- Chimera-users - RBVI Mailing Lists

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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AreaSAS Issue
by Rucco,Dominic J 31 Jul '19

31 Jul '19

Hello, I'll start by saying your software has helped me visualize protein structure for quite some time and overall has been easy to use! I do have a question however: I was recently using the "render by attribute" feature to display areaSAS measurements but have run into an issue. I can no longer select this attribute from the dropdown menu. I noticed this when I attempted to render it on the protein mCherry (PDB 2H5Q). Even when I have gone back to other PDB entries I know have worked for areaSAS rendering, it doesn't appear as an option anymore. The only time I can get it to appear is when I load a session that already has the rendering performed on the protein. Any help would be appreciated, thank you, Dominic Dominic Rucco | Ph.D. Candidate George and Josephine Butler Polymer Research Laboratory Center for Macromolecular Science and Engineering Department of Chemistry University of Florida Leigh Hall 314 | PO Box 117200 | Gainesville, FL 32611-7200 drucco(a)ufl.edu<mailto:drucco@ufl.edu> | www.savin.chem.ufl.edu<http://savin.chem.ufl.edu/>

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--nogui gets permission denied when fetching pdb id
by Ryan Harlich 30 Jul '19

30 Jul '19

Hi Chimera, I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Minimization with sulfur atom
by sara20＠mail.ustc.edu.cn 30 Jul '19

30 Jul '19

Dear users I have complex structure with ligand having sulfur atom in it. I am trying to minimize it but it fails giving the following error: (LIG) /home/usr/.local/UCSF-Chimera64-1.12/bin/amber16/bin/antechamber: Fatal Error! (LIG) Cannot properly run "/home/usr/.local/UCSF-Chimera64-1.12/bin/amber16/bin/sqm -O -i sqm.in -o sqm.out". I assume it's because of sulfur atom in ligand because I tried running it with out sulfur and it worked fine. I checked MMKT Atom database for sulfur file and it's already there: name = 'sulphur' symbol = 'S' mass = [(31.97207070, 95.02), (32.97145843, 0.75), (33.96786665, 4.21), (35.9670806, 0.02)] color = 'yellow' vdW_radius = 0.18 b_coherent = 2.847*fm b_incoherent = 0.188*fm b_coherent_deut = 2.847*fm b_incoherent_deut = 0.188*fm Any help would be highly appreciated. Thanks Sara

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Applying session parameters to another pdb file.
by David Sáez 29 Jul '19

29 Jul '19

Dear Chimera experts, I have saved a session of Chimera showing the perfect angle and size for the molecules of interest. Now I would like to apply the same parameters to visualize another (but similar, only differnet coordinates) pdb file. Is there a way to do that? Thanks in advance. David

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Editing sequences within Chimera
by Joshua Plank 26 Jul '19

26 Jul '19

Hi, I am wondering if it is possible to edit the amino acid sequence somehow? I have a .pdb file of the protein I'm interested in, but would like to change two of the amino acids to something else. Is this possible? thanks, Josh -- *Joshua Plank* *PhD Student* *Department of Electrical and Computer Engineering* *University of California, Riverside* *email: jplan002(a)ucr.edu <jplan002(a)ucr.edu>* *phone: 505-977-9919*

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Measuring the distance between residues and a surface
by Stanley, Julian A 25 Jul '19

25 Jul '19

Hello! I'm fairly new to Chimera, so if you're able to point me towards any resources that can help me answer questions like this one independently in the future, please do! Here's the question: I would like to measure the distance between the ends arginine and lysine residues and a surface, using Chimera's python modules. Typically, I would load my .pdb file, generate a surface, and then use the "measure distance" command and parse the output from the Reply Log. This approach works fine, except since "measure distance" prints to the reply log, I need to run my script in GUI mode. If possible, I'd prefer to run everything from the command line only. I thought that I might be able to do this with the distance() command, but I can't figure out how to pass a surface to that command. Does anyone have any tips/advice? In summary, what I usually do: ``` from chimera import runCommand as rc # load the file rc("open " + pdbFile) # Generate a surface rc("select protein") rc("split") rc("surface allComponents false") rc("~select") # Measure distance between arg and lys and the surface rc("select #0") rc("~select #0:@") rc("measure distance :arg@cd|:lys@ce selection multiple true show true") ``` And then I parse out the distances from the Reply Log. What I would prefer to do: It would be better to have the output to go to STDOUT when I run the script. I imagine that I'd use something like the `distance()` command, of the premade scripts (like here: http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/atomdist.py) but they are designed to measure the distance between atoms or residues, not between residues and a surface. Thanks for your help! Sincerely, Julian

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Modeller Restraints
by Danilo Boškovic 24 Jul '19

24 Jul '19

Dear all, how do i add restraints specific to my templates that i use for comparative modelling in chimera? Specifically what are the names assigned to those templates? Do i need the names to specify the template residues that i want to restrain? Are the names same as in the tab when i choose the templates for the run? Thanks, D. B.

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Re: [Chimera-users] Cannot resample to voxel size of 1
by Tom Goddard 22 Jul '19

22 Jul '19

It sounds like you just want to resample a map at a new grid spacing. Chimera does not have such a feature. The vop resample command is intended make the grids of two different maps match each other. Tom > On Jul 22, 2019, at 1:54 PM, Ryan Harlich <ryanharlich(a)hotmail.com> wrote: > > Hi Tom, > > I need the voxel size to be 1, so subdivideSurface and subdivisionLevel options won’t work. Also, vop new won’t work because I need it to have the same bounding box as the input surface. > > Best, > Ryan Harlich > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, July 22, 2019 1:49:38 PM > To: Ryan Harlich <ryanharlich(a)hotmail.com> > Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Cannot resample to voxel size of 1 > > Hi Ryan, > > Resampling only works on the grid of another map as you can see from the documentation so "vop new" allows you to make that map. If you just want to make the mesh of a surface depiction of a map finer then look at the volume command subdivideSurface and subdivisionLevel options. > > https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.…> > > Tom > > >> On Jul 22, 2019, at 12:03 PM, Ryan Harlich <ryanharlich(a)hotmail.com <mailto:ryanharlich@hotmail.com>> wrote: >> >> Hi Elaine, >> >> I think you missed the point. I am trying to take an existing surface and resample it to a grid Spacing of 1. I am not sure I see the point of making a new map. >> >> Best, >> Ryan Harlich >> >> Sent from Mail <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgo.micros…> for Windows 10 >> >> From: Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> >> Sent: Monday, July 22, 2019 11:59:06 AM >> To: Ryan Harlich <ryanharlich(a)hotmail.com <mailto:ryanharlich@hotmail.com>> >> Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> >> Subject: Re: [Chimera-users] Cannot resample to voxel size of 1 >> >> Hi Ryan, >> You can make a new map of whatever grid spacing you want without any atoms using “vop new”: >> <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u… <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…>> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> > On Jul 22, 2019, at 11:33 AM, Ryan Harlich <ryanharlich(a)hotmail.com <mailto:ryanharlich@hotmail.com>> wrote: >> > >> > Hi Chimera Bug Team, >> > >> > I am unable to resample surface to a grid spacing of 1 to be 1 voxel. >> > >> > Currently I do this: >> > 'molmap #2 6 gridSpacing 1\n' >> > 'vop resample #3 onGrid #2.1\n' >> > >> > But this requires me to have a pdb structure. I would like to do this without a pdb structure. >> > >> > Another alternative is I could automatically without GUI interface make a 3 atom pdb structure with python script that is the size of the surface’s boundary box. Although there is no way to get surface’s boundary box x,y,z. >> > >> > Any help would be much appreciated. Option 1 would be a much better approach. >> > >> > Best, >> > Ryan Harlich >> >> _______________________________________________ >> 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 <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.…>

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Cannot resample to voxel size of 1
by Ryan Harlich 22 Jul '19

22 Jul '19

Hi Chimera Bug Team, I am unable to resample surface to a grid spacing of 1 to be 1 voxel. Currently I do this: 'molmap #2 6 gridSpacing 1\n' 'vop resample #3 onGrid #2.1\n' But this requires me to have a pdb structure. I would like to do this without a pdb structure. Another alternative is I could automatically without GUI interface make a 3 atom pdb structure with python script that is the size of the surface’s boundary box. Although there is no way to get surface’s boundary box x,y,z. Any help would be much appreciated. Option 1 would be a much better approach. Best, Ryan Harlich Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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same volume data values over the entire volume
by Dieter Blaas 22 Jul '19

22 Jul '19

Hi, Trying to color a volume according to "volume data" I get the same numerical values for all colors and a speckled appearance. When using "volume data gradient norm" I get the expected colors, i.e. strong local changes of the volume data are red and spots where there is essentially no change are in blue. How is this possible? If I understand correctly, "volume data gradient norm" colors according to the first derivative of "volume data" or is this wrong? Do I need something like a normalization? Thanks a lot for explanations, best, 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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Fitting the structure into the map after changing origin
by Ahmad Khalifa 22 Jul '19

22 Jul '19

Is there a shortcut way of transforming the model to fit the map after I change, center or reset the origin? Best regards.

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RMSD Chimera
by Ishita Gupta 22 Jul '19

22 Jul '19

Hi, I have a few questions in mind regarding rmsd calculation in chimera: 1. Does the matchmaker tool calculate c alpha? 2. Do we consider RMSD of pruned atoms or the total atoms while reporting? 3. If we use structural comparison match align tool then rmsd is based on multiple sequence alignment? And it also gives C alpha? 4. If we calculate rmsd from multi align viewer by clicking on the structure and then match. What these rmsd values denote? Please elaborate on these points. Thanks Ishita

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Measurement similarity protein structure
by Nail Besli 18 Jul '19

18 Jul '19

Hi I superimposed two proteins in chimera with winch algorithms( blossom62) and p250. The result is the same. Why is the result same for both two proteins, although I tried two different algorithm settings? I am using the chimera's MatchMaker tool. The only thing different is the sequence alignment score. I attached the result file. kind regards

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what laptop configuration should I get for using Chimera and ChimeraX with very large volumes?
by Ilona Nudelman 18 Jul '19

18 Jul '19

Hi, I'm looking for an upgrade to my PC laptop (Windows) and wanted to ask if anyone has any advice on the configuration needed to run Chimera and ChimeraX with very large volumes and lots of heavy pdb's docked in. I am looking for a mobile workstation type laptop but I don't want to spend too much money - maybe 2,500-3,500$. Within these confines what memory, GPU, processor etc. would you recommend? Thanks! Ilona

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how to obtain information regarding complexes
by Quadir, Farhan (MU-Student) 18 Jul '19

18 Jul '19

Hello, I am relatively new to chimera. I am stuck with a problem of how to perform the following from a pdb file which contains multiple chains: 1. I would like to find regions which are 5.0 Angstroms or less between selected chains. 2. After obtaining that I would like to get from (1) a list of the residues and their positions in the chain that are interacting with each other inter-chainwise. Regards, Farhan Quadir PhD Student and Graduate Research Assistant Bioinformatics, Data Mining and Machine Learning (DBM) Lab 304 Engineering Building 1 Electrical Engineering and Computer Science (EECS) Department University of Missouri, Columbia, MO 65201, USA Email: fqg7h(a)mail.missouri.edu Phone (Cell): 573-846-4047

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Finding dimensions of density map
by Ryan Harlich 16 Jul '19

16 Jul '19

Hi Chimera, I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process? Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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energy minimization
by sara20＠mail.ustc.edu.cn 16 Jul '19

16 Jul '19

Dear I am trying to minimize a structure with HEME cofactor. I added heme frcmod and prep files from Amber parameter database in parm and prep folders respectively.I minimized the structure at different steps of steepest descent from 100 to 1000.But in all the structures FE of heme is not well aligned with HEME structure (it is pointed out of structure).I tried with both all atom and united atom frcmod and prep files but the results are same.Please find attached the minimized structure. Kindly tell me where am I wrong. Any help would be appreciated. Thank you Regards Sara

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