- Chimera-users - RBVI Mailing Lists

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>*

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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 12 May '17

12 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 11 May '17

11 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# 09 May '17

09 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 30 Apr '17

30 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

3 2

Hey I'm
by Lia Thompson 22 Apr '17

22 Apr '17

1 0

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

2 1

[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

2 1

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? | | |

2 4

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)*

2 1

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

2 1

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

2 2

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

2 1

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

2 1

Displaying side chains
by Manish Manish 13 Apr '17

13 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

1 0

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.

2 1

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

2 1

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

2 2

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.

2 3

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

2 1

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

2 1

building modeller loops refinement
by ARMIN HODAEI 06 Apr '17

06 Apr '17

Dear Chimera Users, I want to use refining loop option to build missing residues for my target protein. First I get the FASTA file structure of protein then I load it into Chimera, after that in the Structure tab I select load structure, then I see the protein. After that Again in the "Structure" tab I select Modeller(loops/refinement). The rest is easy for creating the new structure PDB. But the problem is that I want whole protein to be treated in this refinement, but it only chose one chain, How can I do this for both chains at once? Sincrely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

2 3

(no subject)
by Kavya Shankar 05 Apr '17

05 Apr '17

Hi, I would like to know how the axis of symmetry is calculated in a dimer as in the precise algorithm that is used to do this. Thank you. Regards, Kavya Shankar

2 1

Defining glycosidic bond of nucleotide objects
by Charles-Alexandre Mattelaer 04 Apr '17

04 Apr '17

Dear Chimera-users I'm currently doing modeling on hexitol nucleic acids and using Chimera to visualize the trajectories. Since the atoms in the hexitol-ring are numbered differently than in the standard ribose, Chimera has some difficulties displaying the correct ribbon (backbone) and slab (bases). I've been able to define my own ribbon style using the Ribbon Style Editor and creating a new ribbon style based on the standard 'nuleic acid' trace and replacing the existing backbone atoms with the corresponding atom names for the non-standard hexitol residues. The main problem is setting a slab object to replace the base atoms. The 'nucleotide objects' settings are based on a glycosidic bond on the C1' of ribose. In HNA the glycosidic bonds are found on C2' of hexitol. I believe this is causing the problem. Additionally, I can add that using the 'ladder'-like objects, a gap between the 'steps' and the backbone occurs. (I've tried setting the base as anchor but to no avail.) I was wondering if there would be a way to redefine the anchor atom of the nucleotide objects? (I searched in the manual but haven't found any ways to redefine the anchor itself.) This would greatly improve visibility of larger oligonucleotides and would help me a lot. Kind regards and thank you in advance Charles-Alexandre Mattelaer

3 2

attributes
by John Mercer, Ph.D. 04 Apr '17

04 Apr '17

Hi, If you have a structure file so large that it needs loaded as two separate files, e. g. a ribosome, is it still the case that a designer attribute file for individual subunits across the whole structure would still be handled by the usual single file attribute mechanism or is something else necessary? Does ChimeraX have an attribute mechanism that is the same as Chimera? Best, -John Mercer Duke University

2 2

another question
by Arthur Szabo 04 Apr '17

04 Apr '17

In the menu used to save images there are two boxes, one for the image width and the other for the image height In the part of the menu below I have set the pixel units for the image width to 5000, with the height being automatically set. These are not the default settings. How can I make them the default settings? In the version of Chimera that I recently downloaded the default settings were 1600 and 796, respectively. The default settings of the former chimera download (my computer had been corrupted so downloaded Chimera again). I can't find anywhere in this image saving menu to change the default settings. Thank you Arthur G. Szabo [cid:image001.png@01D2AD56.F614B2B0]

2 1

[summovie]
by Edoardo D'Imprima 04 Apr '17

04 Apr '17

Hi Oli, one quick question: I noticed the interesting question you posted on the Unblur forum regarding the use of summovie. Did actually worked out the “corrected” version by Tim that should allow you to perform dose weighting and saving the aligned movies? Cheers, Edoardo --------------------------------------------------- Edoardo D'Imprima PhD Student Max Planck Institute of Biophysics Structural Biology Department Max-von-Laue Straße 3 60438 Frankfurt am Main Germany Tel: +49 (0) 69 6303 3015

1 0

(no subject)
by Kavya Shankar 03 Apr '17

03 Apr '17

Hi, I learnt that a dimer axis of symmetry is got by using matchmaker and then the rotation is measured from it. I would like to know the algorithm that is used to calculate the axis of symmetry and how exactly it is done if possible. Thank you. Regards, Kavya Shankar

2 2

active questions
by Arthur Szabo 03 Apr '17

03 Apr '17

I am working with a structure that is largely a protein, and there is a short oligonucleotide associated with it. In the tools menu the sequence of the protein is Chain A and the short oligonucleotide is Chain C. I have shown their respective sequences. I also know how to highlight components of each chain etc. However, there is a short dinucleotide with two thymine residues that are also part of the structure. I was able to select these residues and the two thymine residues in the oligonucleotide by using the SELECT menu: residues: dT. So in total four thymine residues are selected and with the ACTIONS menu I can visualize them. Going to Chain C I can hide the two thymine residues on the longer oligo. How can I select the other two thymine residues that make up the short dinucleotide? One of these thymines is covalently bound to a tyrosine residue through a phosphodiester bond. I can visualize the tyrosine monophosphate through Chain A, and one can see it connected to the relevant thymine residue. But I would like to color the two thymine residues. But I cannot select them or at least I do not know how to select them. I am not an expert at using the command line. Likely there is something there. Again your assistance is sincerely appreciated. Arthur G. Szabo

2 2

Stereo
by Arthur Szabo 03 Apr '17

03 Apr '17

Is it possible to create a stereo view image from a single pdf image. I have colored different segments of the original pdf image. Thanks A G Szabo agszabo(a)outlook.com<mailto:agszabo@outlook.com>

2 3

Residue information failed
by Kunrong Mei 03 Apr '17

03 Apr '17

Hi all, I have met a problem as I used the mouse pointer to show the residue information. Normally, Chimera automatically displays the residue information (residue name, model ID, chain ID, and residue number...) by default when the mouse pointer is placed at a special position. This is ultra helpful when analyzing structures. My problem is that, after I registered to Chimera today, this function lost and it doesn't show the residue information any more. Has anyone met this kind of problem before? Or does anyone know how to fix it? Thanks, Kunrong

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Re: [Chimera-users] Chimera comparing homodimer with flipped homodimer
by Elaine Meng 03 Apr '17

03 Apr '17

Hi Kavya, The “mm” command used to align the structures and “measure rotation” used to report the resulting rotation are fully described in the documentation, see <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> Regards, Elaine > On Apr 3, 2017, at 8:15 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > Hi Elaine, > > I want to know exactly how the axis of symmetry has been calculated for the dimer. What coordinates are used to perform the alignment of the chains? This will really help me out with my research. > > Thank you. > > Regards, > Kavya Shankar > > On Thu, Mar 30, 2017 at 11:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Kavya, > I didn’t have a good example handy yesterday, but here is a more specific example, in commands: > > open 5hvp > open 5hvp > mm #0:.a:.b #1:.b:.a pair ss > show :241.b > measure rotation #0 #1 > > This opens PDB 5HVP twice, matches it to itself except pairing A in one with B in the other and vice versa, shows only residue 241 in chain B so that you can see pairing is A-B, and measures axis of rotation between the two copies of 5HVP. The measurement is also reported in the Reply Log (open from Favorites menu): > > Position of 5hvp (#1) relative to 5hvp (#0) coordinates: > Matrix rotation and translation > -0.32555997 0.82635225 -0.45951350 0.78339640 > 0.82635225 0.01248149 -0.56301524 15.06413576 > -0.45951350 -0.56301524 -0.68692152 28.23994571 > Axis 0.58070648 0.71150597 -0.39565040 > Axis point -5.75571422 -0.00000000 18.30836454 > Rotation angle (degrees) 180.00000000 > Shift along axis 0.00000000 > > I also attach an image below. > 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 > > <flip-axis.png> > >> On Mar 29, 2017, at 10:10 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Kavya, >> I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.” >> Elaine >> >>> On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>> >>> Hi, >>> >>> To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. >>> >>> Thank you. >>> >>> Regards, >>> Kavya Shankar >>> >>> On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>>> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>>> >>>> Hi, >>>> Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. >>>> Thank you. >>>> Regards, >>>> Kavya Shankar >>> >>> Hi Kavya, >>> Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> >>> >>> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> >>> >>> 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 >>> >>> P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues >>> >>> >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> > >

1 0

I figured it out
by Arthur Szabo 03 Apr '17

03 Apr '17

Thanks A G Szabo

1 0

question
by Arthur Szabo 03 Apr '17

03 Apr '17

Previously I had stumbled on how to change the shading on ribbon structures. The default has shading, but with the default setting the colors of the ribbons are shaded and this shading changes when one rotates the structure. Kindly remind me how I can alter the shading of the ribbons. Presumably the settings are through the Tools section. Thank you Arthur G. Szabo

1 0

UCSF Chimera installation - library ubuntu 16.04
by Vasileios Kargas 02 Apr '17

02 Apr '17

Dear Chimera developer, I am trying to install UCSF-Chimera and I have an issue with the libXext.so.6 library I 've installed the library package that contains this and I can locate it at: /usr/lib/x86_64-linux-gnu However I get this error: vk335@hunter:~$ ./chimera-1.11.2-linux.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/vk335' inflating: chimera_install_L6RcLz/installer inflating: chimera_install_L6RcLz/chimera.bin Enter install location: ~/UCSF-Chimera-1.11.2 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /home/vk335/UCSF-Chimera-1.11.2' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu and icon? yes Traceback (most recent call last): File "/home/vk335/UCSF-Chimera-1.11.2/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/vk335/UCSF-Chimera-1.11.2/share/chimeraInit.py", line 603, in init import chimera File "/home/vk335/UCSF-Chimera-1.11.2/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: libXext.so.6: wrong ELF class: ELFCLASS64 ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_L6RcLz' Installation is done; press return. If I install it in the default Chimera directory without desktop icon it proceeds to the installation but I can not run chimera - taking the same error: ImportError: libXext.so.6: cannot open shared object file: No such file or directory Any suggestions how to solve it? Should this be linked to somewhere else in order the Chimera to find it? Thank you very much in advance. Best regards, Vas

2 1

Residue information failed
by Kunrong Mei 31 Mar '17

31 Mar '17

Hi all, I have met a problem as I used the mouse pointer to show the residue information. Normally, Chimera automatically displays the residue information (residue name, model ID, chain ID, and residue number...) by default when the mouse pointer is placed at a special position. This is ultra helpful when analyzing structures. My problem is that, after I registered to Chimera today, this function lost and it doesn't show the residue information any more. Has anyone met this kind of problem before? Or does anyone know how to fix it? Thanks, Kunrong

1 0

Add secondary structure or symbols to headers of multalign viewer (sequence）
by 陈柳青 31 Mar '17

31 Mar '17

Dear all ! Is it possible to add secondary structure or symbols to multalign viewer headers? I know can use "alignment header definition files" do this , but i don't know how to make the definition files, anyone can give me these files or tell me how to do it? thanks! Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

2 1

Re: [Chimera-users] Chimera comparing homodimer with flipped homodimer
by Elaine Meng 31 Mar '17

31 Mar '17

Hi Kavya, Your “mm” command matched A to A and B to B, so there was no rotation between the two copies. It was hard to see if you entered exactly the same “mm” command as in my example (needs to be exactly the same, with colon : dot . and no extra spaces), but it you did, maybe you are using an old version of Chimera that interpreted the command differently. I only started Chimera and entered those 5 exact commands to get the result I showed. Tested in Chimera version 1.11.2 and recent 1.12 daily build. Elaine > On Mar 31, 2017, at 6:55 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > I have attached the screenshots. I have opened the same pdb file. > > Thank you. > > Regards, > Kavya Shankar > > On Fri, Mar 31, 2017 at 9:37 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > Thank you so much. When I do this I get a rotation angle of 0 degrees. Am I doing something wrong? > > Thank you. > > Regards, > Kavya Shankar > > On Thu, Mar 30, 2017 at 11:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Kavya, > I didn’t have a good example handy yesterday, but here is a more specific example, in commands: > > open 5hvp > open 5hvp > mm #0:.a:.b #1:.b:.a pair ss > show :241.b > measure rotation #0 #1 > > This opens PDB 5HVP twice, matches it to itself except pairing A in one with B in the other and vice versa, shows only residue 241 in chain B so that you can see pairing is A-B, and measures axis of rotation between the two copies of 5HVP. The measurement is also reported in the Reply Log (open from Favorites menu): > > Position of 5hvp (#1) relative to 5hvp (#0) coordinates: > Matrix rotation and translation > -0.32555997 0.82635225 -0.45951350 0.78339640 > 0.82635225 0.01248149 -0.56301524 15.06413576 > -0.45951350 -0.56301524 -0.68692152 28.23994571 > Axis 0.58070648 0.71150597 -0.39565040 > Axis point -5.75571422 -0.00000000 18.30836454 > Rotation angle (degrees) 180.00000000 > Shift along axis 0.00000000 > > I also attach an image below. > 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 > > <flip-axis.png> > >> On Mar 29, 2017, at 10:10 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Kavya, >> I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.” >> Elaine >> >>> On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>> >>> Hi, >>> >>> To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. >>> >>> Thank you. >>> >>> Regards, >>> Kavya Shankar >>> >>> On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>>> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>>> >>>> Hi, >>>> Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. >>>> Thank you. >>>> Regards, >>>> Kavya Shankar >>> >>> Hi Kavya, >>> Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> >>> >>> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> >>> >>> 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 >>> >>> P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues >>> >>> >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> > > > > <step1.png><step3.png><step4.png><Step2.png>

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Get side-view model? Or, height of clipping planes?
by Abba E Leffler 31 Mar '17

31 Mar '17

Dear All: I'm making a figure showing a ligand bound deeply in a cryptic pocket of a protein. To show it best, I've oriented the complex so that I am looking down directly on to it. Then, I adjust the hither and yon clipping planes to bracket the ligand so you get a cross-section through the protein containing the ligand and binding site. Is there a way to get the heights of the clipping planes, and then draw planes representing them? Better yet, can the image in the side view planning somehow be saved to high resolution with the yellow clipping planes indicated, but perhaps without the red field of view lines? Basically, for the figure I need some way of showing the viewer where the clipping planes are on the protein. This is critical because viewers need to know in a broad sense where the ligand is located. Thank you for your help

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Collaboratory
by Theodor Emil Gescher 30 Mar '17

30 Mar '17

Dear Chimeramasters and mistresses, I'm having some serious difficulty starting a collaboratory session in UCSF Chimera on Mac. I have tried both an outdated version (build 40427) and the latest (build 41367). I can't find any mention within the program of collaboratory, and because of the Mac OS I don't think it's possible to start a hub from outside Chimera. Is there an additional extension that needs to be downloaded and installed seperately? Yours studiously, Theo

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Re: [Chimera-users] [chimera-dev] (no subject)
by Elaine Meng 30 Mar '17

30 Mar '17

Hi Kavya, I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.” Elaine > On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > Hi, > > To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. > > Thank you. > > Regards, > Kavya Shankar > > On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > > > Hi, > > Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. > > Thank you. > > Regards, > > Kavya Shankar > > Hi Kavya, > Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> > > After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> > > 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 > > P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Scripting commands for existing morph
by Cristina Paulino 29 Mar '17

29 Mar '17

Dear all, I would like to create a movie from an existing morph between two pdb coordinates. I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. Can anyone help me out? I couldn't find any good description for this. Many thanks in advance Cristina

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Re: [Chimera-users] [chimera-dev] (no subject)
by Elaine Meng 29 Mar '17

29 Mar '17

> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > Hi, > Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. > Thank you. > Regards, > Kavya Shankar Hi Kavya, Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> 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 P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues

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ChimeraX Alpha release
by Eric Pettersen 28 Mar '17

28 Mar '17

Hi all, We have released an alpha version of ChimeraX. While it still lacks many features, it has enough useful new and fun features that you might want to take it out for a spin even if it doesn’t prove ready to be your day-to-day workhorse yet. Hope you like it! Home page: http://www.cgl.ucsf.edu/chimerax/ <http://www.cgl.ucsf.edu/chimerax/> Download page: http://www.cgl.ucsf.edu/chimerax/download.html <http://www.cgl.ucsf.edu/chimerax/download.html> —Eric Eric Pettersen UCSF Computer Graphics Lab

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来自"高振飞" <16110440015@fudan.edu.cn>的邮件
by 高振飞 28 Mar '17

28 Mar '17

Dear professor: I'm a student from Fudan University, I want use the software -- chimera. But I can't download it, can you send it to me by using E-mail? thank you very much. with my best regards yours sincerely Zhenfei Gao -- Zhenfei Gao(高振飞) Department of Macromolecular Science Fudan University 310 Yuejin Hall 220 Handan Rd. Shanghai, China 200433 M: +86-18516637266 QQ: 7693692

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Create an entire virus from Octant
by Li, Zongli 28 Mar '17

28 Mar '17

Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli

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MD analysis outputting to file
by Neha Gandhi 23 Mar '17

23 Mar '17

Dear Chimera support, I want to calculate the centroid of the sugar ring and the distance from the centroid to another atom of amino-acid. I know this can be done using the Structure analysis tools in Chimera. I want to use distance command in the MD ensemble analysis and output it to the analysis to the text file. How can I write output per frame to a text file in Chimera? Your insight is appreciated. -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate

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Ensemble models
by Mohamed Noor 20 Mar '17

20 Mar '17

Hello. I have an ensemble of models from phenix.ensemble_refinement. I notice that Chimera automatically loads the models and displays only a subset of atoms as "atoms/bonds". Can I save this as a preset while changing other settings manually so that I can go back to the automatic preset if I make a mistake somewhere? Secondly, is it possible for Chimera to calculate rmsf of each residue and output the values to a CSV file? I would like to replot them in Excel. Thanks. Mohamed

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Looking at docked data with the receptor shows as surface
by Jonathan Y Wang 20 Mar '17

20 Mar '17

To whom it may concern, Hi! I recently docked a ligand onto a receptor using the AutodockVina tool and when I opened the data the ligand seemed to be placed in the middle of the trimer. I showed the receptor as surface and it seems as if the ligand is too big to fit inside any of the holes surrounding the trimer, but somehow it has placed itself inside. I additionally opened it using PyMol to double check the file, but it also seems too small to fit inside any of the holes. My inquiry is this: Does AutodockVina take into account surface projections when performing docking? Thank you so much for your time, Jonathan Wang

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Getting names of selected atoms and renaming
by Vladyslav Dziuba 18 Mar '17

18 Mar '17

Dear Sir or Madam, I have some difficulties with using ORCA and UCSF Chimera together. Let me describe my problem first. I need to freeze some atoms (actually, a lot of atoms) in my calculations (geometry optimization), e.g. make their coordinates constant. To do that I need to specify numbers of atoms from xyz file, which is obtained from pdb-file. The problem is that for every atom in pdb-file OpenBabel generates a new number (for example H27 may become 100th atom in xyz file), so that specifying atoms that must be frozen becomes much more complicated. Given that, I'd like to ask to help me find answer on some questions: 1. How can I rename atoms? It would greatly help me identificate atoms that must be frozen. Can I rename only all selected atoms? 2.Can I modify names of selected atoms? 3. How can I get list of numbers of selected atoms? For instance I've chosen some aminoacids residues and I want to get names or numbers of all atoms chosen. Because if I one wants to get a list of atoms in xyz file, he needs names or numbers of atoms in pdb file, but the last ones are disordered. Manual atom picking and comparison in pdb- and xyz-files is very time-consuming. UCSF Chimera is a truly powerful program so I believe there must exist an elegant solution to my problem. Hope to receive a letter from you soon. Thanks in advance! Best regards, Vladislav Dziuba

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Re: [Chimera-users] Smoothing and binning volume data
by Tom Goddard 16 Mar '17

16 Mar '17

Set "step 1” above the histogram in the Volume Viewer window to display the full resolution of the data. If step is 2 that means only every other density map grid point is shown along each axis. The step gets set automatically to values greater than 1 when the map is large to avoid slowing down the graphics (rotating, zooming…). The initial step it chooses is controlled by the volume viewer menu Features / Data Display Options… , “Adjust step to show at most [N] Mvoxels”. Tom > On Mar 16, 2017, at 11:41 AM, Andrea Fera <andrea.fera(a)gmail.com> wrote: > > Hi Tom! > > Tank you for your information. > Let me try to explain better what I asked. > > What I seem to have revised is that the virtual sections of my maps have a much higher resolution than the rendered images by Chimera. > This should be because, evidently, I didn't understand yet how to control the default smoothing and/or binning in the volume viewer, of which I used until now the default value. > Can you tell me how to do, or what to vary? > > Thank you for the tip about using two colors in the rendering. Going to try immediately. > Thanks, > Andrea > > > > > > > > > > -- > Andrea Fera, PhD – [Senior Research Scientist] > Advanced Molecular Imaging ; DUNS 824-XXX-XXX > Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health > Email: andrea.fera(a)gmail.com <mailto:andrea.fera@gmail.com> > > > On 16 March 2017 at 14:28, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Not sure what you are asking. You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool. > > To color “solid” style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors. > > Tom > > >> On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote: >> >> Dear Tom, >> >> How are you? >> I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering. >> >> Could you please send me some information on where I could look for this information? >> >> Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above) a certain threshold value? >> >> I hope that I am not asking anything too strange. >> Especially the first thing would help me greatly. >> >> Thank you, >> Andrea >> >> -- >> Andrea Fera, PhD – [Senior Research Scientist] >> Advanced Molecular Imaging ; DUNS 824-XXX-XXX >> Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health

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Smoothing and binning volume data
by Tom Goddard 16 Mar '17

16 Mar '17

Not sure what you are asking. You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool. To color “solid” style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors. Tom > On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote: > > Dear Tom, > > How are you? > I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering. > > Could you please send me some information on where I could look for this information? > > Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above) a certain threshold value? > > I hope that I am not asking anything too strange. > Especially the first thing would help me greatly. > > Thank you, > Andrea > > -- > Andrea Fera, PhD – [Senior Research Scientist] > Advanced Molecular Imaging ; DUNS 824-XXX-XXX > Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health >

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VPAT (Voluntary Product Accessibility Template)
by Ashdale, Martin 16 Mar '17

16 Mar '17

Good Morning, I am looking into using your product with my AP Biology classes and I need to get approval to download your software. The IT Department would like the VPAT (Voluntary Product Accessibility Template) so that I can submit it for approval. If you have it available could you please send it to me. I appreciate your time and look forward to teaching with your product. Thanks, Martin Ashdale Biology Teacher Harford Technical High School 200 Thomas Run Road Bel Air, MD 21015 (410) 638-3804

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Selecting certain atoms with exception
by Kelvin Lau 14 Mar '17

14 Mar '17

Dear Chimera users, I'm trying to do the following: -select all the atoms of a single residue (trp) -except for one (residue number 285) I am not sure how to use a negation command to leave out only 285. Any ideas? Cheers Kelvin -- Kelvin Lau Structural Plant Biology Laboratory Department of Botany and Plant Biology Science III University of Geneva 30 Quai E. Ansermet 1211 Geneva Switzerland Email: kelvin.lau(a)unige.ch Phone: +41 22 379 3026

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possible Chimera bug - saving bonds in MOL2 format
by Marek Maly 14 Mar '17

14 Mar '17

Hello, it seems that Chimera (1.11.2) has problem to save some bonds in MOL2 format. If you open attached file "source.mol2" , Chimera reads/show perfectly all the bonds including those where is "Ru" atom present, but when you save it in MOL2 format in Chimera (see attached file "Chimera_MOL2.mol2"), then all the "Ru-x" bonds are omitted and naturally if you open this "Chimera MOL2" file in Chimera no "Ru-x" bonds are shown. Interestingly, if the original MOL2 file "source.mol2" is opened in Chimera and then saved in PDB format ("Chimera_PDB.pdb"), all bonds are written and so if this PDB file is opened in Chimera all bonds are visualized. Would be nice if the perfect bond preservation which works in MOL2->PDB case worked also in MOL2->MOL2 case. Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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chimera 1.11.2 interlaced stereo
by Jean-Marie WURTZ 13 Mar '17

13 Mar '17

Hi, I am a long time user of chimera and had never such a problem. I would like to use the interlaced stereo with a zalman monitor but I get the following error : Unable to turn on stereo viewing (Unable to find hardware stereo support (couldn't choose pixel format Couldn't configure togl widget)). I must say that VMD stereo is working. But I understood also that both programs work differently with regard to steero. My configuration: Dell M4500 precision Windows 10 Quadro FX 1800M driver 342.01 What can I do to get it working? Thanks for your help. Best regards -- Jean-Marie Wurtz Professeur de Bioinformatique Tél : +33 (0)3 69 48 51 04 Fax : +33 (0)3 88 65 32 76 jm.wurtz(a)unistra.fr<mailto:jm.wurtz@unistra.fr> wurtz(a)igbmc.fr<mailto:wurtz@igbmc.fr> IGBMC-CEBGS Département de Biologie et de Génomique Structurales Equipe de Biologie Structurales de Cibles Epigénétiques Parc d'Innovation, 1 rue Laurent Fries BP 10142 F - 67404 ILLKIRCH CEDEX http://archive.igbmc.fr/recherche/Prog_ISB/Eq_JCava/index.html [UniversitÃ© de Strasbourg]<http://www.unistra.fr>

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Re: [Chimera-users] [chimerax-users] animations
by Elaine Meng 12 Mar '17

12 Mar '17

Hi Giorgio, You would still have to use the “export” command that exports one file at a time, but it can be run at every frame by combining it with the “perframe” command. For example, in Chimera the following (should be all one line even though the Mail app may break it up): perframe "export ~/temp/$1.x3d" zero 2; play wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 50; wait 50; ~perframe …where ~/temp is a directory that already exists, will make files 01.x3d …. 50.x3d in that directory. In ChimeraX, there is a “perframe” command and “save” to export X3D, but no “play wiggle” command. <http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> 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 > On Mar 9, 2017, at 11:44 AM, Giorgio Luciano <giorgio.luciano(a)gmail.com> wrote: > > Thanks for the info and sorry for my late reply. I generally export using x3d what I was thinking about is, how can someone export the single model for an animation ? As an example if I make wiggle a molecule play (wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 200 ) may I export in batch the molecules for the single frame ? > Any help will be greatly appreciated :) >

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Re: [Chimera-users] question on MAV
by Elaine Meng 10 Mar '17

10 Mar '17

> On Mar 10, 2017, at 12:59 AM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > I would appreciate it if you could let me know how to make specific residues bold in MAV. Not all of them but only specific residues. > Thank you so much for your help. > Jackie Vitali Hi Jackie, Sorry, MAV (Multalign Viewer) does not have the option to use different fonts for different residues… as you probably saw, the Preferences… Appearance options only change the font of all the residues. To highlight specific residues in MAV, you could draw a box around them to make a region, and then using the Region Browser, change region background color and/or outline color, <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> ...or you could create a custom header to put a symbol above the column. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> 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

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replay morph created with vop morph?
by Oliver Clarke 10 Mar '17

10 Mar '17

Hi all, Is there any way to replay a morph created using vop morph? Or to change the representation of the map prior to playing? I have a sequential morph of multiple different conformations (which I can’t make with the morph map GUI tool), but I would like to change the display of the map before creating a movie (which vop morph does not seem to allow). Example command: vop morph #1,2,3,4,5 interpolateColors false constantVolume true Cheers Oli

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Can you delete a residue attribute?
by Mungo Carstairs (Staff) 08 Mar '17

08 Mar '17

Hi, I would like to be able to set and remove residue attributes (using Chimera commands over the REST service). Setting is fine, but removing seems to be limited to changing the value to either an empty string or None. https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html Is there any way to actually remove attributes after they have been set on residues? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

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running DockPrep and Vina from python
by Lee A.G. 06 Mar '17

06 Mar '17

Hello I have been trying to run DockPrep and Vina from a python script to generate a pdbqt file to be used in subsequent Vina docking studies (with a config file). What I have at present is the following (I have edited DockPrep\_init_.py to make nogui=True ; the receptor has been loaded as model #0, and the ligand as model #1) from DockPrep import prep model=Midas.open('4iaq.pdb') prep(model) modelname='4iaq.mol2' from WriteMol2 import writeMol2 writeMol2(model, modelname) #VinaRun OutFileName='C:/Autodock/5HT/4iaq/Test2/4iaq' rc("vina docking receptor #0 ligand #1 output " + OutFileName + " prep true wait true") The generated 4iaq.receptor.pdb file contains the protein as modified by DockPrep, without the charges etc, and with the original PDB residue numbering. The 4iaq.receptor.pdbqt file contains the unmodified protein with charges etc, and with the original PDB residue numbering. The 4iaq.mol2 file contains the modified protein, with charges etc, but with residue numbering modified to start at 1. What I hoped to produce was a 4iaq.receptor.pdbqt file containing the modified protein with charges etc, and with the original PDB residue numbering, and this is just about the only thing I don't have. Any help would be very gratefully received. Anthony

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Re: [Chimera-users] Moving icosahedron to model
by Tom Goddard 03 Mar '17

03 Mar '17

Hi David, I could not tell from the image if the surface was from a PDB or a density map. If it is from a PDB then the coordinate system is based on the crystal packing. That means the origin could be anywhere and the rotation can be arbitrary. So then getting an icosahedron outline aligned can be a real pain, although sometimes the crystal packing has a virus centered at 0,0,0 and a standard orientation like 2-fold symmetry axes along x,y,z (e.g. 2bbv). In the hard cases there are various tricks. For instance use the shape command to center the icosahedron on the atomic model (e.g. "shape icos radius 200 center #0 mesh true div 1") Tom > On Mar 3, 2017, at 11:12 AM, David Bhella wrote: > > Hi Tom > I think Kok Lian's structure is a surface from a PDB file created using multiscale models. I feel the origin and symmetry should be available from the PDB file in some way, but I too have struggled with getting icosahedral structures from PDB into a sensible orientation. > > Sent from my iPhone > >> On 3 Mar 2017, at 18:38, Tom Goddard wrote: >> >> Is your virus surface from a density map? If so it probably has the origin set in such a way that the center of the virus is not 0,0,0 while the center of your icosahedron outline is 0,0,0. To remedy that you would change the origin of the map in Volume Viewer, menu Features / Coordinates set origin index to for example 128 if the map size is 256 grid points. That is likely to put the map origin at the center of the virus particle. >> >> Tom >> >>> On Mar 3, 2017, at 1:18 AM, KL Ho wrote: >>> >>> Dear All, >>> I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. >>> >>> Best wishes, >>> KokLian >>> <image1.png>_______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Moving icosahedron to model
by KL Ho 03 Mar '17

03 Mar '17

Dear All, I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. Best wishes, KokLian

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move icosahedron surface to a model
by Ho Kok Lian 03 Mar '17

03 Mar '17

Hi All, I am a beginner of chimera. Sorry for the simple question. May I know how to move the icosahedron surface (see attached figure) to the model according to its symmetry? Many thanks. Kok-Lian

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Segmentation fault when issuing chimera command
by Hui Shi 01 Mar '17

01 Mar '17

Hi there, Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here. I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed. But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version. I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work. Any suggestions on how to deal with problem? Thanks a lot in advance! Hui

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Re: [Chimera-users] Error opening larger proteins
by Eric Pettersen 01 Mar '17

01 Mar '17

Hi Catherine, It turns out that the singular value decomposition function that Chimera uses to get the eigenvectors and eigenvalues for the plane computation uses a lot of memory if you use a large number of atoms to define the plane (or axis for that matter). There is a non-default setting for that svd function that I just discovered that uses much less memory and seems to produce identical results, so I have switched Chimera to using that setting. The switched version will be available as the next daily build. Look for daily builds dated March 1 or newer. Also, you may be able to get your current version to work if you simply use less atoms to compute the plane. The selection you were using — “sel :.A,.B,.C,.D” — will not only select all the protein but also all the waters, ligands, and ions. Perhaps just “sel protein” would be more appropriate (depending on what you want the plane for) and might work in your current build. —Eric Eric Pettersen UCSF Computer Graphics Lab > On Mar 1, 2017, at 9:09 AM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > Hello, > > When I try to open large protein in Chimera, and try to define plane for the protein, It is throwing me an error saying "Memory Error". Can you please help me with this error? > > Note: Attached a snapshot of the error. > > Thanks, > Catherine > <Screenshot.png>

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MMTK/Chimera interface error
by ADIL AHIRI 27 Feb '17

27 Feb '17

hi everyone, I work on the modeling of the effect of phosphorylation on segment peptide. I had a problem when i use this interface MMTK/Chimera interface because when i use a doubly phosphorylated peptide i have this message: KeyError: 'No parameters for bond Atom 0.ARG_12__0_0_1_286__B.peptide.C (atom type C) - Atom 0.TPO_13__0_0_1_287__B.N (atom type n)' You will find attached a sample problem source file. Is there anyone who can help me solve this problem please. Codially

2 1

coloring a surface based on proximity to a point
by Hamish Todd 27 Feb '17

27 Feb '17

Hey everyone. So I have a coloration for a set of surfaces that is very close to what I want. I want to make a change to it though: I want parts of the surfaces close to certain points to change their color. And I want the rest of the surface to be unchanged from the current coloring. Is this possible? Would be much obliged if any advice could be offered! Hamish Todd -- @hamish_todd

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starting pre-existing morph
by Elena Zehr 27 Feb '17

27 Feb '17

Hi, I have a chimera session with a morph between two structures. I wish to start playing the morph from the command line. What would be the argument for this? Many thanks, Elena

2 1

FW: Commercial Chimera
by Williams, Joanne 27 Feb '17

27 Feb '17

On 2/26/17, 10:29 PM, "Agnieszka Dobinska" <adobinska(a)okinawa-pt.com> wrote: >Dear Sir/Ma'am, > >I have a questions regarding commercial use of Chimera. > >Provided that we are commercial users of Chimera (subject to commercial >agreement), and we are creating files using Chimera, does our customers >need to >have the commercial Chimera to browse the files we have sent them, or >they can >use the free one. > >Best regards, >Agnieszka Dobinska > >~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~ >Agnieszka Dobinska >Sales & Marketing Manager >Okinawa Protein Tomography Ltd. >1919-1 Tancha, Onna Village, Kunigami, >Okinawa Prefecture 904-0411 Japan >Tel. +81-98-982-3359 　FAX +81-98-982-3361 >Skype: okpt.sales >http://www.okinawa-pt.com >~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~ > > >

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models disappear after using "split"
by Leschziner, Andres 24 Feb '17

24 Feb '17

Hi, I used “split” to break a model into its 19 component chains. The chains appear in the Model Panel and are marked as “Shown" but are gone from the display. Everything else I have in the session works normally but nothing I have tried so far makes the split models show up. Any help solving this would be much appreciated! -Andres ______________________________________ Andres Leschziner Professor Department of Cellular and Molecular Medicine and Section of Molecular Biology, Division of Biological Sciences University of California, San Diego Leichtag 483 9500 Gilman Dr. La Jolla, CA 92093-0694 aleschziner(a)ucsd.edu<mailto:aleschziner@ucsd.edu> 858-246-1252 ______________________________________

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density maps
by Antonio Coluccia 24 Feb '17

24 Feb '17

Dear all I have computed a molecular dynamic and i would like to have the density maps for some molecules of the system. I tried with isopropanol molecules and I obtain the map for each atom type: H; C3; O3, CH and another called density map_iso.mcr My concerns are about the last one map. What does it mean? Is it the map for the whole molecules, while the other maps are for each atom type? Is it possible to analyse the maps contemporary thus I am able to visualize just three per time? Any help will be really appreciated. Antonio Antonio Coluccia Ph.D. Department of Chemistry and Drugs Technology Rome 00185 Piazzale Aldo Moro 5 antonio.coluccia(a)uniroma1.it

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Two questions about a model
by Steven D. Aird 23 Feb '17

23 Feb '17

Dear Elaine, I have a couple of questions about the attached model set. These are catalytic residues and residues forming the hydrophobic channel in four phospholipases. The first question almost seems silly. I decided to experiment with the label command and labeled one residue in the lower right enzyme of the figure. I didn’t like the position or form of the label. I couldn’t get rid of the “.A” on the label and when I tried to delete the entire label, I couldn’t. Selecting the residue and then selecting LABEL>Off, doesn’t work. In all four plots there are fine lines that resemble the earlier ribspline problem, but they are not resolved by "ribspline cardinal.” Any idea as to what these are? As always, thank you for your tutelage. I am making steady progress. Sincerely yours, Steve Steven D. Aird Technical Editor Faculty Affairs Division Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp

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Windows & dialogues outside the screen
by Hernando J Sosa 22 Feb '17

22 Feb '17

Dear UCSF-Chimera, I have noticed (perhaps since I upgraded, currently running v1.11.2) that when opening new windows/dialogues many times they pop-up outside the screen. This seems to happen more often when many windows are opened simultaneously. It is more of a nuisance than a real problem but it can get annoying having to continuously search for those elusive windows. So I wonder if there is a way to fix this behavior (e.g. to force newly opened windows to always appear on top and within the screen boundaries) . I am running Windows 64 UCSF-Chimera version 1.11.2 on a Windows 7 and Windows 10 machine (problem occurs in both computers) Thanks Hernando

2 1

Converting a part of a molecule in pdb to xyz format
by Vladyslav Dziuba 22 Feb '17

22 Feb '17

2 1

Re: [Chimera-users] MatchMaker working beautifully, and Transform Coordinates definitely does move things....
by Elaine Meng 17 Feb '17

17 Feb '17

> On Feb 17, 2017, at 3:47 AM, Steven D. Aird <steven.d.aird(a)gmail.com> wrote: > > Dear Elaine, > I apologize for the deluge of Email, but within minutes of writing you, I figured out how to use MatchMaker to align two ribbon models of interest. Again, it’s simple and elegant. > > I also found the transform coordinates command, which I had missed earlier. That enables me to move one of the models relative to the other. But moving a model is tricky because it seems impossible to know what relationship the two models have with a Cartesian coordinate system. I had assumed that x, y, and z would be relative to the monitor surface, but that is not the case. > > Is there a more intuitive way to move molecules while maintaining the same relative orientation? > Thanks very much for your help. > Sincerely yours, > Steve Hi Steve, Thanks for the kind words! After you use Matchmaker (or matrixcopy or the mouse or some other method) to position structures relative to one another, you shouldn’t have to do anything special… now when you move “everything” they will still retain their relationships. I.e. you can rotate and translate everything with the mouse and structures will still be superimposed, docked, etc. as they were after you moved them separately. Personally I never use the Transform Coordinates tool and I don’t understand why you wanted to use it. You can translate and rotate relative to screen coordinates (X horizontal Y vertical Z normal to screen) using commands “move” and “turn” and these can apply to everything or only certain models (they have a “models” keyword option). You can also move only certain models with the mouse by activating/deactivating (freezing) them with the “A” checkboxes in the Model Panel, which can be opened from the Favorites menu. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> Also, for future reference, we really prefer questions to be sent to chimera-users (CC’d here) so that other people can benefit from the answers, and also give you better support if I don’t know the answer or am away. 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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Chimera refuses to attach short peptide to protein C-terminus
by Steven Douglas Aird 16 Feb '17

16 Feb '17

Dear Sirs: I am modeling novel proteins on homologous structures from other organisms using SWISS-MODEL. After the model is completed I import the PDB file into Chimera to form disulfides and to produce publication quality graphics. I thought all was going well until I discovered that SWISS-MODEL was actually truncating one or both termini of my target sequences by 1-5 residues. In one case, I created the missing C-terminal tripeptide using MacPyMol, but MacPyMol will not not add the tripeptide to the C-terminus, because it is designed only to create intramolecular bonds. So I imported the protein and the tripeptide into Chimera. I selected the C-terminal oxygen of the protein and the N-terminal nitrogen of the tripeptide and tried to create a peptide bond using Build Structure>Adjust Bonds>Add Bond. Chimera claims that only one atom is selected, but in fact, both are selected. I do not want to try to build a tripeptide one atom at a time. Is there any way to do ligate the tripeptide? Thanks very much! Steve Aird Steven D. Aird Technical Editor Faculty Affairs Division Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp<mailto:steven.aird@oist.jp>

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Visualisation of membrane proteins
by James Starlight 15 Feb '17

15 Feb '17

Dear Chimera users! I am on the preparation of interactive molecular visualisation, focusing on ligand-binding representation in GPCRs system. Working with the X-ray structures of the receptor bound with the ligand, I wonder to ask some suggestions: 1 - I need to move ligand from ligand binding pocket burried within receptor (as on default in the X-ray structure) towards the selected position outside of it - e.g in case where I would like to depict "vestibule" for the ligand enterance. As I understood for the realisation I should to select ligand within the current model and than to copy it to new model (layer) which then should be moved against the structure, shouldn't it? 2- Is it possible using some Chimera tool to indicate "approximate" membrane plane assuming that GPCRs structure is shown in latteral perspective? Thanks so much for the help! James

2 3

electrostatic surface
by chemocev marker 13 Feb '17

13 Feb '17

Hi I am calculating the electrostatic surface of the protein that has a peptide bound inside the catalytic camber. There are two ways to calculate, either i can split the molecule in indivual chain and calculate their surface indivdually and run the APBS server for the electrostatic potential, or i can do it use the surfcat command. Both of them works but the results are different. To me the results are more logical by splitting the molecule in indivual chain, but u am not sure if its right to do that specially when you want to measure the electrostatic potential. What is your opinion. best Jiri

2 1

Write out coordinates for Centre of mass
by Soumya Govinda Remesh 10 Feb '17

10 Feb '17

Hello, I wanted to know if I can write out the coordinates for the object placed at the 'centre of mass' of selected atoms from a domain. I used the following command to place a marker at the location of interest. - measure center sel mark true 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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Re: [Chimera-users] CHIMERA ERROR
by Eric Pettersen 10 Feb '17

10 Feb '17

> On Feb 8, 2017, at 9:07 AM, Stellamaris Sotomayor Burneo <stellamaris_sb(a)yahoo.com> wrote: > > > Dear Dr. Eric, > > My name is Stellamaris. I am an undergraduate student from Ecuador. There is almost no one working in molecular docking in my country so far. So, it is very difficult to find somebody to ask for help. I would like to kindly ask you a question about the problem I am having with Chimera and I would really appreciate your help. > > I am trying to convert a set of receptors (named receptor.pdb) to receptor.mol2. using chimera. However i am having problems with the charges of FAD, NAD, NDP, and FMN. Receptors that have problems in those groups are not being transformed. > > Is there a way to transform those files without having to change to charges? I have tried changing the charges and it seems to work. However, I am very afraid of changing the conditions of my simulations if I change the charges. > > I have gotten the following message: > NAD) Error: cannot run "/opt/UCSF/Chimera64-1.10.2/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit > Failure running ANTECHAMBER for residue NAD Hi Stellamaris, As you have discovered, the underlying tools that Chimera relies on to derive charges (AmberTools/antechamber/sqm) sometimes fail for entities with concentrated areas of negative charge. It is for this reason that Chimera already includes pre-calculated charges for ADP, ATP, GDP, and GTP. These charges were taken from the AMBER parameter database <http://research.bmh.manchester.ac.uk/bryce/amber>. Charges for the moieties you mentioned are also in that database, and I’ve gone ahead and added NAD and NDP to the ones that Chimera knows about without needing to do a calculation. Precalculated NAD/NDP charges will be available in daily builds dated Feb. 9 or later. Unfortunately, FMN and FAD are more problematic in that Chimera doesn’t protonate them in the standard way used in the database. It adds a proton (and positive charge) to the isoalloxazine ring system so that the central ring becomes aromatic. Obviously, the simplest way to deal with this if you don’t need FAD/FMN as a cofactor is to simply delete them. If you do need them then things get hairy. I guess what I would do is: 1) Delete FMN/FAD. 2) Run Dock Prep which will get you a Mol2 file of the remainder of the system with charges. 3) Close your system and reopen it. 4) Delete everything but the FMN/FAD. 5) Set the IDATM types of the FMN/FAD so that they correspond to the standard protonation pattern. 6) Add hydrogens. 7) Write another Mol2 file with just FMN/FAD. 8) Edit this second Mol2 file and transcribe the charges found in the corresponding Amber parameter database file to the atoms. 9) Combine your two Mol2 files. Step 6 is a little tricky in that the atom names in the “OFF” parameter files aren’t all the same as the PDB standard names, but there is connectivity information in the OFF file, so you can figure out which atom is which. You can do step 5 by running the “defattr” command with the file I have attached, which will set the types of FMN/FAD heavy atoms to the standard protonation pattern. Also, instead of step 8, you could work up another “defattr” file to assign charges to the FMN/FAD before you write out the Mol2 file. Probably easier. —Eric Eric Pettersen UCSF Computer Graphics Lab

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large structures and two letter chain IDs
by Petr Leiman 09 Feb '17

09 Feb '17

Dear Chimera Users and Developers, I am writing to ask if there is a way to animate multiple conformations of a structure containing 144 chains (~300,000 atoms)? Is it possible to read in such a structure into Chimera and preserve chain IDs? We have to use two-letter chain IDs, something that Chimera does not seem to like. Thank you, Petr -------------- Petr Leiman UTMB Galveston, TX77555

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Re: [Chimera-users] Fwd: chimera MAV
by Elaine Meng 09 Feb '17

09 Feb '17

Hi Jackie, Yes, see the sequence window menu: "Preferences… Appearance. " There are several options for spacing, font, and coloring, including “Space between wrapped blocks.” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Best, Elaine > On Feb 9, 2017, at 12:45 AM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > > Thank you so much. Doing it by hand is the easiest. > Also, is there a way to increase the distance between wrapped blocks? > > Jackie Vitali > Cleveland State University > > On Wed, Feb 8, 2017 at 1:39 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > You can also: > > (1) hide/show the header lines (Conservation, Consensus, etc.) using the sequence window Headers menu > (2) change how Conservation is calculated (sequence window Preferences… Headers) > (3) add your own headers with quantities or symbols, e.g. put stars over the columns with superfamily-conserved residues > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > Elaine > > > On Feb 8, 2017, at 8:30 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > Hi Jackie, > > You can draw boxes (we call them “regions”) in the alignment wherever you want with click and drag, and then change their colors using the Region Browser. > > > > Multalign Viewer: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> > > > > Regions, including how to create them manually: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > > > Region Browser (click the square color wells to change colors): > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > > > I hope this helps, > > Elaine > > > > > >> On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > >> > >> Elaine, > >> > >> I would appreciate it very much if you could let me know how to highlight specific conserved residues in a sequence alignment between 2 proteins with chimera using the MAV? I highlight helices and beta sheets with colors, conservation between the 2 proteins is shown with the blocks on top. But there are 15-20 residues conserved in the superfamily of proteins and i would like to use blocks around them or highlight them in different color. In other words, 60 residues are conserved between the 2 proteins and 20 are special and need to be shown in a different way. > >> > >> I hope my question is clear. > >> > >> Thank you in advance. > >> > >> Jackie Vitali > >> Cleveland State University > >

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Re: [Chimera-users] Fwd: chimera MAV
by Elaine Meng 08 Feb '17

08 Feb '17

Hi Jackie, You can draw boxes (we call them “regions”) in the alignment wherever you want with click and drag, and then change their colors using the Region Browser. Multalign Viewer: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> Regions, including how to create them manually: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Region Browser (click the square color wells to change colors): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> 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 > On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > > I would appreciate it very much if you could let me know how to highlight specific conserved residues in a sequence alignment between 2 proteins with chimera using the MAV? I highlight helices and beta sheets with colors, conservation between the 2 proteins is shown with the blocks on top. But there are 15-20 residues conserved in the superfamily of proteins and i would like to use blocks around them or highlight them in different color. In other words, 60 residues are conserved between the 2 proteins and 20 are special and need to be shown in a different way. > > I hope my question is clear. > > Thank you in advance. > > Jackie Vitali > Cleveland State University >

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Re: [Chimera-users] Upgrade to Sierra
by Elaine Meng 06 Feb '17

06 Feb '17

> -------- Forwarded Message -------- > Subject: Upgrade to Sierra > Date: Sun, 5 Feb 2017 17:58:53 +0100 > From: F.Xavier Gomis-Rüth <fxgr(a)ibmb.csic.es> > > Dear Elaine, > I recently had to upgrade to Sierra from Mountain Lion and now I find that ions are displayed as black spheres only > in Chimera v. 1.9. Any ideas on what I should change? > Kind regards, > Xavier > On Feb 5, 2017, at 9:11 AM, F.Xavier Gomis-Rüth <fxgr(a)ibmb.csic.es> wrote: > > Elaine, it's not only the ions, its all the atoms and bonds. > Ribbon appear fine though.... > Dear Xavier, I’m not an expert on this kind of thing, so I’m forwarding to the chimera-users list. (Sending to the list is always recommended… I will still answer it if I can, just as fast!) Although I don’t know if it’s related, maybe you should get a newer version of Chimera. Using Chimera versions 1.11.2 and 1.12 daily build on both a laptop and a desktop running Sierra, I do not have this problem. 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

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Re: [Chimera-users] Contour level animation ?
by Elaine Meng 04 Feb '17

04 Feb '17

> On Feb 3, 2017, at 4:21 PM, esserlo(a)helix.nih.gov wrote: > > Hi Elaine, > for a small demonstration, I want to make a movie in chimera where I animate > a change in contour level. I have an EM map with noisy features that improve > upon changing the level. I can do it by hand in the volume section but I > cannot figure out what parameter it is even if I wanted to set it on the > command line. > Setting it on the command line I suppose would be the first step but then my > question is: can this parameter be changed during an animation? > Thanks, > Lothar Hi Lothar, Yes, you can use the “volume” command “level” option to change the contour level. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> The “volume” command doesn’t itself have frames option, but you can combine it with the “perframe” command to perform a gradual change in a single line, as illustrated with this video mini-example: <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.htm…> We generally encourage emailing questions to chimera-users (CC’d here) unless they involve private data, since others may like to know the answer. 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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Re: [Chimera-users] [chimera-dev] (no subject)
by Tom Goddard 02 Feb '17

02 Feb '17

Hi Kavya, How about just measuring the distance between the two monomer center of mass points of the homodimer and dividing that distance by 2 since the line between the two monomers will intersect the symmetry axis in the middle. For example for monomer chains A and B "measure center :.A ; measure center :.B ; distance #1,2”. Send this type of question to chimera-users instead of the chimera-dev list which is for developer programming questions. Tom > On Feb 2, 2017, at 1:39 PM, Kavya Shankar wrote: > > Hi, > > Is it possible to find the distance between a point and a line in chimera? I am trying to find the distance from the center of mass of the protein to the 2 fold axis of the homodimer. > > Thanks. > > Regards, > Kavya > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

1 0

3D movies for projects
by Kenward Vaughan 02 Feb '17

02 Feb '17

Hello, I'm developing a project for my class which feels like it's taking on Chimera (as in the creature) like proportions for the students. The thought is to have presentations of their visualization studies presented in a conference like setting at our school, open to all students. The question that has pounced into my thoughts is the possibility of using some settings within Chimera allowing them to record a movie (even as simple as a screen capture) which can then be played using an Oculus headset (or similar) with a phone. This would be a simple way to get the technology out into the street, so to speak. I do not yet have one of these myself so really don't know this first hand, but thought using wall-eye stereo made sense...?? Has anyone tried this, hopefully successfully? Kenward ps. Is there a way to use the phone as a monitor so one can manipulate the images via an external device, or use a Bluetooth hand controller? (I expect this is not possible given the graphics constraints of phones...) -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

4 9

Help with coordinates please
by drew richardson 01 Feb '17

01 Feb '17

Hi, I am very new chimera and I am having to use it for a project at university. I have to create a picture from chimera and then list commands so anybody can recreate it just by typing in the commands in the command box. The problem I am having is: once I have rotated and zoomed manually using the mouse I don't know how to recreate that position and view by using typed commands. I can't even seem to find anywhere the coordinates of the new rotation. Could you please help me? How do I recreate the zoom and rotation using commands only, so that anyone wanting to recreate the view I have can do it just by typing in a list of commands after loading my original PDB file? Kind regards Drew Richardson ID: 27927431 (1st year biochemistry)

3 3

Help!
by Kempfer, Jamie E. 31 Jan '17

31 Jan '17

i cannot get chimera to work on my windows computer!

3 2

Re: [Chimera-users] on chimera unit cell function
by Elaine Meng 31 Jan '17

31 Jan '17

Hi Smith, The Unit Cell results for a structure with and without “pack” are equivalent because the symmetry describes a repeating pattern: each single copy could be shown in any of several places around the first copy. In other words, as I said before, there are multiple equally correct ways of presenting the same information. Although I cannot spend a lot of time looking at your specific data, I see the 3 structures are all the same space group with similar unit cell dimensions and angles, and the paper says “we could present nucleotide-induced conformational changes in the same crystal lattice by eliminating possible artificial structural differences because of different crystal packing.” Therefore I infer that the crystal packing is approximately the same in the 3 structures. It cannot be EXACTLY the same, however, since there are conformational changes between the structures. Since I didn’t write the Unit Cell code or look at the symmetry matrices in detail, I don’t know why the structures don’t give the same arrangement without “pack,” but I don’t think it is important, since the different possible arrangements for a single structure are equally correct. I hope this helps, Elaine P.S. please send questions to chimera-users rather than to me individually - thanks > Begin forwarded message: > > From: "Smith Liu" <smith_liu123(a)163.com> > Subject: Fw:Re: [Chimera-users] on chimera unit cell function > Date: January 31, 2017 at 7:01:54 AM PST > To: meng(a)cgl.ucsf.edu > > Dear Elaine, > > Related to our previous communication on "on chimera unit cell function" , here I have more to discuss with you. > > Attached 1 was the paper “Nucleotide-Dependent Conformational Changes and > Assembly of the AAA ATPase SKD1/VPS4B” published in Traffic 2008. PDB ID 2ZAM, 2ZAN, 2ZAO were 3 pdbs from this paper, and 2ZAM was the VPS4B without any nucleotide, 2ZAN was the VPS4B bound with ATP, 2ZAO as the VPS4B bound with ADP. > > As the paper wrote, “Because our attempts to crystallize SKD1 (VPS4B) in the presence > of ATP or ADP failed, we soaked the apo form crystals in solutions of ATP or ADP”, thus the 2ZAN and 2ZAO were got by soaking the crystal for 2ZAM with ATP and ADP separately. All 3 crystals were with space group P 65. > > The pdb for the 6 mates for each of 2ZAM, 2ZAN and 2ZAO are attached in attachment 2, 3, 4 separately (prepared without clicking ""Pack molecules in unit cell"). If viewed by Chimera, you will find the mates of 2ZAM arrange in the same way as the mates of 2ZAO, i.e., the 6 mates connect each other closely (side by side) and packed in a screw way. However for the 6 mates of 2ZAN, although still in screw way, the 6 mates arrange not closely but have a space between the adjacent mates. Correspondingly, the diameters of the z-axis projection of the 6 mates of 2ZAM and 2ZAO were much smaller than that of the 6 mates of 2ZAN. > > However, if we by Chimera we click the "Pack molecules in unit cell",we will find the 6 mates of 2ZAN displayed exactly (or very similarly) as the 6 mates of 2ZAM and 2ZAO (Am I right). > > Then my question would be, in the crystal for 2ZAN and 2ZAO, do the proteins arranged in exactly the same pattern? And why if we did not click ""Pack molecules in unit cell", the mates of 2ZAN and 2ZAO were displayed differently, and with clicking ""Pack molecules in unit cell",the mates of 2ZAN and 2ZAO were displayed similarly? > > If the protein arranged differently in the crystal for 2ZAN and 2ZAO, then in the crystal packing of 2ZAN, how can I identify the 6 protein which were from the 6 screwed mates in 2ZAM? > > I am looking forward to getting a reply from you. > Smith > -------- Forwarding messages -------- > From: "Elaine Meng" <meng(a)cgl.ucsf.edu> > Date: 2017-01-30 04:05:22 > To: "Smith Liu" <smith_liu123(a)163.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] on chimera unit cell function > Hi Smith, > The number of copies and their positions are all correct no matter whether you choose the “pack” option or not. If you cut out a part of the real crystal, there will be a real copy in the same place as the copy from Chimera. So imagine if you had specified an infinite (or large) number of unit cells in Chimera, a chunk from the middle of the result would look the same as some chunk of the real idealized crystal, regardless of whether you used “pack”. However, since you are probably specifying 1 x 1 x 1 or some small number of unit cells, yes choose the “pack” option to show the copies packed together, instead of with some spaces where a copy is shown inside a neighboring box rather than in the central outline box. > Best, > Elaine > > > On Jan 29, 2017, at 5:10 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > > > Dear Elaine, > > > > I am still confusing on the function of "Pack molecules in unit cell" in Chimera. If we cut out a cube (or a volume) of crystal based on which a pdb was got, do you think the molecules packed in the cube in the way without "Pack molecules in unit cell" clicked, or the molecules packed in the cube in the way with "Pack molecules in unit cell" clicked? > > > > I am looking forward to getting a reply from you. > > > > Smith > > > > > > At 2017-01-29 00:50:44, "Elaine Meng" <meng(a)cgl.ucsf.edu> wrote: > > >Hi Smith, > > >It is my understanding that you will get the same number of copies whether or not you choose the “pack” option, and that there are multiple equally correct ways in which the copies will be positioned according to the symmetry information. The “pack” option simply chooses, out of these many equally correct alternatives, a configuration that places the centers of all the copies inside one unit cell outline box instead of spreading them out among neighboring boxes. > > >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 > > > > > >> On Jan 28, 2017, at 1:47 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > >> > > >> Dear All, > > >> > > >> In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly? > > >> > > >> I am looking forward to getting a reply from you. > > >> > > >> Smith >

2 1

Save marker sets from command line or python
by Kyle Morris 30 Jan '17

30 Jan '17

Dear Chimera dev and community, I would like to save a marker set from the command line and ultimately do so in a script. Using the write command which I would use for PDB's, marker sets get saved in PDB format, of course. Is there a command to save the marker set as XML .cmm as it would from the volume tracer menu? I notice at the bottom of the following page this is a suggested development: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/… - supply Python code for reading and writing the XML files containing saved marker sets Is it there already and I can't find perhaps? Thanks for your help as ever! Best wishes, Kyle

3 2

on chimera unit cell function
by Smith Liu 29 Jan '17

29 Jan '17

Dear All, In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly? I am looking forward to getting a reply from you. Smith

2 3

Metal Geometry Analysis - per frame
by Ilkow, Veronica 27 Jan '17

27 Jan '17

Dear All, Is there a way I could include the metal geometry analysis as a per frame script for a MD movie? Ideally I would like to have an output file which lists the best geometry and essentially prints out the co-ordination table for two atom selections per frame. I am trying to figure out how to use the python or chimera per-frame commands to specifically select an atom and then print an output file. Any hints and suggestions on how to do this will be greatly appreciated. Thank you in advance for your help. -Veronica

2 1

Re: [Chimera-users] dipoles
by Tom Goddard 25 Jan '17

25 Jan '17

Hi Vatsala, To change the arrow thickness change the line of code in the dipole.py script bildString = ".arrow %g %g %g %g %g %g .1 .2 .9" The values at the end control the shape, the “.1” is the cylinder radius, the “.2” is the arrow tip cone radius, and the “.9” is the fraction of the arrow length taken by the cylinder. This is described in the Chimera BILD format documentation here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> Tom > On Jan 25, 2017, at 10:02 AM, Sagar, Vatsala (NIH/NEI) [E] wrote: > > Hi Tom, > Do you know how to change the dipole vector thickness. I am using dipole.py program to calculate dipoles in Chimera, and it is giving me a very thin line. > Thanks a lot, I sincerely appreciate it, > Vatsala Sagar > > From: "Sagar, Vatsala (NIH/NEI) [F]" > Date: Friday, January 6, 2017 at 10:09 AM > To: Tom Goddard , "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>>, "Sagar, Vatsala (NIH/NEI) [F]" > Subject: Re: [Chimera-users] dipoles > > Hi Tom, > I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think, > Thanks, > Vatsala > From: Tom Goddard > Date: Thursday, January 5, 2017 at 7:07 PM > To: "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>>, "Sagar, Vatsala (NIH/NEI) [F]" > Subject: Re: [Chimera-users] dipoles > > Hi Vatsala, > > I guess you are refering to the dipole.py script on the Chimera Python scripts web page: > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong. > > Tom > > >> On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote: >> >> Hi, >> Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? >> Thanks, >> Vatsala Sagar >> _______________________________________________ >> 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> >

1 0

on Multiscale Models
by Smith Liu 23 Jan '17

23 Jan '17

Dear Al, In the "Mutiscale Models" Windows , will you please tell me what does it mean for the item "Range"? I am looking forward to getting a reply from you. Smith

2 1

Python script for reading volume values at atom positions
by Kyle Morris 20 Jan '17

20 Jan '17

Dear chimera dev and users, Can anyone confirm with the latest chimera version (i’m running v1.11.2 build 41376) if this python script for measuring map values at atoms works for them? The script was reported previously on the users list here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001587.html For me I get a python import error: from VolumeViewer import Data_Region, full_region, Rendering_Options Thanks for your insight! Best wishes, Kyle

3 6

beta sheet to loop
by chemocev marker 19 Jan '17

19 Jan '17

Hi I am looking at some region of the protein in chimera and it looks like a loop but the from the procheck analysis it shows a beta-hair pin like structure. In the electron density, its shows a hydrogen bonding between the main chain atom. Why is this difference and how to overcome on it. best Jiri

2 1

forget last question
by A G Szabo 19 Jan '17

19 Jan '17

Forget the last question regarding visualizing nucleotides as balls and sticks. Figured it out. ags

1 0

quick question
by A G Szabo 19 Jan '17

19 Jan '17

I am looking at a protein polynucleotide structure. How do I turn the rectangles that represent the individual nucleotide into balls and sticks? Thanks Arthur G. Szabo

1 0

Autodock vina + modeller + ATOM syntax error
by Zirpel, Bastian 18 Jan '17

18 Jan '17

Hi everyone, I'm using Chimera 1.11.2 on windows. I am experience following error after my workflow. I fetched a known pdb model from the servers and generated several structural models of similar sequences using the integrated MODELLER script. Since my pdb model contains a covalently attached cofactor in the active site, I let MODELLER include non-water HETATM into my structural models as well. Afterwards I tried to do substrate/product binding studies with the known pdb model as well as with the generated structural models using the AutoDockVina script. However, when I run the script with the known pdb model, everything works fine. But when I'm running the script with the structural models, I receive following error msg: "Parse error on line 8553 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive." It should be noted that this error does not occur if I won't include non-water HETATM by MODELLER. Makes sense, since having a look at the generated pdbqt file, the FAD lines are generating the error. " HETATM 8554 HO3' FAD 525 62.339 60.023 -29.788 1.00 0.00 0.238 Ho HETATM 8555 HO2' FAD 525 66.741 58.106 -28.406 1.00 0.00 0.397 Ho HETATM 8556 HO3B FAD 525 60.634 66.984 -32.274 1.00 0.00 0.221 Ho HETATM 8557 HO4' FAD 525 65.182 62.428 -29.602 1.00 0.00 0.217 Ho HETATM 8558 1H6A FAD 525 68.751 67.392 -38.565 1.00 0.00 0.157 HD HETATM 8559 2H6A FAD 525 68.156 65.783 -38.183 1.00 0.00 0.157 HD HETATM 8560 HO2B FAD 525 62.183 68.217 -34.408 1.00 0.00 0.253 Ho " I found that AutoDockVina needs a "HD" instead of a "Ho" entry at these positions? Is this correct? So my question is, why is AutoDock vina generating a pdbqt file in the first place which it cannot read properly in the next step? How can I prevent this? I cannot just change the pdbqt entries as AutoDockVina will overwrite it again. Thanks in advance for any help! Bastian

2 1

model panel: long 'clicking time'
by Julian von der Ecken 18 Jan '17

18 Jan '17

Dear Chimera Team, there is a long delay between on and off of the ’S’-checkbox (show button) in the model panel. I mean the model it self vanished instantly but the ckeckbox takes much longer to be set to on/off. Mac OS X 64-bit Version tested (1.11 2016-06-30, 1.11.2 2016-12-02; ): very slow. In older versions (1.10.2 2015-07-23) it was much faster. It is kind unfortunate when you click very fast through all models manually or you just want to alternatively show and hide one model very fast to see differences. Is it possible to set the speed somewhere/somehow? Thanks a lot for your advise Julian ————————————————————————————————— Julian von der Ecken, Ph.D. Max-Planck-Institute of Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund, Germany room: B2.27 tel: (+49) (0)231 133-2306 e-mail: julian.von-der-ecken(a)mpi-dortmund.mpg.de<mailto:julian.von-der-ecken@mpi-dortmund.mpg.de> institute: http://www.mpi-dortmund.mpg.de group: http://www.mpi-dortmund.mpg.de/forschungsgruppen/raunser

2 2

Transparency of surface colored with electrostatic potential file
by Sarah Piper 18 Jan '17

18 Jan '17

Hi, I was wondering if you can make a surface transparent, which contains an electrostatic potential file (.dx), calculated with APBS? It would be nice to be able to see the ribbon structure of my .pdb file within the coloured surface. I’m using mol maps or SES to create the surface (my surface calculations (MSMS) usually fails, probably because of too large .pdb files) and then color this surface (Surface Color) with the submitted potential file from APBS. If I then want to make the surface with the potential colouring transparent, it doesn’t work. It just works to make the ’normal’ surface color itself transparent (e.g. transp 70,s #1). Does anyone have an idea if I can make the potential file or surface with electrostatic potential transparent as well? Many thanks for your help. Best regards, Sarah

2 2

Visualization Martini coarse grained model in Chimera
by MOHD HOMAIDUR RAHMAN 17 Jan '17

17 Jan '17

Dear All It is possible to visualize martini coarse grained bead of proteins and lipid in Chimera? if yes please guide me for same. Thanks & 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* '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''

3 6

on Unit Cell function
by Smith Liu 17 Jan '17

17 Jan '17

Dear All, Once we load a PDB in chimera, in Tools-Higher order structure-Unit Cell, if we click "Make copies", the copies of the PDB would be created based on space group, with each copy has a specific # (0,1,2,3..., for example). Will you please let me know is any rule available for how the number of # for each copy of PDB was defined? It seems the PDB copies with consecutive specific # were not most closely related in the Chimera display. I am looking forward to getting a reply from you. Smith

2 1

Fixing the Frame size
by chemocev marker 17 Jan '17

17 Jan '17

Hi I am making some images and I would like to know how to fix the zoom size so that in all the images size of the secondary structure should be similar. best Jiri

2 1

Preference/default for H-bond representation
by Markus Heller 16 Jan '17

16 Jan '17

Hello, Is there a way to set the preference for H-bonds to be represented as dashed lines, not as solid lines? I don't seem to be able to find anything in the Preferences or the documentation. Thanks and Cheers Markus

3 5

virtualization project - UCSF
by Scholz, Sebastian 16 Jan '17

16 Jan '17

Dear Sir or Madam, we, the COMPAREX AG, are a German Reseller. For one of our clients we conduct an evaluation license and have a list of questions provided, in the answer we need your help. This involves essentially the question whether the software can be virtualized and, if so, on what terms. These are crucial questions for the future orientation of its IT strategy for our customer. The Software: (for every Software is one questionnaire) Chimera 1.x Please note, that our questions refer to the latest software version. I therefore kindly ask for a timely response to the questionnaire, which you can found in the appendix (in German and English), but not later than January 23rd 2017. Kindly forward our request to whom it may concern, if you are not the responsible contact person. Thank you for your support. I look forward hearing from you soon. Kind regards / Mit freundlichen Grüßen Sebastian Scholz International Sales Team ______________________________________ COMPAREX AG Software Inside Sales Blochstraße 1 04329 Leipzig Direct contact: Sebastian Scholz mobile: +49 341 2568 6643 email: Sebastian.Scholz(a)comparex.de<mailto:Sebastian.Scholz@comparex.de> COMPAREX AG | Blochstraße 1 | 04329 Leipzig | Amtsgericht Leipzig | HRB: 15064 | USt-ID: DE 141626867 | Vorstand: Mag. Wilfried Pruschak (Vorstandsvorsitzender, CEO) | Marc Betgem (CSO) | Dr. Thomas Reich (CFO) | Aufsichtsratsvorsitzender: Mag. Wilhelm Doupnik | phone: +49 341 2568 000 | fax: +49 341 2568 999 | email: info(a)comparex.de<mailto:info@comparex.de> | web: www.comparex.de<http://www.comparex.de/>

1 0

Docking license
by Farah Yousef 13 Jan '17

13 Jan '17

Hello, I need an assisdtance in what I faced in submitting after I filled the required info for DOCK 6. Pages cannot be opened though I checked my net connection and I know DOCK program is free of charge and available for academic projects. Hope I get help in obtaining the license for DOCK 6, please. Best wishes,Farah Yousef

3 2

Web services (Modeller, Blast, etc.) running
by Elaine Meng 13 Jan '17

13 Jan '17

Hello users, I believe the RBVI web services called from Chimera are now running, thanks to the efforts of my coworkers. I just now verified running Modeller, Blast (requires Chimera 1.11.2 or later), and sequence realignment with Clustal Omega or Muscle. 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

2 1

Deleting a surface on command line, not just hiding it
by Rebecca Swett 12 Jan '17

12 Jan '17

Hi all, I'm working on an animation, and I'd like to know if there's a way I can delete or close a calculated surface from the command line. For my purposes, I'd like to show the surface representation of the protein, remove it, then show a dynamics trajectory, and show the surface again at a separate point (while the trajectory is stopped). Currently, without being able to close the surface, it tries to recalculate the surface at each trajectory frame, which doesn't work for my purposes. Let me know if this is possible. Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

2 2

Re: [Chimera-users] dipoles
by Sagar, Vatsala (NIH/NEI) [E] 12 Jan '17

12 Jan '17

Hi Tom, So if you align the pdb files of the rotated proteins, they have an exact match. But when you make the PQR files, it adds hydrogens differently to the rotated proteins, resulting in a charge difference in the said histidine. Should the program be adding hydrogens differently to the rotated proteins, and is there a way to remedy this> Thanks a lot, Vatsala Sagar From: "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> Date: Friday, January 6, 2017 at 10:27 AM To: "chimera-bugs(a)cgl.ucsf.edu <mailto:chimera-bugs@cgl.ucsf.edu>" <chimera-bugs(a)cgl.ucsf.edu <mailto:chimera-bugs@cgl.ucsf.edu>> Subject: FW: [Chimera-users] dipoles Hi Tom, I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think, Thanks, Vatsala From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> Date: Thursday, January 5, 2017 at 7:07 PM To: "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>>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> Subject: Re: [Chimera-users] dipoles Hi Vatsala, I guess you are refering to the dipole.py script on the Chimera Python scripts web page: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong. Tom > On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote: > > Hi, > Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? > Thanks, > Vatsala Sagar > _______________________________________________ > 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

Re: [Chimera-users] dipoles
by Tom Goddard 10 Jan '17

10 Jan '17

Hi Vatsala, If you run the Chimera pdb2pqr command or graphical interface on a molecule and a rotated copy of the same molecule and it gives different protonation states for histidine that seems like a bug. As described in the Chimera documentation this uses the PDB2PQR web service provided by the National Biomedical Computation Resource (NBCR). https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdb2pqr.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdb2pqr.html> You might want to contact the developers of PDB2PQR to pursue this matter further http://www.poissonboltzmann.org/support/home/ <http://www.poissonboltzmann.org/support/home/> Chimera can also add hydrogens and compute charges using the Chimera DockPrep tool so maybe that is an option for you to avoid this problem in pdb2pqr. Tom > On Jan 10, 2017, at 7:35 AM, Sagar, Vatsala (NIH/NEI) [E] <vatsala.sagar(a)nih.gov> wrote: > > Hi Tom, > So if you align the pdb files of the rotated proteins, they have an exact match. But when you make the PQR files, it adds hydrogens differently to the rotated proteins, resulting in a charge difference in the said histidine. Should the program be adding hydrogens differently to the rotated proteins, and is there a way to remedy this> > Thanks a lot, > Vatsala Sagar > > From: "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> > Date: Friday, January 6, 2017 at 10:09 AM > To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>, "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>>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> > Subject: Re: [Chimera-users] dipoles > > Hi Tom, > I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think, > Thanks, > Vatsala > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Date: Thursday, January 5, 2017 at 7:07 PM > To: "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>>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> > Subject: Re: [Chimera-users] dipoles > > Hi Vatsala, > > I guess you are refering to the dipole.py script on the Chimera Python scripts web page: > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong. > > Tom > > >> On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote: >> >> Hi, >> Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? >> Thanks, >> Vatsala Sagar >> _______________________________________________ >> 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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Map conservation of my sequence compared to sequence alignment
by mfellner＠msu.edu 09 Jan '17

09 Jan '17

Good day I like the mapping sequence conservation tool in chimera, however I ran into a problem that IÂ could not overcome with anything IÂ found online. I have the consensus mapped onto my protein but that is not what IÂ want. IÂ want to show how the residues of my protein are conserved. For example at a particular residue the consensus is a C but in my structure its a W. at the moment the W is colored to be highly conserved based on the consenus of the C. The W is maybe 15% conserved, how can IÂ map the conservation of my sequence compared to all the other sequences. IÂ hope IÂ explained what my issue is Thank you for this great tool Matthias Fellner

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dipoles
by Sagar, Vatsala (NIH/NEI) [F] 06 Jan '17

06 Jan '17

Hi, Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? Thanks, Vatsala Sagar

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Mutation in Chimera
by Islam, Tanzila 06 Jan '17

06 Jan '17

Hi I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time. I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work. Thanks Tanzila Islam Graduate Student Washington State University

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Problem opening DOI from Protein Data Bank
by Tones,Jason R 06 Jan '17

06 Jan '17

Hello, I am a student and recently downloaded chimera to use for a class, when I clicked to open the DOI of a search on the protein database I picked the wrong file under chimera to use to open it and it wouldn't open. I tried uninstalling and reinstalling and it keeps going to the file that won't open what I'm trying to do. Thank you for any help or suggestions you may have for me. Jason

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Measuring hexamer asymmetry
by Tom Goddard 06 Jan '17

06 Jan '17

Hi Elena, Ok. The “measure rotation” command shows the rotation axis defined by the rigid motion of one subunit onto another — it has nothing to do with the hexamer axis. I think you are asking for is that if you take subunit 1, rotate it 60 degrees about the hexamer axis, then compare the orientation and translation of subunit 2 to that moved copy of subunit 1. Then do the same for subunits 3,4,5,6. To do this take subunit 1 and make 5 rotated copies by 60,120,180,240,300 degrees and save that as a new hexamer PDB file. Now open the asymmetric hexamer and this symmetric hexamer. If the subunits are chain ids A,B,C,D,E,F then use “measure rotation #0:.B #1:.B”, “measure rotation #0:.C #1:.C", …. This will still show a rotation axis that is not the hexamer axis which indicates the rotation needed to make the exact symmetry copy of subunit 1 rotate onto the asymmetric subunit 2, and it will give the translation, rotation axis and angle in the reply log. Maybe you are not interested in how the symmetric copies of subunit 1 rotate when being aligned to asymmetric subunits 2,3,4…. Then you can just ignore this rotation information and get the translation from the reply log. Tom > On Jan 5, 2017, at 7:38 AM, Elena Zehr wrote: > > Hi Tom, > > Thank you very much for you response. Yes within the asymmetric hexamer subunits have different conformations. To test your advice on RMSD, I first generated hexamer by using six copies of the same subunit to align to the original hexametric structure, then I closed the original hexametric structure. The asymmetric hexamer now consisted of subunits with identical conformation, please note the hexamer is still asymmetric. Then I opened a monomer with the same conformation as the subunits within the newly-generated hexamer, and calculated rotation and translation matrices between the first protomer within the hexamer and the rest of the subunits (#2-6). The central axis for each of the calculations deviated from each other. > > My issue is the following: to make the calculations reliable I wish to have the same central axis running through the center of the hexamer and not the axes between #1 and #2 or #1 and #4, etc. which deviate from each other due to the asymmetry of the hexametric structure. Is it possible? For example I wish to calculate the central axis of the whole hexamer and then use it as a reference to calculate rotation and translation for each subunit (#2-5) around the ring with respect to the subunit #1 and the central axis of the whole hexamer. Is it possible to define parameters for the central axis in the command line together with “measure rotation #1 #2 or #1 and #4” ? > > > Many thanks, > Elena > > > On Jan 4, 2017, at 4:47 PM, Tom Goddard wrote: > >> Hi Elena, >> >> Elaine asked me to look at your problem measuring orientation of subunits of a hexamer. Does your hexamer have cyclic symmetry? If so I think the reason the displayed axes don’t appear to align with the hexamer symmetry axis is because your alignment of one subunit to another is not good. You can get the root mean square deviation of C-alpha positions for the alignment by looking in the Reply Log (menu Favorites) after running the match maker command, for example, >> >> RMSD between 308 pruned atom pairs is 0.361 angstroms; (across all 308 pairs: 0.361) >> >> From your picture with blue and tan complexes it does not appear they are aligned at all. If the sequences of the subunits are very different then match maker may not be able to align them. >> >> Tom >> >> >> >> Begin forwarded message: >> >>> From: Elena Zehr >>> Subject: Re: user-defined rotation axis >>> Date: January 4, 2017 at 1:09:10 PM PST >>> To: Elaine Meng >>> >>> Dea Elaine, >>> >>> Thank you for getting back to me so soon. Sorry for sending you my question again. >>> >>> I am getting the following (see attached image) Where the central axis between protomer A and B is different than the one between protomer A and F. I wish to have the same central axis that would be the central axis of the hexamer, otherwise I assume my measurements are not accurate. I get the same if I use the hexamers or separate monomers >>> >>> >> <axis.tiff> >>> On Jan 4, 2017, at 1:15 PM, Elaine Meng wrote: >>> >>> Begin forwarded message: >>> >>>> From: Elena Zehr >>>> Subject: Re: user-defined rotation axis >>>> Date: January 4, 2017 at 1:09:10 PM PST >>>> To: Elaine Meng >>>> >>>> Dea Elaine, >>>> >>>> Thank you for getting back to me so soon. Sorry for sending you my question again. >>>> >>>> I am getting the following (see attached image) Where the central axis between protomer A and B is different than the one between protomer A and F. I wish to have the same central axis that would be the central axis of the hexamer, otherwise I assume my measurements are not accurate. I get the same if I use the hexamers or separate monomers >>>> >>>> >>> <axis.tif> >> >

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Showing color key programatically colouring from a volume...
by Pablo Conesa 31 Dec '16

31 Dec '16

Dear all We have this simple script to open a volume (#0) coloured using values from a second volume (#1): open betaGal.mrc open extra/MG_Chimera_resolution.vol volume #1 voxelSize 3.54 vol #1 hide scolor #0 volume #1 cmap rainbow reverseColors True For scolor command we are using a volume. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#volume It would be nice to achieve something like this at start up (note the color key is based on the volume): I've did it dragging the mouse over the canvas while "Color key" utility is open. And, is there a posibility to round up the values. Some kind of: Psaudocode: Give the resulting color key for each round values display the color key I guess that if there is a way to get the color key, then rest can be done through commands. Cheers, Pablo.

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color zone on command line
by Kyle Morris 24 Dec '16

24 Dec '16

Hi Chimera dev, Following on from this post back from 2009: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003514.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003514.html> How would one also split map in this python script? Thanks! Kyle

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Re: [Chimera-users] Chimera-users Digest, Vol 164, Issue 26
by Healey, Joe 23 Dec '16

23 Dec '16

I might be able to offer a bit of help here, the Chimera team and Jaime helped me with basically this exact problem. I have a script here https://github.com/jrjhealey/bioinfo-tools/blob/master/strucfit.py that you could take from. You'll probably want to look specifically at lines 216-240. (Note - you'll also need to look at the relevant module imports for match and pychimera etc. The script will need Jaime's implementation of pychimera too (he's super helpful!) https://github.com/insilichem/pychimera The script gives output as below, as the script automatically finds the best matching PDB file (that's what the first 150 lines or so is looking for), there is additional information there. Best Model I'm Hit Comparing RMSD Assorted homology metrics 2k4r PAK_01796_model5.pdb 2.81843275676 37.5 13 0.00035 21.5 2k4r PAK_01796_model4.pdb 12.6869844869 37.5 13 0.00035 21.5 2k4r PAK_01796_model3.pdb 14.4133021316 37.5 13 0.00035 21.5 2k4r PAK_01796_model1.pdb 0.459177533295 37.5 13 0.00035 21.5 2k4r PAK_01796_model2.pdb 15.1861411912 37.5 13 0.00035 21.5 Hope that's useful! Happy to offer more help (though I'm sure the chimera team have it covered!) Joe 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 ________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: 22 December 2016 20:00 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 164, Issue 26 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Saving Output From Match Align (Muk, Sanychen) ---------------------------------------------------------------------- Message: 1 Date: Thu, 22 Dec 2016 16:11:00 +0000 From: "Muk, Sanychen" <smuk(a)coh.org> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] Saving Output From Match Align Message-ID: <A69D81CB04F0734E96302AA9E36F9B233E521BEE(a)ppwexch2kx03.coh.org> Content-Type: text/plain; charset="iso-8859-1" Hello, I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays. Best, Sanychen Muk --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wi! sh to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) ---------------------------------------------------------------------

1 0

Saving Output From Match Align
by Muk, Sanychen 23 Dec '16

23 Dec '16

Hello, I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays. Best, Sanychen Muk --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) ---------------------------------------------------------------------

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ChimeraX daily builds available!
by Elaine Meng 23 Dec '16

23 Dec '16

Prerelease daily builds of UCSF ChimeraX are now available to the public! UCSF ChimeraX home: http://www.rbvi.ucsf.edu/chimerax/ Download: http://www.rbvi.ucsf.edu/chimerax/download.html Please keep in mind that ChimeraX features are currently quite limited, that ChimeraX may not work on older machines and/or graphics cards, and that due to the upcoming holidays, responses may be slow if you contact us. On behalf of the Chimera/ChimeraX team, 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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change default color maps
by Michał Kadlof 21 Dec '16

21 Dec '16

I found Palette Editor Tool, but I don't know how to use it. How can I apply chosen pallete in Surface Color Tool or load colors from palette into rainbow tool? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 1

Crossfade and disp
by Daniel Asarnow 21 Dec '16

21 Dec '16

Hello Chimera experts, Here is another movie making question. I noticed that disp and ~disp trigger frames to be recorded, without a call to wait. For example: disp #2 movie crossfade 25 ~disp #2 disp #3 This would produce a movie that crossfades from model #2 to blank, with #3 suddenly appearing. To get crossfades between two ligands, I had to use: disp #2 movie crossfade 25 perframe "~disp #2" frames 1 disp #3 movie crossfade 25 Based on the documentation I wasn't sure if this was intended behavior or a bug. Did I miss a more elegant way to crossfade between two models? Thanks, -da

3 3

Multiscale models command
by Ian Holmes 21 Dec '16

21 Dec '16

Hello Chimera gurus, I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module. Here is the rough order of what I am doing from the graphical user interface: Open model 2QA0 Tools menu -> Higher-order structure -> Multiscale Models panel (The following actions are all in the Multiscale Models panel) Click "Make models" button in "Models from molecules and matrices" section Click "All" button in "Select chains:" section Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection Click "All" button in "Select chains:" section (again) Select "Ribbon" from "Style" menu in "Act on selected chains" section (then back to the main view) Zoom out (with mouse wheel) Favorites menu -> Command Line Type "select :10,20,30" (amino acids I want to highlight) Here is what I've got so far in terms of equivalent Python code: import os from chimera import runCommand as rc rc("open 2QA0") # make multiscale model here? rc("select :10,20,30") # select some residues Your help would be appreciated - thanks! Ian

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(no subject)
by Kartheek 19 Dec '16

19 Dec '16

Hi UCSF CHIMERA users, I am trying to make a movie in chimera using MD movie and pdb option. However I have been stumbled with the following error "Residue 256.C not in first model on line 20792 of /tmp/tmpvr4a2t.pdb". I do not have any end records, how can I rectify the error ?? -- Sincerely, P.Kartheek, Research Scholar, IIIT-H, Hyderabad, INDIA.

2 2

Surface clip coloring
by Michał Kadlof 16 Dec '16

16 Dec '16

How can color volume by value with binning several values into single color? I achived the effect partialy by opening several times the same map. set different thresholds and colors to each one and playing with Per-Model Clipping tool, but it have some drawbacks. Planes can't be at exact same level because I observe artifacts. So I tried to move slightly inner layers upp, but still I observe "staris" effect. I also tried with Surface color tool, but it uses interpolation and blends colors togather. In other words I need something like this: https://1.bp.blogspot.com/-5B5ueLHCBPY/T4II4IddvwI/AAAAAAAAB_w/rYwqsJNldY0/… instead of something like this: https://i.stack.imgur.com/hQmry.png -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 1

probably a bug
by Michał Kadlof 16 Dec '16

16 Dec '16

Hello, I visualize density of my data two different way with the same thresholds and observe different sizes of regions. Isn't it a bug? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 1

Hide side chain
by Zhu, Xiaoyan 12 Dec '16

12 Dec '16

Hello, I am using UCSF Chimera to generate figures of protein crystal structures. Some crystals, if open in Chimera, automatically show the side chains of some amino acids. I want to hide those side chains in my figures. I wonder if there's an easy way to do it. Thank you! Have a good one, Xiaoyan Zhu Ph.D. Candidate Department of Biological Sciences, Marquette University

2 2

Multiple transparent objects
by Daniel Asarnow 12 Dec '16

12 Dec '16

Hi, I'm having some trouble with a movie of a morph between structures of the same protein bound to two different ligands. The basic idea is a closeup of the binding pocket, and as the morph progresses the initial ligand becomes transparent while the second one becomes opaque. The result is a similar effect to crossfade, only the morph animation is playing simultaneously. I've tried both the screen capture and ray tracing methods, with the following results: Screen capture - When a ligand is almost entirely transparent, a white silhouette is shown at the highest z-order, blocking what's behind. - There is a "pop up" effect when the ligands suddenly switch z-order at the beginning and end of my animation. - Single-layer and flat transparency options don't help. Ray tracing - Multiple transparency is fine. - Reflections and shadows are not made transparent. - E.g. when one ligand is 100% transparent, the reflections and shadows are still visible as white lines and dark spots. Maybe someone here has some insights on my transparency problems? A way to use crossfade instead would be even better. I can record movies with the two ligands separately and then crossfade them manually with ffmpeg. However, it would be nice to have this working entirely in chimera, especially for some more complicated animations I have in the works. Best, -da

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.pyc session file
by Luca Pellegrini 12 Dec '16

12 Dec '16

Hi, How can I open in Chimera a saved .pyc session file? When I try, Chimera reports the following error message: Error while processing /Users/lp212/Dropbox/<filename.pyc>: .pyc files are not portable; please use .py file instead Unfortunately I don’t have the .py file, Chimera doesn’t seem to have saved it (not sure why). Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

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Selective lighting
by Oliver Grant 12 Dec '16

12 Dec '16

Hi all, Is it possible to use the lighting command and have it apply only to particular models? I'd like my ligand to "pop" out by having a light that only shines on it, and not the protein. Oliver

2 2

Fit-to-window for procedurally generated images
by Mike Sivley 09 Dec '16

09 Dec '16

I am procedurally generating images of protein structures using a Chimera python script. I can center the protein structure within the viewing window, align the protein to emphasize certain elements, set the output size of the final image, and manually apply a scale factor to the view, but I have not found a way to ensure that the protein structure is maximized (but fully contained) within the final image. Is there a "fit-to-window" command that will automatically scale the view in this way? Thanks! Mike Sivley

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How to find symmetry parameters for icosahedral molecule
by Haselbach, David 08 Dec '16

08 Dec '16

Hi everyone, sorry to ask such a basic question. I have a cryo EM density map 3.2 A of a icosahedral molecule and I already build the model of the monomer. I would like to place the remaining 59 copies and calculate the BioMT matrix for it. I started playing around with the sym command, but I couldn't get it working nicely. It's probably a problem of the coordinate system, but I couldn't figure it out. Than I thought there must be an automatic way and I tried Multifit but also this failed me miserably as the runs fail continuously with "stderr". So I was wondering is there a protocol to do this? Already thank you for any suggestions, David Dr. David Haselbach Max-Planck-Institute for biophysical Chemistry Department for structural Dynamics Am Fassberg 11 37077 Germany Tel. +495512011302

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symmetry axis
by chemocev marker 08 Dec '16

08 Dec '16

Hi All I am interested to measure the symmetry axis of individual sub-unit (chain A & chain B) along with the symmetry axis of the heterodimer (AB). Each chain has 2 domains and 2 fold rotations axis, and I can measure by removing 1 chain and measure for the other. Is there way to measure the inter-domain symmetry axis of the heterodimer molecule. best Jiri

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Fwd: chimera minimize option
by Jacqueline Vitali 07 Dec '16

07 Dec '16

It puckers ASN and ASP (and probably other amino acids). (I run it to relieve steric conflicts only) How do you fix this? And can you run it with the whole protein selected?

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question
by A G Szabo 06 Dec '16

06 Dec '16

You have been very helpful in explaining different items that use the command line. I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc. So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number. I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model. Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec <frameatom_spec.html> I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1. So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly. Thank you Arthur G. Szabo

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Re: [Chimera-users] Chimera -> Povray
by Elaine Meng 05 Dec '16

05 Dec '16

Hi Lothar, If you use "File… Export Scene” (instead of Save Image) or the “export” command, there is an option to save a file for POV-Ray without rendering: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> 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 > On Dec 5, 2016, at 3:07 PM, esserlo(a)helix.nih.gov wrote: > > Hi, > currently, I am using chimera to make a figure for publication and render > the result in povray. However the figure is a bit complex - with a gradient > background just to mention one thing- so that I have to edit the .pov file. > Is there a way to ask chimera to output the .pov file but not render it in > povray right away (that would save time as I need to edit it first!). > > Unfortunately in the "save image" menu, using povray, I did not find a > checkbox that would enable chimera to write out .pov only. > Thanks for any advice. > Lothar >

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difficulty in using chimera for large PDB files
by Shruti Khare 05 Dec '16

05 Dec '16

Dear Sir/Madam, When we use chimera to visualize PDB files with ~18,000 atoms (PDB ID 5FUU) even rotating the molecule is slow in chimera. The computer has 6GB RAM. Would upgrading RAM help or we need to get a graphics card installed? Graphics card capacity should be 2GB or higher? Could you please tell me the minimum computer configuration required by chimera to handle large PDB files? Also what is chimera's maximum limit for handling PDB files given a computer with very good configuration? Thank you. -- Shruti Khare Graduate Student Prof. Raghavan Varadarajan Lab Molecular Biophysics Unit Indian Institute of Science Bangalore +91-80-2293-2612 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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pipes and planks
by Kyle Morris 03 Dec '16

03 Dec '16

Dear Chimera dev, I am using the pipes representation. In this case is it still possible to color/highlight a segment by residue number? Using the normal commands when displaying pipes doesn’t update the color, only on the original model. Thanks for your help! Best wishes, Kyle

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Selected measure angles
by Soumya Govinda Remesh 02 Dec '16

02 Dec '16

Hello, I have just modified the loop script available here ( http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html) to measure certain angles and distances. I just want to know if there is a way to export the individual values of angles and distances to a file other than parsing from the reply-log. Thank you. 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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saving pdb with transformed coordinates
by Michael Elbaum 01 Dec '16

01 Dec '16

Dear Chimera people, I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates. I've tried the following: for i in xrange(0,90,10): rc("rock " + "y " + str(i) + " 1") fn = basefn + str(i) + '.pdb' rc("write format pdb 0 " + fn) and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11. thanks for your help, Michael

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Unit cell
by Neha Gandhi 01 Dec '16

01 Dec '16

Hi Elaine, I have tried to look at the unit cell information of pdb Id :3HR2. It is a fiber diffraction structure of collagen with only CA coordinates. I tried using different programs like VMD to visualise unit cell, the unit cell is at the beginning of N terminus in agreement with experimental paper. Whereas in Chimera it is not the case. How can I visualize the unit cell of 3HR2 structure in Chimera and also number of molecules within one unit cell? Many thanks, Neha -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate

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Re: [Chimera-users] failing to open saved PDBs
by Healey, Joe 01 Dec '16

01 Dec '16

Hi Elaine, OK, that is what I had expected to happen yes - and that NMR ensemble looks to be what I was anticipating. I've attached the PDB chimera created here. I'm no expert on PDB internal formatting but it at least looks to me like there are coordinates, sequence information etc etc. I had thought that I had taken care to make sure whole models were saved (not just sel atoms), but I'll replicate it to make sure. Applying the preset in any event didn't work. Maybe you can spot what's wrong with it? Joe Healey M.Sc. B.Sc. (Hons) 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>

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more questions about visualizing the backbone.
by A G Szabo 30 Nov '16

30 Nov '16

Last week I asked a question regarding about how to visualize the backbone atoms. I have figured that out. I am working with a peptide that forms an amyloid structure. The peptide strands form a beta sheet. When I select two of the peptide units that are hydrogen bonded to form two strands in the beta sheet, the strands are shown as a coil type structure rather than a flat beta strand. How can I change the coil backbone to a beta strand structure? Second part is there a simple way to suppress the side chains but leaving the backbone atoms? I have included two peptide units that are hydrogen bonded to one another. Thanks Arthur G. Szabo

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Ca-Ca difference plot
by Luca Pellegrini 30 Nov '16

30 Nov '16

Hi, I have superimposed two structures of the same protein in two different conformations, and now I would like to calculate a plot of the distances between alpha carbons for each residue in the two conformations, to quantify the relative movement of different domains in the protein structure. Can anyone please explain a simple way of doing this in Chimera? Apologies if I missed something obvious, I tried 'RR distance maps' but couldn’t figure out how to do this simple task. Best regards, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

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Visualizing Orientation of Side Chains
by Christian Bock 30 Nov '16

30 Nov '16

Hello, I am new to Chimera and want to visualize how the side chain orientation for a specific residue changes in different structure predictions. Means I have a correct structure and several predictions and I want to see how different the orientations are among the predictions with reference to the correct structure. I was looking at the MD movie but I am not sure if it's smart to put the correct structure and all predictions into one .pdb file to make a movie. Does anyone has other suggestions? Thanks, Christian

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using Chimera to superimpose structures using sequence alignments
by Elaine Meng 28 Nov '16

28 Nov '16

Hi Deepak, You would still have to show the Chimera GUI (it cannot be done running Chimera with no GUI), but if you mean using a script instead of interactively choosing menu items, it may be possible. However, there is no Chimera command to do this. It would require a Python script. For future reference, we recommend sending Chimera questions to the chimera-users(a)cgl.ucsf.edu list (which I CC’d here, so you do not need to re-send this question). Since today is a holiday, and I do not know Python, somebody may be able to help you with this question next week. 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 Nov 24, 2016, at 3:08 PM, Deepak Kumar <deepakk1(a)andrew.cmu.edu> wrote: > Dear Dr. Meng, > I am a Bioinformatician at the Computational Biology Department of Carnegie Mellon University. I have been using Chimera for visualization purposes and for many other of its features. I got to learn about your expertise from here: > > http://www.cgl.ucsf.edu/home/meng/index.html > > May I please request you to give your suggestions on this problem mentioned below: > > I know of one feature "multialign viewer" which uses a fasta alignment file to superimpose two pdb structures in Chimera. However, I have been using this feature through the GUI of Chimera. I am in need of using this feature standalone i.e superimpose two pdb structures based on a fasta alignment file. May I please request you to let me know, how can I perform this step standalone and not through Chimera GUI. > > Thank you so much for your time and consideration. > Yours Sincerely, > Deepak

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On the adding of the dynamics effect on the static structure
by James Starlight 28 Nov '16

28 Nov '16

Dear Chimera Users! I am interesting whether it possible to add some impression of the dynamics to some static elements of the pdb? Assuming that I am working with the visualisation of static x-ray structure and would like via some vizualisation trick to add some element of the conformational dynamism (like what can be obtained from the md trajectory or nmr ensemble) to the selected fragment of the structure (e.g loops or alpha-helix) eventually making impression of the several conformers superimposed on the structure? Thanks so much for any suggestions! James

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FW: Channel and normal mode calculations
by Williams, Joanne 28 Nov '16

28 Nov '16

On 11/28/16, 8:43 AM, "Mohamed Noor" <mohamed.noor(a)ul.ie> wrote: >Hello. > >I am wondering whether Chimera can do these calculations natively? Or do >I need some plug ins? > >Thanks. >Mohamed

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failing to open saved PDBs
by Healey, Joe 28 Nov '16

28 Nov '16

Hi (again) Chimera Team! Encountered a problem where chimera seems to fail to open PDBs that it created. I saved multiple PDBs to a single file as I wanted to open them and have them behave like a single structure. I started a new session with another PDB open that I want to compare the multiple PDBs to, went to open the multiple PDBs from before that I saved as a single file and nothing appears. Chimera claims to have opened the files successfully and I get no errors etc. Am I maybe misunderstanding the point/use of the multiPDB file form? Joe Healey M.Sc. B.Sc. (Hons) 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>

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Fit in map equivalent for surfaces?
by Healey, Joe 28 Nov '16

28 Nov '16

Hi Chimera Team, Is it possible/does a function exist to fit one structure inside the calculated surface of another? To be clear, i don't mean inside a density map, I mean an MSMS surface calculated from a PDB inside chimera itself. I have 2 proteins that are sequentially very different, but I suspect fulfilling the same role. They don't overlay via MatchMaker well, but they look to have quite similar space occupation, so I'd like to see how well they fit in one anothers 'map'. Any alternative suggestions appreciated! Thanks, Joe Joe Healey M.Sc. B.Sc. (Hons) 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>

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angle between subunits
by chemocev marker 26 Nov '16

26 Nov '16

Hi All I am interested to measure the angle between chain A and chain B of heterodimer, and both sequence identity is around 14%. I can measure the angle by selecting 3 atoms on chain A and chain B but this is bias because, if I change the residues then the angle will be different. I can also measure by structure measurement options and defining the axes and all the create axes for all the helices in the chain A and chain B and measure the angle between two helices on chain A and chain B. I am not sure if its a right way to claim the angle between chain A and chain B in one PDB file. I also try to use the "match :.A at CA <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> :.B at CA <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> move false show true" But it gives the rotation angle. As I am comparing the different homologous structureswhere chain B shows more identity but the each structure have a different state giving a unique angle between chains. What can be best option to measure this??? best Jiri

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simple question
by A G Szabo 25 Nov '16

25 Nov '16

I should be able to find this but haven't looked too hard. I am interested in a salt bridge between the C-terminal carboxylate and a Lys residue in the protein. I know how to visualize the Lys side chain, and the C-terminal residue. How do I visualize the carboxylate terminus? I tried backbone only actions, but nothing worked. Thanks AGSzabo

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Sequence tool
by Hernando J Sosa 23 Nov '16

23 Nov '16

Dear all Is there a way using the sequence (or any other) tool in chimera to save a text file with sequence and corresponding secondary structure assignments as displayed in the sequence tool. Thanks Hernando

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usage of mcopy
by Jiying Jia 23 Nov '16

23 Nov '16

Hi, I want to use python script to adjust the bond angle randomly and only accept the case if the random new angle is larger than old one. I use "mcopy" to recover the old angle if the new is smaller. But I encounter a problem: if I use "mcopy #old #new setting a" or "x" or "y", the after "adjust angle anglenew" command, the angle adjusted is not the anglenew, but a different one. I don't know why. I hope anyone can solve my problem.. Below is the python script and init.mol2. PYTHON SCRIPT: import os import time import chimera import random from chimera import runCommand as rc from chimera.tkgui import saveReplyLog import MoleculeTransform from MoleculeTransform import transform_atom_coordinates import numpy as np import sys import re #open initial conformation init.mol2 opened = chimera.openModels.open("init.mol2")# opened as model 0 in chimera chimera.openModels.open("init.mol2") # opened as model 1 in chimera, used to store old conformation in monte carlo simulation rho = opened[0] print "angleold anglenew angle_after_adjust" for pdbi in range(0,20): random_atom = 1 an0 = rho.atoms[random_atom-1] an1 = rho.atoms[random_atom] an2 = rho.atoms[random_atom+1] angleold = chimera.angle(an0.xformCoord(),an1.xformCoord(),an2.xformCoord()) anglenew = random.random()*180 rc("adjust angle %f %s %s %s"%(anglenew,an0.oslIdent(),an1.oslIdent(),an2.oslIdent())) angleafter = chimera.angle(an0.xformCoord(),an1.xformCoord(),an2.xformCoord()) print str(angleold)+" "+str(anglenew)+" "+str(angleafter) if anglenew>angleold: rc("mcopy #0 #1 settings x") else: rc("mcopy #1 #0 settings x") rc("close all") rc("stop now") INIT.MOL2: @<TRIPOS>MOLECULE init.mol2 3 2 3 0 0 NUCLEIC_ACID NO_CHARGES @<TRIPOS>ATOM 1 C 1.7324 -0.5083 0.8663 C.3 1 DA 0.0000 2 C -0.6180 0.4940 -0.0060 C.3 2 DA 0.0000 3 C 1.2450 0.9460 1.8950 C.3 3 DA 0.0000 @<TRIPOS>BOND 1 1 2 1 2 2 3 1 @<TRIPOS>SUBSTRUCTURE 1 DA 1 RESIDUE 4 A DA 1 ROOT 2 DA 2 RESIDUE 4 A DA 2 3 DA 3 RESIDUE 4 A DA 1

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How to place a small volumed object in place of markers in marker set?
by BRANDEN WAYMON WEST 23 Nov '16

23 Nov '16

How do I place an object with small volume in the locations of markers in a marker set? Essentially, I would like to replace the sphere markers with copies of my own object. This is my first post in this mailing list. I very much appreciate all of your help. Thank you. Branden West

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how to find clashes/contacts for residue of our interest?
by Seera Suryanarayana 23 Nov '16

23 Nov '16

Dear chimera users, I am new to chimera and I looked into the manual. But I did not get perfectly that how to use find clashes command. I would like to know clashes/contacts of residue of my interest. But I am not able to select the residue in graphical interface under select tool. Kindly tell me how to find clashes/contacts ASP32 in a protein. Thanks in advance Surya Graduate student India.

2 1

Rotating marker sets
by Kacher, Joshua P 23 Nov '16

23 Nov '16

Hello, Is there a way to rotate marker sets? I have a 3D crystal system that is defined by a hexagonal coordinate system. I can load in a marker set in the form of a hexagon to act as the coordinate axes, but I need to then rotate the marker set to align it with my system. So far, I've only been able to see how to move one marker at a time, not the entire marker set. Thanks, Josh -- Josh Kacher Assistant professor Georgia Institute of Technology KacherLab.gatech.edu

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Render by Attribute - Radii and individual radius for each HETATM
by Kuda Ondřej 22 Nov '16

22 Nov '16

Hello, I have a path (chain of heteroatoms with defined radii, see below) forming a pore in a protein. I would like to create an envelope (surface view) to illustrate the 3D path within the protein. My problem is that Chimera uses default vdw value and not the values I defined. Therefore, the "pore" has a constant diameter. According to https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm… , I tried "Render by Attribute - Occupancy - Radii". I assumed that the VDW values are rendered for each HETATM according to the input, but it seems that the VDW values are sorted (smallest > largest) and then applied on the chain starting from #1. Therefore, it creates kind of a funnel structure. Could you please suggest how to create this tunnel with variable width? Thank you. Best, Ondrej REMARK ATOM NAM RES TUNID X Y Z Distnm RadiusA HETATM 1 X TUN T 1 -45.770 -35.888 -4.154 0.00 2.01 HETATM 2 X TUN T 1 -45.766 -35.893 -4.132 0.02 2.03 HETATM 3 X TUN T 1 -45.762 -35.897 -4.111 0.04 2.11 HETATM 4 X TUN T 1 -45.759 -35.901 -4.091 0.07 2.16 HETATM 5 X TUN T 1 -45.756 -35.903 -4.073 0.08 2.14 HETATM 6 X TUN T 1 -45.755 -35.903 -4.057 0.10 2.17 HETATM 7 X TUN T 1 -45.756 -35.901 -4.045 0.11 2.10 HETATM 8 X TUN T 1 -45.758 -35.896 -4.037 0.12 2.01 HETATM 9 X TUN T 1 -45.763 -35.888 -4.032 0.13 2.01 HETATM 10 X TUN T 1 -45.770 -35.876 -4.033 0.15 2.00 HETATM 11 X TUN T 1 -45.779 -35.861 -4.037 0.16 1.99 HETATM 12 X TUN T 1 -45.787 -35.843 -4.039 0.18 1.97 HETATM 13 X TUN T 1 -45.794 -35.822 -4.034 0.21 1.95 HETATM 14 X TUN T 1 -45.796 -35.800 -4.017 0.23 1.93 HETATM 15 X TUN T 1 -45.792 -35.777 -3.984 0.27 1.92 ________________________________ This email was scanned by Bitdefender Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato E-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Fyziologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Fyziologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Physiology CAS. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract; nor does it create any pre-contractual liability on the part of Institute of Physiology CAS.

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read dcd from openMM simulations
by Michał Kadlof 22 Nov '16

22 Nov '16

Is there any way to read dcd trajectory from openMM simulation? Example in attachment. OpenMM does not produce psf or prmtop files :( -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 1

Reflection symmetric
by Grzegorz Bokota 22 Nov '16

22 Nov '16

Hi, I need to apply isometry and shift to volume data. In cmap file format it is possible to do rotation but to have isometry I need to can do symmetric reflection. Ir is possible with any chimera format? I found that there is "symmetries" parameter in cmap file format, but i do not seen any effect. Sincerely, Grzegorz Bokota

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merging maps
by Elaine Meng 21 Nov '16

21 Nov '16

> On Nov 21, 2016, at 6:46 AM, Ignatiou, Athanasios <athanasios.ignatiou.13(a)ucl.ac.uk> wrote: > > Hello Elaine, > I have a quick question: > do you know how to merge 2 separate cryo-EM maps (of the same object which are are scale correctly) into one new cryo-EM map in Chimera. > cheers > Thanos Hello Thanos, If by merging you mean simply adding the values, take a look at the “vop” (volume operations) command. It includes “vop add” and several other subcommands: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html> We recommend sending Chimera questions to the chimera-users(a)cgl.ucsf.edu address (CC’d on this message). 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

surface transparency to particular residues
by chemocev marker 20 Nov '16

20 Nov '16

HI All I am completely new to chimera and I am wondering if there is a way to set the surface transparency to just a particular region, not to the whole surface. best Jiri

2 2

scrolling
by Dougherty, Matthew T 18 Nov '16

18 Nov '16

I want to completely avoid changing the scale factor keeping it at 1.0. Instead I want to rely on z translation of the camera. I disable scrolling on the mouse in the chimera preferences. This works. On my Mac laptop I am noticing zoom on the trackpad changing the scale factor. How do I stop that? I have zoom disabled in Mac system preferences. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

2 1

REST Server
by Anatoly Chernyshev 18 Nov '16

18 Nov '16

Hello, is there a way to specify a port number when starting REST Server? Thank you. Anatoly

2 1

Chimera-Modeller interface, template selection
by Dina Schneidman 17 Nov '16

17 Nov '16

Hi, Currently it is only possible to select a template from PDB based on the PDB code. Would it be possible to have an option to use one of the currently open PDB files in Chimera? Thanks! Dina

3 4

split ligands and H-bonds
by Markus Heller 16 Nov '16

16 Nov '16

Hi, I have a structure of a complex (I tried with several, but here's one example: 3t07). I want the stick radii for protein and ligand to be different, so I "split ligands" and then set the stick scale in the attributes of the respective model. When I then try to detect H-bonds between the ligand and the protein, none are found! They are found, however, when detecting them prior to splitting the model with "split ligands". I've tried several settings in the Find Hbond dialog: Find inter-model, intra-model, both: no difference. Restrict to the models the H-bonds are between: no difference. Select the ligand and the protein residue participating in the H bonds and using "Only find H bonds with both ends selected": nothing, no H bonds found. Why is that? Thanks and Cheers Markus

2 2

Question: Dock Prep
by wang_q＠tib.cas.cn 14 Nov '16

14 Nov '16

Dear Colleagues, I am a beginner in docking(using DOCK 6.7). I learned from DOCK6 tutorial that I could use UCSF chimera to prepare my inputs file for DOCK6 and I prepared the inputs mol2 format file ( converting from PDB to mol2) successfully indeed. And now I have a question, is there a way that I can use in commend line to convert PDB to mol2 format file in chimera, because I want to use this format conversion function in server. I would be very grateful if someone could help me solve the puzzle. Thanks very much! Aaran 发送自 Windows 10 版邮件应用

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