structural Biology Institute of Genetics and Molecular and Cellular Biology IGBMC - UMR 7104 - U 1258 1, rue Laurent Fries BP 10142 67404 ILLKIRCH CEDEX FRANCE Phone: +33 3 6948 5103 Email: Albert.Weixlbaumer(a)igbmc.fr<mailto:Albert.Weixlbaumer@igbmc.fr> OpenPGP KeyID: 0x7F644168

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Making PDBs with over 10,000 atoms
by Ryan Harlich 07 Aug '19

07 Aug '19

Hi Chimera, I am trying to make a PDB with over 10,000 atoms. Currently we have this marked as a limitation to our project. I am researching to see if there is a way around this. Our current idea is to make the next 10,000 atoms another chain. Although when I apply this to a sample I get a break point between chain A and chain B. I do want them connected and to be different chains. So: 9,998.A 9,999.A 0.B 1.B connect. In addition, I would need helices and sheets to span over these two chains. So helix or sheet would start at 9,998.A and end at 1.B. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Superimpose protein chains
by Peter Snyder 07 Aug '19

07 Aug '19

How can I superimpose two (or three) chains from a single structure (ie two homologous subunits that form a multimeric protein)? Thank you Pete

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Is "volume #0 voxelSize 1" a isosurface display changes
by Ryan Harlich 06 Aug '19

06 Aug '19

Hi Chimera, Is "volume #0 voxelSize 1" a isosurface display changes? So if I volume save this would it save this change? Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Morphing, ligands, and secondary structure
by Yan Kung 06 Aug '19

06 Aug '19

Hi Chimera, I’m a new-ish user, and I’ve found that morphing structures is usually very straightforward and easy to use. But I’m now running into an issue with morphing and ligands (and secondary structure). I’d like to make a single morph composed of states A-B-C-B-A (so 4 movements between 5 states). These movements are: (1) A-B: domain opens, (2) B-C: a ligand flies out, (3) C-B: the same ligand flies back in, and (4) B-A: domain closes. First problem: the ligand does not appear in the resulting morph, a problem suggested by the documentation, which I have tried (and failed) to solve using the tips I found in archived posts from this mailing list. Also, because the ligand has to fly in and out, I can’t simply superimpose the ligand from any of the individual states over the morph. So I tried a workaround: make each movement a separate morph. This works for movements 2 and 3 (where the ligand flies out and in). But the ligand still does not appear in movements 1 and 4 (where the ligand remains in place and the domain moves). I’m not sure why the ligand’s appearance would depend on whether it flies in/out, or whether a domain moves… But it seems to. Moreover, a second problem emerges that has to do with secondary structure and is difficult to explain. (Essentially: a few protein regions are on the border between helices and loops such that they appear as helices in some states but as loops in others, and vice versa. If possible, I’d like the secondary structure to remain constant across all states, or else it’s distracting. Even still, I’ve tried to embrace this and use ksdssp to show the helices/loop switching back and forth, but this is distracting as they flicker between helices and loops, each region at its own separate frame. Specifying ksdssp only in certain frames to minimize the flickering doesn’t work either, as different regions switch back and forth at different times.) The only solution I can think of that would maintain the same secondary structure throughout is to just make a single morph of all movements (and not use ksdssp). But this puts me back where I started! Any ideas? (Separately, I realize that I could make a simpler morph of just A-B-C, then record it as “roundtrip”, i.e. forward and backwards, to achieve the same thing as A-B-C-B-A. But this doesn’t solve the problems above.) Thanks very much, Yan -- Yan Kung Assistant Professor Department of Chemistry Bryn Mawr College http://www.brynmawr.edu/people/yan-kung Follow: @KungLab<https://twitter.com/KungLab>

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Nvidia 3D Vision on a large display
by Tom Goddard 02 Aug '19

02 Aug '19

Krish Raman asked what kind of large displays might work with Nvidia 3D Vision stereo glasses with Chimera. Hi Krish, I believe any display capable of a high refresh rate, at least 120 Hz (even 100Hz would do) will be able to show stereo with Nvidia 3D vision. Conventional 60 Hz displays could only show stereo at 30 Hz in each eye (since the display first shows the left eye, then shows the right eye in sequence), and 30 Hz is too slow causing flicker. Video gaming displays are usually advertised as 144 Hz and I believe any of those would work. It is hard to find big displays at 144 Hz, but here is an example, 49 inch ultra wide Samsung CHG90 https://www.amazon.com/Samsung-49-Inch-Curved-Monitor-LC49HG90DMNXZA/dp/B07… <https://www.amazon.com/Samsung-49-Inch-Curved-Monitor-LC49HG90DMNXZA/dp/B07…> If one person is using this sitting at a desk it is very wide and would probably give very nice immersive stereo because of the width. It is not ideal for your use with an audience standing further back because of its extreme 32:0 aspect ratio. You could look for a video gaming TV, such as these https://www.tomsguide.com/us/best-4k-gaming-tv,review-4837.html <https://www.tomsguide.com/us/best-4k-gaming-tv,review-4837.html> Keep in mind your Nvidia 3DVision system may not work with any of these. I would strongly recommend testing at a store with your 3DVision before buying. Stereo is an an extremely obscure niche product and there is no telling if it will work without testing. Another option is to use a high refresh rate projector. That is what we use at my lab -- (ours is a $50,000 Christie, so I don't recommend it). Also I am sure you are aware that Nvidia discontinued support for 3D Vision and it will not work with any Nvidia drivers released after April 2019. So the 3D Vision system is going to be dead soon. Tom

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crash on using Preset Publication 2
by Dieter Blaas 02 Aug '19

02 Aug '19

Hi, I have been using the Publication Preset 2 for making figures of a number of pdb structures without problems. However, I now have a pdb that shows up well in Chimera and does not have any obvious problems. However, when trying rendering it with the Preset Publication 2 (and only with this one) Chimera crashes with the error message below: *** stack smashing detected +++: /home/blaas/.local/UCSF-Chimera64-1.10.2/bin/python2.7 terminated Since I have prepared the other figures with this setting I'd like using it as well for the next figure but how? Thanks a lot, best regards, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Chimera Viewdock Bug
by Sacco, Michael 02 Aug '19

02 Aug '19

Hello all, I would like to report a bug. When using Chimera in dual monitor mode on windows OS and loading the viewdock module, Chimera becomes unresponsive. However, when the second monitor is unplugged, it functions normally. I have confirmed this on multiple computers. After force closing Chimera a pop-up appears with the message "Chimera exited abnormally; the exit code was: 1.". Thanks everyone! Michael

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OBJ files are exported too small and won't open on other programs.
by Josh Moon 01 Aug '19

01 Aug '19

Hello! I am a relatively new and inexperienced user of Chimera. I am having a difficult time working with obj files. The Scenes I'm exporting as obj's end up having a very small file size (67 bytes in one case) and are being processed very quickly. The resulting file won't open successfully on any program that should understand an obj. Stl's are fine. Conversely, when I try to open an obj file into Chimera, it asks me to manually "Designate the File Type" as though it doesn't know what to do with it. Can someone please suggest what features I'm missing so that I can successfully export an OBJ? I'm also interested in how best to handle color information. Thank you! Josh ----------------------------------------- Josh Moon, Ph.D. (he/him/his) Educational Technology Specialist Kalamazoo College (269) 337-7415

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inquire about molecular docking
by Mohamed Hegazy 31 Jul '19

31 Jul '19

Hey , My name is Mohamed Hegazy, beginner in molecular docking , recently I performed a molecular docking procedure using chimera and I found that the initial structure of the ligand differs from the minimized one , and the binding score for a ligand would change during my different runs. The binding score you obtain from my docking cannot be a constant number. Sent from Mail for Windows 10 Mohamed Said Hegazy --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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