- Chimera-users - RBVI Mailing Lists

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

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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

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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

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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

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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 ================================================= =================================================

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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

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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

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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

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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

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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

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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

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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

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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.

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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]

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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> >> >

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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

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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

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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 > >

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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

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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.

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Distance measurement file
by Marco Sette 08 May '17

08 May '17

Dear all, I have to measure the same interatomic distances in different molecules: it is possible to create a file like distance ... distance ... distance ... and use as input, just to avoid typing the same command many times? Thanks for your help, Marco

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hbonds and distances movie script questions
by mfellner＠msu.edu 05 May '17

05 May '17

Good day I am making a movie by writing a chimera command script and I searched through existing chimera topics but I could not find a solution for these issues: Is there a command to display hbonds, I have made a script now to select residues and find the hbonds, even color + line width them and then I get rid of them later by ~hbonds. What I would prefer is to have them premade (so I dont need to select residues during the movie) but not displayed, later I then displayed and undisplayed them with a scipt command. Also I could not get the lineType command to work inside the hbond script (lineWidth worked fine), I had to use the setattribute command in a second script line, so for a splitsecond I have a different linetype displayed. The second question is about distance labelling. I can set the options in the gui and then distances are displaed by a script with the distance in Angstrom shown. Is there a way to undisplay the distance label later but keep the dashed line, so change the gui option with a script? Also I assume this is not possible, is there a script to change where the label will show up next to the line? I have not looked into displaying and undisplaying 2D labels with scripts, maybe that is a possibility? Lastly which is not that important, is there any way to trim the corners easily? I think I am recording a lot of white space to the left and right throughout the movie, if I resize the window the molecule gets focused, so its no longer exactly where I had it related to the corners and I think I would have to adjust the script. Thank you so much, I hope I made my questions clear, chimera is an awesome program, movie is 21 minutes at the moment. Best wishes Matthias Fellner Michigan State University

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Sub-region selection
by Soumya Govinda Remesh 05 May '17

05 May '17

Hello, I am analyzing some tomography data. I am working with multiple maps - one which defines several cells and another that defines their inner organelles. I want to be able to select and save the map for individual cells and their corresponding map for the organelles. In addition to using the sub-region selection in Volume-viewer is there another way to select the cells? Thanks Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh(a)lbl.gov

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Contact Maps (RRdistance Maps) questions:
by Nicole Persky 03 May '17

03 May '17

Hi All, I've just found the RRdistance Map function on Chimera and would like to compare between structures. I would like to: 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms 3- compare these two contact maps using the colors available for the whole contact map. I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms. Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way. ALSO: Anyone know of a way to map defined attributes onto a contact map? Thanks so much! Sincerely, Nicky

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Working with Electron density map
by MOHD HOMAIDUR RAHMAN 03 May '17

03 May '17

Dear Chimera user's I am trying to super impose molecular dynamics calculated density on cryo EM density and then slice densities to visualize each in different colors. I fitted density successfully now during slicing their X Y Z co-ordinate is not matching. The similar analysis were publish in Marzinek et al., 2016, Structure 24, 1–11 August 2, 2016 http://dx.doi.org/10.1016/j.str.2016.05.014 Please see figure 3 for more details and image attached here. Thank Regards Rahman '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' *M*d* H*omaidur* R**ahman *( Research Scholar ) Lab No. 510, Computational Biophysics Lab. Department of Biotechnology Indian Institute of Technology-Madras Chennai-600 036, India *Mobile No = +91- 7845991785 <078459%2091785>* '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''

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Issue with docking in chimera and autodock vina
by Miss Charles 02 May '17

02 May '17

Dear Chimera Team, I have been trying to dock the small molecules pino-stilbene and trans-stilbene to chainA of the estrogen receptor on chimera using autdick vina. Suddenly, with almost no changes to my protocols I have been getting error message 13 permission of pino-stilbene denied or error message 134 permission of trans-stilbene denied. What am I supposed to do to avoid getting that error message? Thank you so much for your time and your help. Sincerely, Alexis Charles

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assistance
by Arthur Szabo 01 May '17

01 May '17

I asked this question several months ago, but rarely have applied the answer. I have a structure that has a long stretch that is disordered. In the structure it appears as a dashed line. If I highlight this section of the total sequence and then apply a color (red) the whole structure is then colored red. So how can I make the dashes slightly larger, and secondly color that stretch of dashes with a particular color without coloring the rest of the molecule? Thank you Arthur G. Szabo

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Re: [Chimera-users] [chimerax-users] animations
by Elaine Meng 01 May '17

01 May '17

> On Mar 6, 2017, at 6:21 AM, Giorgio Luciano <giorgio.luciano(a)gmail.com> wrote: > > Hello ! In the effort to create a more integrated pipeline with vastly used 3d software (I use mainly C4D and modo) is there a way to export animation from chimera in a format that other software can interpret. To make an example. If I wiggle a molecule in chimera, can I export the animation in a format that does not lot this info ? And eventually are there plan to create this feature in chimeraX ? > Giorgio Hi Giorgio, Chimera supports several export formats, see “File… Export Scene” in the menu or the “export” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> However, these are for individual conformations, not for a whole animation, so you’d have to export at each step. Although ChimeraX is in early development, currently the “save” command formats include STL and X3D. The command “save formats” lists all the formats that can be saved. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> These may be subject to the same limitations mentioned in the Chimera manual links above. 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

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independent rotation of multiple models
by Stefano Luciano Ciurli 01 May '17

01 May '17

Hello, if I have more than one structure in the same session, is there a way to rotate all models together along their respective axes (for example their intrinsic y-axis) without having to do so after selecting each individual model from the model panel? Regards and thanks, Stefano Ciurli

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coloumbic coloring when surface can't be calculated?
by Oliver Clarke 29 Apr '17

29 Apr '17

Hi, I have a structure (well, lots of structures) for which surface calculation fails in Chimera. I can rescue surface calculation using the ‘grid’ option (e.g. surf #0 grid 1), but then I can’t figure out how to apply coulombic coloring to that surface. I could use APBS, but PDB2PQR seems to choke on especially large/complicated structures. Is there any way around this? Would it be possible to export the coloumbic potential as a .dx file and use that for electrostatic surface coloring? Cheers Oli

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Pipes and Planks
by chemocev marker 27 Apr '17

27 Apr '17

Hi Chimera users I am wondering if its possible to assign 2 different color to 2 different helix when use the pipes and planks option in depiction. best Jiri

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file opening problem
by Arthur Szabo 27 Apr '17

27 Apr '17

I had a major problem with my computer - too long a story - Needless to say a computer shop technician had to reinstall my operating system, Windows 7, install Microsoft Office 2016. Of course there were several other programs that had to be reinstalled. So recently I downloaded the latest version of Chimera and have been able to work with PDB files and do all the things that I am used to doing. However, I always save the sessions that I have worked on. They are saved to the desktop C:\users\user\desktop The session files are saved to the desktop. Now comes the problem. When I double click on the file I want [cid:image002.png@01D2A987.C67BFFE0] I get the following message [cid:image001.png@01D2A986.AAC7D360] If I right click on the file then in the menu window click on open with Another window opens with Chimera being the recommended program. Click on OK and the same window as above comes up. This happens even with a .py file that I worked on today. I am puzzled. Ideas will be appreciated. Arthur G. Szabo

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Hey I'm
by Lia Thompson 21 Apr '17

21 Apr '17

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cutting the structure
by Dmitry Semchonok 20 Apr '17

20 Apr '17

Dear colleagues, I did a fit using the predicted models. Now I would like to cut the those parts which don't ft in my EM map. How can I do that? (My EM model has C2 symmetry). Thank you! Sincerely, Dmitry

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[chimerax-users] Chimera bug report submission
by shumaila 19 Apr '17

19 Apr '17

Hi, I want to add oxygen molecule to iron atom in chimera . Kindly help me out how should I add O2 molecule? I tried by Addd bond option but the oxygen molecule is not attached at the desired place. Attached is the protein complex to which I want to attach O2 molecule.Kindly find the attachment. Thank You File attachment: pro time_15000ps.pdb _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

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Re: [Chimera-users] How to install package in chimera python?
by hy liao 19 Apr '17

19 Apr '17

Hi, this was posted here, but where exactly do I invoke the said chimera command? I open chimera with IDLE; a python shell opens with the following Python 2.7.10 (default, May 4 2016, 01:09:35) [GCC 4.6.2] on linux2Type "copyright", "credits" or "license()" for more information.==== No Subprocess ====>>> >>> import chimera>>> I tried what the posting said, but got an error>>> chimera --nogui --script get-pip.pyTraceback (most recent call last): File "<pyshell#3>", line 1, in <module> chimera --nogui --script get-pip.pyNameError: name 'nogui' is not defined Thanks,SL [Chimera-users] How to install package in chimera python? | | | [Chimera-users] How to install package in chimera python? | | |

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SAS exposure question
by Kyle Novakowski 17 Apr '17

17 Apr '17

Hi there, I'm hoping to get some clarification on how to calculate the SAS of a defined set of residues within a molecular structure. I currently have 3 molecular structures in a chimera file and was hoping to compare the SAS of a specific region within 2 mutant proteins relative to that same region of the wildtype protein. Thanks. Kyle -- *Kyle Novakowski, B.Sc.* *Ph.D. Candidate: Medical Science (Infection & Immunity) and Laboratory Manager* *Faculty of Health ScienceDepartment of Pathology and Molecular MedicineMcMaster UniversityE: novakoke(a)mcmaster.ca <novakoke(a)mcmaster.ca>P: 905-525-9140 ext. 21551 <905-525-9140%20ext.%2021551> (work/laboratory)*

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How to show local agreement between cryo-EM map and model
by #AHMED TOFAYEL# 17 Apr '17

17 Apr '17

Dear developers and users, Is it possible to generate/color a cryo-EM map to show local agreement between the map and the model generated using the same map? If I am not wrong, the following figure had accomplished the job but I don't understand how to generate a similar figure for my project: http://d2ni3bh4dzb2ig.cloudfront.net/content/embojnl/28/6/755/DC7/embed/inl… Best regards, Tofayel NTU Singapore

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How DMIN, DMAX, DMEAN is re-calculated if particular portion of MRC is chopped in Chimera
by SALIM SAZZED 13 Apr '17

13 Apr '17

Hello, I am a Ph.D. student of Computer Science department at Old Dominion University, USA. I am using Chimera for my research. Can you please tell me how Chimera calculates *DMIN, DMAX, DMEAN *value of MRC header after chopping a portion of original MRC/MAP*?* My understanding about that- *DMIN: T*he minimum density value of the voxels in the MRC/MAP Cube. *DMAX: T*he maximum density value of the voxels in the MRC/MAP Cube. *DMEAN: *The average density of voxels (add all the voxels density value and divide it by the number of voxels). It will be really helpful if you clarify. Thanks Salim Sazzed

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Gold atoms
by Dominique Matt 13 Apr '17

13 Apr '17

Dear Colleagues, I am an enthusiastic Chimera user. I recently got some structures of gold complexes and noticed that the when using the ball&stick or the sphere representation, gold atoms are too small, while palladium atoms are absolutely OK. What can I do to increase the size of the gold atoms ? Or could you correct this directly in the online program ? I thank you for your help Sincerely, Dominique MATT CNRS Research Director Laboratoire de Chimie Inorganique Moléculaire et Catalyse Institut de Chimie de Strasbourg UMR 7177 CNRS-Université de Strasbourg 4 rue Blaise Pascal, 67070 Strasbourg cedex, France Phone : + 33 3 68 85 17 19 E-mail : dmatt(a)unistra.fr web: http://lcimc.u-strasbg.fr

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saving the session
by Dmitry Semchonok 13 Apr '17

13 Apr '17

Dear colleagues, How to save the session and in the same time all pdb + volume maps in it (all at once)? Thank you Sincerely, Dmitry

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Re: [Chimera-users] Displaying side chains
by Mark J. van Raaij 13 Apr '17

13 Apr '17

As I understand it, Chimera by default displays those side-chains that are near ligands, and assumes that any non-water, non-protein molecule is a ligand. Mark J van RaaijCNB-CSICwwwuser.csic.es/~mjvanraaij -------- Original message --------From: Manish Manish <manishjnu8(a)gmail.com> Date: 13/04/2017 08:55 (GMT+01:00) To: Chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Displaying side chains I have opened PDB ID 1iep using "fetch structure by ID from PDB" through chimera GUI menu. I can see the side chain of few residues such as PHE 317.A and Valine 299.A are automatically displayed. Also by moving the mouse cursor, one can find the distance between different atom types such as between CA and CB. Whereas side chain of many residues such as Lysine 274.A and ASP.276 have not been displayed. My question is how the chimera decides this differential display? Whether chimera directly uses information from PDB files to differentially display the side chains and distance. Or chimera has its own algorithms to decide this. It will be a great help for me if one can point me toward the portions of PDB file or source code from Chimera which does this. I have also attached the image file. Sincerely Manish

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Displaying side chains
by Manish Manish 12 Apr '17

12 Apr '17

I have opened PDB ID 1iep using "fetch structure by ID from PDB" through chimera GUI menu. I can see the side chain of few residues such as PHE 317.A and Valine 299.A are automatically displayed. Also by moving the mouse cursor, one can find the distance between different atom types such as between CA and CB. Whereas side chain of many residues such as Lysine 274.A and ASP.276 have not been displayed. My question is how the chimera decides this differential display? Whether chimera directly uses information from PDB files to differentially display the side chains and distance. Or chimera has its own algorithms to decide this. It will be a great help for me if one can point me toward the portions of PDB file or source code from Chimera which does this. I have also attached the image file. Sincerely Manish

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How to open four volumes simultaneously in Chimera
by Barnali Waugh 12 Apr '17

12 Apr '17

Hi All, I am using Chimera volume viewer to open four volume simultaneously (*.mrc tomogram; 256 256 256 voxel). However, I can open any three volumes at a time. When I try to open the fourth one, it replaces one of the open volumes. I would be thankful for any suggestion. Regards, Barnali.

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given viewing angle
by hy liao 11 Apr '17

11 Apr '17

Hi, How can I specify the elevation and the azimuth angles to view my density map on chimera? In Matplotlib, one can specify the elevation and azimuth, so I was hoping chimera can do something similar that is based on INPUT ANGLES and not having to get involved with tedious transformation matrices and such. Thanks,SL

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Radius of Gyration questions
by George Tzotzos 10 Apr '17

10 Apr '17

Taking a reference PDBID 3n7h, I’ve generated for an MD simulation topology and restart files. I’ve loaded on Chimera 3n7h and then the starting frame of the MD simulation. Used the MatchMaker and found perfect superposition of the protein backbone and two ligands (3n7h is #0 and the ligands #0:129.A and #0.132.B I run the radius of gyration script (see attached). I found that the radii of gyration for the ligands in the two models are completely different. #0 center of mass: 12.6543 10.4356 15.4086, radius of gyration: 21.182 #1 center of mass: 42.7381 42.5171 42.6163, radius of gyration: 37.390 I don’t follow why this is so. Any explanation would be most welcome. A second question regards the units of the radii of gyration. Are they Angstrom or nm? Thank you in advance George

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mysteries
by Arthur Szabo 10 Apr '17

10 Apr '17

After several different occurrences at different times of the same thing I finally decided to ask 1) What happened ?2) How can I reverse it? Now the hard part is to try to described what happened. I was working on a figure - it does not seem to depend on its complexity. I had a figure on the screen, ribbons colored, selected amino acids visualized. I did something with the mouse I believe, though it might have been that my finger touched something on the keypad - what happened was that the majority of the structure disappeared. Parts of it were there. I could rotate it and different parts of the structure would come into view and what had just been visible faded away. It was like on rotation portions of the structure would be moving in the plane of the view, but could move out of that plane I was also able to enlarge whatever portion of the image was on the screen. I know that this is difficult to answer because one really has to see the result of whatever I clicked or something else. It is not just a random event. Thanks for any tips. Arthur G Szabo

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question about Chimera
by Richard Collins 10 Apr '17

10 Apr '17

Hello I would like to highlight certain residues of interest in my molecule, preferably by colorizing them in Chimera. Is there a way to do this? Richard Collins Lab Research Project Coordinator Department of Cell Biology Peter Gilgan Centre for Research and Learning Room 199420, bench HH Hospital for Sick Children 686 Bay St. Toronto, ON CANADA M5G 0A4 T (ext): 416 813-8474 T (int): 308474 E: rcollins(a)sickkids.ca ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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FINDING SALT BRIDGE
by Qistina Hassan 08 Apr '17

08 Apr '17

Hi, 1. How to find salt bridges of 50 selected residues in a protein using Chimera? 2. How to measure distances of one residue to another residues to determine if the residues could form salt bridge or not? Thank you, Qistina

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Non-ASCII error
by ARMIN HODAEI 06 Apr '17

06 Apr '17

Dear Chimera users, My PDBhas some extra HOH water molecules in it. when I delete them manually from the pdb I could not open the PDB with Chimera, it gives the error Non-ASCII file. What can I do to fix it? Or is there any way to delete extra HOH atoms from the PDBfile inside the Chimera software? Cheers, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

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