- Chimera-users - RBVI Mailing Lists

saving rotated volume
by Reginald McNulty 18 May '17

18 May '17

Dear Users, I have two objects open in Chimera. One is a .bild file that shows axes x,y,z. The other is a volume of a virus with a tail. I used “activate only” to manipulate the volume relative to the axis.bild object. After rotating the virus to align the tail to the Z-axis, I try to save the map but it’s always back in the original position when I re-open it in Chimera. Is there a way to save this transformed map? -Reggie

3 4

morphed conformation movie?
by esserlo＠helix.nih.gov 18 May '17

18 May '17

For this one, I found a solution: >Also is there a commandline version to access the conformations and to re-run >kdssp on each interpolated conformation? I read you need the perframe command >for that. Does anyone have a working example ? There is a good example (and several more) in http://www.cgl.ucsf.edu/chimera/animations/animations.html (for instance leucyl-tRNA.cmd ) However, I still don't know how to re-open a morphing menu that disappeared and the per-frame kdssp is not yet clear to me yet. Thanks, Lothar

2 2

morphed conformation movie?
by esserlo＠helix.nih.gov 18 May '17

18 May '17

Hi, I used Tools->Structure Comparison->Morph Conformations and it worked well. However, I somehow lost the menu that opens up after the morph is complete. Well, I cannot find it. How can you re-open it to run through the morphed conformations again ? Also is there a commandline version to access the conformations and to re-run kdssp on each interpolated conformation? I read you need the perframe command for that. Does anyone have a working example ? Thanks, Lothar

2 1

reading in electron density map H32 vs R32
by Christine Gee 17 May '17

17 May '17

Hi, I have a structure in the space group H32. I wrote out a map, which lists it as space group 155. I was wondering if chimera would read that in as space group H32 (R32:h) or as R32 (R32:r). Regards Christine

2 1

Open file interface suggestion
by Dan Kool 15 May '17

15 May '17

Hello, I have been using your software for a while. I love the features and general user interface. There is one thing that drives me nuts, though. The side-by-side list interface when I go to open files.A window-based one would be much easier. Is there an option for that that I am not seeing? If not, I suggest adding the option. Thank you for your software! Best, Dan ---------------------------------------------------- Daniel Kool Graduate Research Assistant, Jernigan Lab Bioinformatics and Computational Biology Iowa State University *kool(a)iastate.edu <kool(a)iastate.edu>*

3 3

error or bug
by Arthur Szabo 15 May '17

15 May '17

Continuing my earlier question. I tried the suggestions sent to me neither split nor surfcat seemed to work. After some attempts I received this window and reported the bug [cid:image001.png@01D2CD74.26A7D780] I then tried to use molmap and I did get a surface and saw how by moving the cursor in the molmap window I could get the surface to progressively disappear leaving the selected domains that were colored previously. The surface was for the entire protein, one of the models #0. I could also change the surface color. Then I went looking at some of the tabs on the molmap window and cannot describe the sequence, but ended up with another window that I eventually found out was for visualizing Cryo EM maps. Now I have a surface that is multicolored and looks like jelly beans. Somehow perhaps by selecting one of the models from the command lines, (#0) I was able to pull out a surface of the entire molecule, rotate it etc, and progressively remove the surface, til the selected domains remained. Stuck!!! This is one model: [cid:image003.png@01D2CD79.3D09E040] [cid:image004.jpg@01D2CD79.3D09E040] HERE IS ANOTHER which is #1 or #2 [cid:image005.jpg@01D2CD79.3D09E040] [cid:image006.png@01D2CD79.3D09E040] Arthur Szabo

2 4

Visualizing specific atoms in autodock-vina output
by Francesco Pietra 15 May '17

15 May '17

I am trying to investigate the protein surrounding a docked (autodock-vina, alpha chimera 1.1 build 40505 linux 64) ligand. I am interested in the environment of specific atoms of the ligand. With command sel #1.1@N z<5 I can investigate the protein at 5A from BOTH nitrogen atoms of model 1.1. How to select one of the two existing N atoms in the ligand? Same questions for other ligand atoms (there are many O-atoms) Is that possible without elaborating the vina output? thanks francesco pietra

4 8

Saving multiscale models only?
by Healey, Joe 12 May '17

12 May '17

Hi Chimera team, Is it possible to save a multiscale model without the atomic coordinates that generated it in the first place? I've seen that the multiscale models can be saved within Scenes, but I'd like to save it as a 'structure' such that I can continue to use it in subsequent sessions. At present, when I close the PDB model that generated the MultiScale map, the map also closes. Thanks, Joe Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

2 1

surface transparency animation
by esserlo＠helix.nih.gov 12 May '17

12 May '17

Hi, I am trying to animate a transition of a surface from 100% transparent to opaque. In a test (the real case is more complicated) I did this: open 1hen.pdb # Lysozyme test # Chimera shows a blue ribbon model on gray background surface #0 scolor #0 color green # chimera shows a green surface over a (now invisible) blue ribbon model # According to the manual the following (I think) should work: transparency 80,s #0 # I expected to see the green surface to become 80% transparent and the blue ribbon model to shine through. # No luck. What am I missing ? BTW the page https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/transparency… seems to be missing the last example concerning transparency of surface patches. Thanks, Lothar

2 3

scripting & density
by Dougherty, Matthew T 12 May '17

12 May '17

Hi, I have a dataset, its values are 1-255. I would like to modify the density values using a script. Specifically, I would like to set density values 50-74 & 90-110 to the value of zero. Is there a way to do that using scripting, or do I need to do that using python? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

2 3

surfaces
by Arthur Szabo 12 May '17

12 May '17

Working with a structure that has many domains. I would like to show the surface of three of the domains. I have hidden the ribbon residues of all but the ribbons of three domains. I receive the following error message [cid:image001.png@01D2CB26.2CA19B30] The domains are not contiguous in the structure, but even if I try to show the surface of only one domain I get the same message. And going to the Selection inspector is not helpful since it is not obvious as to how that option assists the surface representation. Over to you Thanks Arthur G. Szabo

2 1

vop scale and vop morph (maybe chimeraX?)
by Oliver Clarke 11 May '17

11 May '17

Hi, When I morph two maps, if they have different mean/sd, I always have to scale the mean and sd of the second map to that of the first, otherwise the morph looks very non-linear - nothing happens until fraction 0.9, and then the morphing happens increasingly fast (so not ideal for visualization). If I normalize one map to the other I get a beautiful, smooth, linear morph. Would it be possible in either chimera or chimeraX to automate this? Either to add an option to vop scale to scale one map directly to the parameters of another (rather than having to use vop measure mapstats) or to have an option for vop morph to put both maps on the same scale? Cheers Oli

2 1

suggestion: if clip planes cross, swap them?
by Oliver Clarke 11 May '17

11 May '17

Hi, Quite often, in aliases and scripts where I am adjusting the clip planes, I get the error “far clip plane placed in front of near clip plane”, or words to that effect. I’ve tried various ways to remedy this but it has to be done on a case by case basis and sometimes I just can’t figure it out. Would there be any possibility for Chimera to rather than triggering an error in such a case, just swap the clip planes when this happens, so the near plane becomes the far plane, and vice-versa? Or is there some other foolproof way to avoid this? I get this error when I want to adjust the hither and yon planes successively - would it be possible to add a command that adjusts them both at the same time, like `section` but with simultaneous independent control over both clip planes? Cheers Oli

2 1

morph map fails with solid representation
by Oliver Clarke 10 May '17

10 May '17

Hi, When I create (using the latest nightly build) a morph between two maps using the “Morph map” GUI, and then I change the representation of the resultant volume to solid, the morph no longer runs, or rather, it appears to run, but the solid volume does not update. This used to work - I used it to create quite a few movies - so I guess it is a bug? Cheers Oli

2 1

symmetrical fit of maps
by Oleksiy Kovtun 10 May '17

10 May '17

Hi all, is there is a way to do symmetrical fit and add symmetrical copies for map to map fitting? The standard symmetrical fitting protocol (measure symmetry. #0...; sym #1 group #0 update true; fitmap...) only works for molecule to map fit. Thank you, Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

2 1

translation and rotation in MATLAB using transformation matrices from chimera
by Oleksiy Kovtun 10 May '17

10 May '17

Dear all, I need to merge two maps in MATLAB using alignment data from chimera. Inputs: two maps of the same box size, origin. I use matrixget - to report translation and rotation matrices for the aligned map . Translation operation works well when transferred into MATLAB (briefly, translation matrix gets converted in eulers and pased on to tom_rotate command in MATLAB, TOM package). However the x y z translation coordinates (the fourth column top to bottom in matrixget - output) are way off the real translation when using tom_shift command in MATLAB, TOM. I found out that if I open the rotated map and fit it again, it gives close to correct translation matrix. What's going wrong here? Does anyone have a solution how to overlay 3D arrays in MATLAB using chimera-reported transformation matrices? Many thanks, Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

3 4

Multiple fitting of structures in to EM densities
by Healey, Joe 10 May '17

10 May '17

Dear chimera team, I have a large EM density I would like to fully populate with a number of copies of a protein. To be more specific, the EM density is of 2 concentric protein rings (EMDB-6720), and each concentric ring is stacked 3 or 4 times. Each ring is a hexamer, so I would like to populate every single ring with 6 copies of each protein (but the inner and outer rings are 2 different proteins). What would be the best mechanism to iteratively import a protein, populate an EM density space, then move on to the next one? Currently, I think if I was to simply open several copies of the protein, they would probably all try to fit within the same EM density position, leaving the rest of the structure empty? My apologies if this isn't totally clear, I've tried to explain it as best as I think I can. I'm happy to accept solutions in 'chimera language', python (or I also have Jaime's Pychimera installed). Many thanks Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

2 3

Re: [Chimera-users] Wire thickness
by Oliver Clarke 10 May '17

10 May '17

Hi Hernando, I used the ca_and_sidechains alias in this script (you should be able to get the individual commands from that). https://github.com/olibclarke/chimera-trimmings/blob/master/chimera_aliases… Cheers Oli > Dear Chimera > How do you set the thickness of the backbone and side chains independently to produce figures like the ones below (sorry I hijacked the picture used in blurred-display discussion). > > Thanks > > H.

3 2

Wire thickness
by Hernando J Sosa 10 May '17

10 May '17

Dear Chimera How do you set the thickness of the backbone and side chains independently to produce figures like the ones below (sorry I hijacked the picture used in blurred-display discussion). Thanks H. [cid:image001.jpg@01D2C8F6.BEA06B60][cid:image002.jpg@01D2C8F6.BEA06B60]

1 0

Re: [Chimera-users] Gaussian blur depth cueing? (ChimeraX)
by Tom Goddard 09 May '17

09 May '17

Before/after pair - at large size, I think the blur is helpful, but YMMV > On May 9, 2017, at 12:09 PM, Oliver Clarke <olibclarke(a)gmail.com <mailto:olibclarke@gmail.com>> wrote: > > Perhaps a better example: > > <brightness_blur.jpg> >> On May 8, 2017, at 10:07 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Oliver, >> >> The depth of field blur images I have seen of maps and molecules have all struck me as cool looking and less useful then conventional brightness based depth cuing. Brightness depth cue allows you to include more of the structure in back while reducing the obscuring effect it has on stuff in front. Blurring depth cue interferes much more with the stuff you want to be in focus. Your image minimizes the badness by not having any blurring in the central region of the image, but the periphery where there is blurring may be artistically nice, but I hope you are not looking at the structure there. >> >> That said the technique could be done using the depth buffer that assigns depth to each pixel — it can’t be done really well that way because that depth only gives the front-most object and if transparency is present the pixel shows multiple objects at different depths. I think it would require a compelling mock-up image to make it worth spending effort on this effect. It is relatively easy to make a mock-up image by using clip planes to save several images representing slabs at different depths, then blur each slab image differently depending on depth in a photo editor and composite. >> >> Tom >> >> >>> On May 5, 2017, at 6:42 AM, Oliver Clarke <olibclarke(a)gmail.com <mailto:olibclarke@gmail.com>> wrote: >>> >>> Hi, >>> >>> I was wondering if you have thought about implementing depth-dependent gaussian blur as a depth cueing mechanism in ChimeraX? >>> >>> The idea would be to blur the image in a manner dependent on the distance from the plane intersecting with the center of rotation, to mimick depth of field in a camera. >>> >>> Mocked up in the attached using a tilt/shift effect, but without access to real depth information - I wonder if it might better convey depth information than distance-dependent changes in brightness/contrast under some circumstances? >>> >>> Cheers >>> Oli >>> >>> <test_image_tilt_shift.png> >>> _______________________________________________ >>> 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> >> >

2 1

Gaussian blur depth cueing? (ChimeraX)
by Oliver Clarke 09 May '17

09 May '17

Hi, I was wondering if you have thought about implementing depth-dependent gaussian blur as a depth cueing mechanism in ChimeraX? The idea would be to blur the image in a manner dependent on the distance from the plane intersecting with the center of rotation, to mimick depth of field in a camera. Mocked up in the attached using a tilt/shift effect, but without access to real depth information - I wonder if it might better convey depth information than distance-dependent changes in brightness/contrast under some circumstances? Cheers Oli

2 4

Re: [Chimera-users] Query regarding chimera tool
by Elaine Meng 09 May '17

09 May '17

On May 8, 2017, at 10:54 PM, bushra TAJ <bushraistaj(a)gmail.com> wrote: > Hello Sir > I want to do some docking studies of my own synthesized compounds. I found them very active in some anti-cancer assays. > I will use AUTODOCK for this purpose. I have got the Pdb file of my target protein from PDB database. > My problem is how to make pdb of my molecule (input file for autodock) can I use chimera for that?? > I have chem-draw file format of my molecules will that open in chimera to make their pdb format. > Regards > In the menu under Tools….. Surface/Binding Analysis: There is a “Dock Prep” tool for preparing PDB files. There is also an “Autodock Vina” tool that will make prepared files in pdbqt format, but it will also run Autodock Vina docking (in other words, the prepared pdbqt files are a by-product but you could also use them as input to something else). You should look at the manual pages for more information. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Also in the future please send Chimera questions to chimera-users(a)cgl.ucsf.edu and include a useful subject line like “preparing molecules for docking.” Messages to my individual email address may not get answered. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

All-by-all distances
by Elaine Meng 09 May '17

09 May '17

> From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Chimera Question > Date: May 8, 2017 at 6:03:55 PM PDT > > Hi Shawn, > I’m out sick… please send Chimera questions to chimera-users(a)cgl.ucsf.edu list. On second thought, I think I can answer quickly. However, for future reference please use the user list for Chimera questions and include a informative “subject” line to make it easier for others to find … thanks! Command: findclash :lys@n test self overlap -99999 log true … will put all the Lys N -> Lys N distances (within about 1000 A … just use a larger-magnitude negative overlap if you think there are longer distances) in the Log. It won’t be a table, though, just a list of distances that you would have to process yourself. Or instead of “log true” (or in addition to it) you could use the “saveFile” option to specify putting the same output into a text file. Command and options described here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>> Output is like the following example for PDB 2gbp, with distances in the last column: 464 contacts atom1 atom2 overlap distance LYS 191.A N LYS 189.A N -1.010 4.290 LYS 223.A N LYS 227.A N -1.505 4.785 LYS 246.A N LYS 300.A N -3.378 6.658 […etc…] However I suspect maybe you meant NZ (the end of the sidechain) instead of the backbone N, in which case the command would be something like findclash :lys@nz test self overlap -99999 log true … with output like: 465 contacts atom1 atom2 overlap distance LYS 270.A NZ LYS 276.A NZ -1.932 5.212 LYS 308.A NZ LYS 246.A NZ -2.262 5.542 […etc…] Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > >> On May 8, 2017, at 4:14 PM, Shawn Sternisha <ssternisha(a)chem.fsu.edu> wrote: >> >> Hello Dr. Meng, >> >> Sorry to bother you but I have a question about Chimera that I have not been able to find an answer to, despite intensive web searches. I have seen your name on a lot of useful posts and answers so I figured I would give emailing you a shot. I have been searching for a method to measure all possible distance between Lys residues in a protein in a high-throughput manner. >> >> For example, if my protein has 17 Lys residues, is it possible to generate a table that has distance measurements between the N atoms of all of them. I believe that would be 231 possible distances. Any advice you could provide would be greatly appreciated. Thank you for your time in advance. >> >> Best, >> Shawn Sternisha >> PhD Candidate, Miller Laboratory >> Dept. of Chemistry and Biochemistry >> Florida State University > >

2 1

calculate FSC curve between experimental cryo EM map and model
by #AHMED TOFAYEL# 08 May '17

08 May '17

Dear all, If I want to calculate FSC curve between experimental cryo EM map and model, what is the correct procedure to do so? I will explain what I have tried so far. Although I have variable local resolution in my map, according to FSC=0.143 criterion I have a 4 Ang map (say 1.mrc), I have used 'molmap' command in Chimera to generate a simulated map at 4 Ang. Then I used "vop resample" to take care of the pixel and box values ( then saved as 2.mrc). Thereafter, I have used "e2proc3d.py 1.mrc fsc.txt --calcfsc=2.mrc and plotted the fsc.txt file to get the curve. I am not sure if I am on the right track. My pixel size is 1.28. Best regards, Tofayel

3 3

MD file naming
by P. Buscemi Ph.D. 08 May '17

08 May '17

Please,,,, How does one specify the output file name and location for molecular dynamics output ? regards Paul Buscemi, Ph.D.

3 2