- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Cannot resample to voxel size of 1
by Tom Goddard 23 Jul '19

23 Jul '19

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

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

22 Jul '19

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

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

22 Jul '19

Hi, Trying to color a volume according to "volume data" I get the same numerical values for all colors and a speckled appearance. When using "volume data gradient norm" I get the expected colors, i.e. strong local changes of the volume data are red and spots where there is essentially no change are in blue. How is this possible? If I understand correctly, "volume data gradient norm" colors according to the first derivative of "volume data" or is this wrong? Do I need something like a normalization? Thanks a lot for explanations, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Fitting the structure into the map after changing origin
by Ahmad Khalifa 22 Jul '19

22 Jul '19

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

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RMSD Chimera
by Ishita Gupta 22 Jul '19

22 Jul '19

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

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Measurement similarity protein structure
by Nail Besli 19 Jul '19

19 Jul '19

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

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

19 Jul '19

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

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

18 Jul '19

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

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

16 Jul '19

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

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

16 Jul '19

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

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visualizing distance restraints using Chimera
by Matthew Fountain 16 Jul '19

16 Jul '19

Is there any way to import a list of distance restraints and have Chimera display them based on the restraint violation. -- Matthew Fountain Professor and Chair Fredonia State University of New York Chemistry and Biochemistry Department

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Export morph confirmation scene to 3D Studio Max
by Edel Fenix 16 Jul '19

16 Jul '19

Hi, I just discovered Chimera and love the morph confirmation function! Amazing! I would like to export a full morph confirmation scene with surface render from Chimera with all frames in a format that I can import in 3D Studio Max as a complete animation. I can import individual OBJ but not what I am looking for with higher number of frames. I've tried all formats Chimera can natively export as but I can not open any of them in 3D Studio Max. Has anyone done this? Didn't find a relevant prior post when I searched. Is there a way to export formats multiple times to achieve this? Deeply appreciate any help in finding a solution. Best regards, Edel

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command lines to replace "joint models"
by wangdj7＠mail.ustc.edu.cn 15 Jul '19

15 Jul '19

Dear Chimera developers, I'm so sorry to interrupt you. I have to run Chimera in Linux,but there is no command line of "joint modeles".I need to get 2 modified amino acids or peptides together and not creating crashes.In windows,"joint models" is my best choice,it's very convient and perfect.But in Linux,I tried some command line,such as "combine","bond",but it can't automatically repositioning the models and the structure was not right. So,could you please tell me how to use command lines to replace "joint models" function? Thanks in advance Best Regards Daojiong Wang

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Parse error Chimera
by Dorfner, Maja 15 Jul '19

15 Jul '19

To whom it may concern, Using Swissmodel, I have constructed a model based on an original PDB file. NAP is part of this model. The docking works when the option of either "Ignore chains of non-standart residues" or "Ignore all non-standart residues" is chosen as false. The Problem is that in the PDBQT file of the receptor shows that NAP was not considered during the docking, making the Substrate float either within the NAP or to far from it. The docking worked fine with the original PDB file but not with the newly modeled one. Could the problem be that the NAP is a separate chain? I have already tried to erase the H before using AutoDock Vina. Here is the Reply log: Running AutoDock Vina for PmWT.pdb failed; see Reply Log for more information Application stderr ----- Parse error on line 3578 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. ----- Application stdout ----- ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, Journal of Computational Chemistry 31 (2010) # # 455-461 # # # # DOI 10.1002/jcc.21334 # # # # Please see http://vina.scripps.edu for more information. # ################################################################# Detected 4 CPUs Reading input ... ----- Thank you for your patience. Sincerely, Maja Dorfner

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Surface render error in MD movie for morph conformation
by Edel Fenix 15 Jul '19

15 Jul '19

Everything works at the basic level and has produced very useful data and animations. I am most grateful for these tools and your help. The BIG problem I have is that for some frames no surface is rendered at all. Other parts "magically" disappear and reappear during the transformation. *What I would want to do:* 1. There are missing structures/regions in need of repairs in the PDB files I work with (see attached screenshot example). The files are for the same protein but different regions missing in different models and they differ some, ideally they shouldn't. I am using Chimera and Modeller to repair these with loops/refinement. Ideally I would want to match/alter the proteins so the gaps connect correctly and their amino acid structure is the same for all models. I feel like this may be the/one cause for the surface errors when rendering? I've tried using modeller both locally and the web service so I have verified installation, integration and function. Must I generate multiple drafts and manually review and select the one best corresponding or is there a way to get it performed for all models loaded of the same protein? Further, if I want them to have the same genetic makeup, can I somehow use one as reference to alter the others? 2. Align the protein snapshots from the configurational change using matchmaker (works great!). 3. Use morph conformation to generate an animation of the configurational change with surface rendered. Works sort of, with errors for some frames where no surface is rendered at all or regions magically appearing/disappearing. 4. Solve the surface error I get, see attached error message :( If I use split copying from the example page, the model looks nothing like it should look like and more like boiling gruel. I am not experienced with Chimera but I feel like if I ensure the files have no gaps and are structurally identical with the same amino acid makeup it may work as is? *The problems with existing suggested solutions:* The link below present 4 possible solutions linked from the error message. Solution 1 looks nothing like what I want when rendered in my test. Solution 2 does not solve the issue of disappearing structures magically appearing again. I am not sure of the cause but could be because the models have different structure/missing parts. If repaired and matched across all protein models in the animation might work? If so, might not even give an error message? Looks viable but does not solve the problem. Solution 3 is not viable as I am looking to render the surface in details, not "overall" look for large structures. Solution 4 is not applicable as I do not want CPK. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html Any help would be greatly appreciated, Edel [image: Screenshot 2019-07-15 at 12.05.12.png] [image: Screenshot 2019-07-15 at 14.30.00.png] )

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Integer Values instead of Floats in Render by Attribute
by Daniil Prigozhin 11 Jul '19

11 Jul '19

Hello, I am using the latest nightly build and in the Render/Select by attribute window the values in the Value box (defining the color scheme) are reported as integers and accept only integer input, when in fact the Attribute that I defined is a float, and shows up as a float. This does not happen with "native" attributes, only with the newly defined one. Is it a problem with the defattr function not determining/passing the data type correctly? I am pasting the top of the attribute deffinition file below. Many thanks, - Daniil attribute: shannonEntropy match mode: 1-to-1 recipient: residues #0:1.L 0.865 #0:2.L 0.743

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Issue regarding Chimera-Vina
by Prabuddha Bhattacharya 11 Jul '19

11 Jul '19

Dear Sir, I am a beginner in the field of molecular docking. However, I started doing it using Chimera Vina. UCSF Chimera 1.13rc provides the interface while AutoDock Vina does the docking part. For a couple of cases I have found that inspite of keeping all the parameters same, the best obtained dock scores are coming different for each individual job-run. Is it so because it is a stocastic method? With such different dock scores, what should I do? I will be extremely grateful of you can kindly address this issue. Thanking you in advance, Best regards -- *Prabuddha Bhattacharya *

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Structure overlay
by Chakraborty, Joydeep 11 Jul '19

11 Jul '19

Dear all, I am trying to overlay two structures. 1. Wild type enzyme and 2. A mutant, with a single point mutation on the wild type. However, somehow when I am opening the structures, both are overlapping automatically and showing as one structure. I need to have two separate strands overlay, so I can show the change in the active site pocket. I was hoping if anyone could shed some light on this issue. Thanks, Joydeep.

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Volumes comparison
by Dmitry A. Semchonok 09 Jul '19

09 Jul '19

Dear colleagues, How to compare 2 volumes in Chimera by cross-correlation? Thank you. Sincerely, Dmitry

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Associate Scientist/Scientist Position in Protein Engineering
by Andrew Waight 07 Jul '19

07 Jul '19

Dear Chimera Users We are seeking a fresh phD graduate or postdoc with a structural, biophysics or computational background to join our group. This is an excellent opportunity for anyone looking to break into the extremely desirable field of antibody engineering for immuno-oncology. The position entails the design, cloning, purification and in vitro testing of multispecific antibody type molecules. The training involves in silico design (including MD analysis) molecular biology, HEK and CHO expression, Antibody purification and biophysical analysis including SEC, MALS, DLS, RP, Mass Spec, Kinetic analysis (Octet) Binning, Humanization, and *in vitro* validation including FACs analysis, immune cell activation and cancer cell line killing assays. Although experience is not necessary, we expect interview candidates to have researched the above topics thoroughly and to express and explicit interest in the field of protein engineering for immuno-oncology. If interested, please see the link below and feel free to contact me personally with any questions. So sorry to the rest of Chimera-users for the spam. https://www.linkedin.com/jobs/view/1358848339/

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Question regarding RR Distance Maps
by Meysam T. Chorsi 03 Jul '19

03 Jul '19

Hello, I need to use Chimera to determine the distance map, but for some reason the output matrix is not symmetric. I used other software as well, they all giving a symmetric matrix which makes sense to me. Could you please let me know how can I fix this? Thank you Sincerely, Meysam -- *Meysam T. Chorsi* *University of Connecticut * *191 Auditorium Road, Storrs, CT 06269, USA*

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Cylinder coloring extension
by Thomas Marcellino 03 Jul '19

03 Jul '19

Dear Chimera Team, I am aiming to color a stucture according to the B factor and represent it as a cylinder (pipes and planks) is there any possibility to apply different colors within the same cylinder or assign the coloring scheme to the cylinder representation in the same way as doing it with surface ? Looking forward to an answer, Thank you for your time reading my suggestion. Thomas M

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Creating a smooth disk
by Henrique C. S. Junior 02 Jul '19

02 Jul '19

Dear list, I'd like to create a disk that didn't show lines in the surface depending on the orientation angle (see the image attached). Right now I can clearly see that the circle is formed by several triangles, so I'd like to smooth things up. I can actually get rid of the triangles by disabling the silhouette of the plane, but I'd like to keep it to show where the plane ends. Thanks in advance -- *Henrique C. S. Junior*

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Volume save after volume changes
by Ryan Harlich 01 Jul '19

01 Jul '19

Hi Chimera, I am having problems saving changes of volume. Here is my script: 1. open C:\Users\ Desktop\density.map 2. volume #0 level 1.0 3. sel #0 4. volume sel save C:\Users\ Desktop\density2.mrc This does not save the change at line 2. How can I go about to save the change? Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Saving .pdb file in location of .mrc file
by Ryan Harlich 27 Jun '19

27 Jun '19

Hi Chimera, I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1. So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1. An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Looking for an image...
by David Cohen 27 Jun '19

27 Jun '19

Hello, Let me preface this by saying that I am not a user of Chimera, I just find the images it creates interesting. My name is Dave and I have a metal band we have named Entropathy. Don't go looking for us on the internet, we aren't anywhere yet, just a bunch of guys in my studio making loud crazy music. The band name is a mashup of Entropy and the suffix "pathy" a condition we have defined as "A degenerative fixation on the ultimate disintegration of all matter". I was surfing the internet looking for some kind of images that would fit as an album cover and came across a few of Chimera's images. I was wondering if you might have some older images sitting around nobody has licensed that might be considered an artistic rendering of molecular entropy. We don't really have any money to spend, but I thought I would reach out and see if you had something that would be of interest to us and would not be an issue to share. Thank you for your time, David Cohen Progammer, Writer, Musician, Dad (not necessarily in that order) djcohen66(a)gmail.com

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Re: [Chimera-users] Sudden Chimera issues with OSX Mojave?
by Geoffrey Sametz 27 Jun '19

27 Jun '19

You may already know this, but: the latest Tk (8.6.9) doesn't play well with tkinter. Python's solution seems to have been to bundle 8.6.8 with new installs. In my own projects I installed 8.6.8 to regain functionality. I posted an answer to a related question on stackoverflow and included links: https://stackoverflow.com/questions/54957374/tkinter-window-opens-as-black-… --Geoff Sametz On Wed, Jun 26, 2019 at 2:41 PM <chimera-users-request(a)cgl.ucsf.edu> wrote: > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 26 Jun 2019 10:58:21 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: Neil Rzechorzek <njr48(a)cam.ac.uk> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Sudden Chimera issues with OSX Mojave? > Message-ID: <E66B6410-56F4-46D9-8596-C5AD33EE4C8D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Neil, > I don?t know why your systems would have started having problems > in the last 48 hours. Nonetheless, I suggest you try using the daily build > instead of the production release. The daily build uses a newer version of > the Tk windowing toolkit that Chimera relies on to draw windows, handle > scrolling, etc. and that newer version in particular has some fixes for bad > scrolling behavior. If the daily build fails to remedy the problem, try > using Chimera?s Help?Report a Bug to make a bug report. The bug report > will include many details of your hardware and software setup that will > help us investigate the problem. > > ?Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > > > > -- Dr. Geoffrey Sametz QDH 104 Department of Chemistry and Biochemistry University of Delaware sametz(a)udel.edu (302) 831-3621

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coloring mmCIF files
by Josef Sprinzak 27 Jun '19

27 Jun '19

Dear Chimera Support I am a developer of consurf (http://consurf.tau.ac.il/) for displaying evolutionary conservation of amino/nucleic acid positions in a protein/DNA. Till now we have been working with PDB files and inserting the coloring values in the b-factor (temperature) field in the ATOM part. In the chimera script we use the color commands: color CONS1 @/bfactor=1 color CONS2 @/bfactor=2 color CONS3 @/bfactor=3 ... Now we wish to start using mmCIF files. Where should we insert the coloring values in the mmCIF file, and how do we reference then with the chimera commands ? Best Josef

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Sudden Chimera issues with OSX Mojave?
by Neil Rzechorzek 27 Jun '19

27 Jun '19

Dear Chimera users, Has anyone else started seeing issues with the latest stable version of Chimera on OSX Mojave? We have two new identical systems that were running perfectly as recently as 48 hours ago, but now Chimera is constantly crashing whenever we do something as trivial as File>Open or if we attempt to save a map. To our knowledge there has been no update to Mojave, and we haven't changed our Chimera installation. An example of the error log generated by Chimera when trying to, for example, save a map is: while executing "4642906592_scrollBothNow" ("after" script) File>Open windows do not scroll properly, and will instantly crash the entire program unless we change preferences to 'Open dialog starts in directory from last session = false' Does anyone know of any recent (last ~36 hours...) changes to any supporting software? We're wondering whether there has been some silent security update at Apple that has interefered with, for example, the windowing toolkit? Many thanks, Neil -- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk Biochemistry Enterprise Champion www.enterprise.cam.ac.uk Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk Email: njr48(a)cam.ac.uk Tel: +44 (0)1223 333652

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time counter
by CLARA BLANES MIRA 27 Jun '19

27 Jun '19

Thank you all!!!. I am going to try all your suggestions, with chimera commands script and with chimera python script (this is still too much for me!!, but I will try with your directions). Thank you all again for your fantastic work and your attention! All the best, clara

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time counter
by CLARA BLANES MIRA 26 Jun '19

26 Jun '19

Dear chimera users, I have two doubts regarding per-frame actions: 1) I am trying to add a counter in my script (commands script, no python script). It works when I do it as a per-frame action in the MD Movie window (just as Elaine does in the’Trajectory and ensemble Analysis Tutorial’) but I am not able to do insert it in my command script: Something like this: movie record 2dlabels create timer text “frame 0" size 40 color white alias ^actions 2dlabels change timer text "frame <FRAME>" perframe actions; coordset #0 1,216000,1000 load false; wait 216; ~perframe movie encode movie.mp4 2) What I really want is to show nanoseconds, not frames. In my case 1000 frames = 1 ns. When I write frame <FRAME>/1000 in MD Movie window, obviously, it does not work. Any suggestion to make it work and insert it in the commands script? Thank you very much!, Clara

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Unsubscribe
by Ina Oestroem 26 Jun '19

26 Jun '19

Hi, I'd like to unsubscribed. Thank you Ina

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installing vintage chimera
by Francesco Pietra 25 Jun '19

25 Jun '19

Hello Although, as a chimera user, i use the latest linux release, I was also interested to install chimera-1.1442-linux.exe francesco@vaio64:~/tmp$ chmod 755 chimera-1.1442-linux.exe francesco@vaio64:~/tmp$ ./chimera-1.1442-linux.exe bash: ./chimera-1.1442-linux.exe: No such file or directory francesco@vaio64:~/tmp$ ls -ls 20420 -rwxr-xr-x 1 francesco francesco 20909040 Jun 25 10:59 chimera-1.1442-linux.exe I also tried chimera-1.1602-linux.exe and chimera-1.5-linux.bin with the same problem. I must confess that I am quite confused about that. In contrast, no problem with the current stable version for linux. Thanks for advice francesco

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full pdb path
by petra wendler 24 Jun '19

24 Jun '19

Dear All, I have a silly question. Having opened a three year old chimera session, I unfortunately have no clue which pdbs on my computer the pdb names in my session refer to (pdbs in session are renamed). Is there a way to somehow open the session in a verbose manner or get the full path of the session pdbs? Cheers, Petra ------------------------------------------------------------ Petra Wendler, Prof. Dr. Dipl. Ing. Universität Potsdam Institut für Biochemie und Biologie Biochemie Karl-Liebknecht-Str. 24-25 D-14476 Potsdam- Golm email: petra.wendler(a)uni-potsdam.de phone: 0049 331 9775130 fax: 0049 331 9775128 ------------------------------------------------------------

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segment and group density together
by Yangqi Gu 21 Jun '19

21 Jun '19

Hi Chinera users, I have a density map of a filament. After I segmented the map, I want to group all the outer globular domain (which is part of a monomer) together. Instead of group them one by one, is there a quicker way to do this? I have the helical symmetry of the filaments. Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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chimera help in spacing out two structures within the same session
by #LAI KEI ONN# 21 Jun '19

21 Jun '19

Dear Chimera team would appreciate if you have any advice in spacing out two/or more structures within the same chimera session (e.g. the green structure away from the beige ones) so as to clearly visualise the intercrosslinks (red and blue sticks) between two different structures. Currently everything is superimposed with one another and i tried separating all the structures into different sessions and recombining it again but it didnt work. I am using xlinkanalyzer plugin with chimera. Would appreciate your kind advice, [cid:a79ad9c6-047a-493c-abc9-3ac3d537f4df] thank you! Best Regards Kei Onn LAI|黎啟諳 Phd Student Lee Kong Chian School of Medicine

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Chimera - mask after vop
by Ryan Harlich 18 Jun '19

18 Jun '19

Hi Chimera team, Is it possible to mask after vop. I got it to work in Chimera’s command line in the gui but when I run it from my python script it does not work. I am trying to change this working solution to this solution without ground truth: WORKING SOLUTION #chimera_script.write('open ' + paths['input'] + '\n' # 'open ' + paths['ground_truth'] + '\n' # 'molmap #1 6 gridSpacing 1\n' # 'volume #1.1 level 0.1\n' # 'mask #0 #1.1\n' # 'vop resample #2 onGrid #1.1\n' # 'volume #3 save ' + paths['cleaned_map']) NEW SOLUTION chimera_script.write('open ' + paths['input'] + '\n' 'vop gaussian #0 sDev 2\n' 'vop median #1 iterations 5 modelId #2.1\n' 'volume #2.1 level 0.1\n' 'mask #0 #2.1\n' 'vop resample #3 onGrid #2.1\n' 'volume #4 save ' + paths['cleaned_map']) While mask after vop works with GUI command line it gets a NoneType error when doing this: subprocess.run(['/usr/local/bin/chimera', '--nogui', chimera_script.name]). It seems like this might be a bug of chimera? Since it tries to return None to a tuple and crashes. For some reason no triangles in the new surface with vop. Here is a snippet from the depthmask.py where it crashes. [cid:image001.png@01D525AB.830ADC20] Thank you, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Chimera local resolution color
by Dmitry Semchonok 14 Jun '19

14 Jun '19

Dear colleagues, I have a cryo-em map after resmap local resolution. I would like to see not just the 2D colored slices but the hole model (not in the movie mode). How to color the model model in chimera based o remap? I would like the final result be similar to https://discuss.cryosparc.com/t/view-coloured-3d-map-in-chimera-using-outpu… <https://discuss.cryosparc.com/t/view-coloured-3d-map-in-chimera-using-outpu…> Thank you. Sincerely, Dmitry

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Stereo glasses
by Jonathan Sheehan 14 Jun '19

14 Jun '19

Hi all, What stereo setup are people recommending these days? It seems that NVIDIA has discontinued the 3D Vision 2 goggles+emitter. Is there something else that is available and works well? Thanks for any advice! -Jonathan

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Script to generate and fit structures
by Ahmad Khalifa 12 Jun '19

12 Jun '19

I want to write a script that can copy combine my structure, translate it up, down, left or right a certain distance, fit it into its new place. Is it feasible, how can I do it? Regards.

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counter ions
by patrizio.arrigo＠ge.ismac.cnr.it 12 Jun '19

12 Jun '19

Dear All I would like to use counter ions of nucleic acids not included in the default list of Chimera. I do not know how to perform this action. The option add ions offers only a limited set of ionic species I guess that is necessary to use amber18. Can you give me some suggestions Dr. Patrizio Arrigo CNR SMAC

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Chimera silent installer options for RHEL 7.6
by Darin Lory 11 Jun '19

11 Jun '19

Chimera Gurus, Are there linux silent install options for the Chimera so I can specify the installation directory, etc. I have chimera working via the regular installation method. My team and I are trying to automate the installation via Ansible playbook. Kindly advise, -Darin "The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...'" -Issac Asimov [image: --] Darin S. Lory [image: https://]about.me/darin.lory <https://about.me/darin.lory?promo=email_sig&utm_source=email_sig&utm_medium…>

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Chimera - can I tweak the red color on the Red-cyan stereo view
by Tweten, Rodney K. (HSC) 11 Jun '19

11 Jun '19

We are displaying our protein structures on a large TV in the Red-Cyan stereo view, which works pretty good for 3D viewing (except the required loss of specific colors). We tend to see a bit of ghosting of the red structure, which I suspect is that the red color lens of the Red-Cyan glasses we have (we’ve tried a few with the same results) is not quite matched to that being used by Chimera in its Red-Cyan stereo view. I was wondering if there is any way the user could tweak the red color being used by chimera in this stereo view to more closely match that of the glasses (assuming that this is responsible for the ghosting of the red structure). Thanks! Rodney Tweten George Lynn Cross Professor "Anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that my ignorance is just as good as your knowledge.” Isaac Asimov BMSB-1053 940 Stanton L. Young Blvd. The University of Oklahoma Health Sciences Center Oklahoma City OK 73104 USA Work phone: 405 271-1205 FAX: 405 271-3117 Skype: toxlab1

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APBS
by Karl R Voigtritter 11 Jun '19

11 Jun '19

Hello, I am trying to display an APBS surface. I loaded a .pqr file that was generated using the http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1 server. I then ran the APBS tool in the surface/binding analysis tab in Chimera. I left everything to default and clicked OK. It launched the executable and then executed it. The newly generated files came into the Surface Color window correctly. Upon trying to color the surface with the "color" nothing happens. -Karl Voigtritter, Ph.D. California State University, Chico

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Regarding MD simulation
by Divakar S 11 Jun '19

11 Jun '19

Hi, I have been trying to do MD simulation in chimera. However, i could not understand the exact procedure from the user help menu. Plz give us a detailed procedure for simulation and analysis if possible. I also tried to learn the procedures from previously published papers but i couldn't find any articles using MD simulation from chimera. Thank you -- *Dr. Divakar S, M. Pharm (Pharmacology), PhD.,* *Lecturer, **Department of Pharmacology,* *JSS College of Pharmacy,* *(A Constitute College of JSS Academy of Higher Education and Research, Mysuru)* *Ooty, The Nilgris, Tamilnadu.* *Mobile: +91-9944036345* *Email: divakar.s(a)jssuni.edu.in <divakar.s(a)jssuni.edu.in>, diva.niru(a)gmail.com <diva.niru(a)gmail.com>*

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viewing same size atoms within multiple molecules
by Andrew Garven 10 Jun '19

10 Jun '19

Hi, I am trying to implement a script so that each individual atom in each molecule I view on chimera is the same size (ie each carbon atom i view, regardless of the size of the molecule views a the same size). I realize this must be a function of the scale factor which changes the size of the molecules to appropriate viewing size. Is there a way to properly scale each molecule so that they have a standard atom viewing size. I would appreciate any help in this regard. Andrew

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voxel coordinates
by Andrew Garven 07 Jun '19

07 Jun '19

Hi I am trying to get a voxel encodings (coordinates) of molecules that are run through Chimera, as a deep learning model will have an easier time with such data. I am unsure how to retrieve such data from chimera. Any help would be greatly appreciated Andrew

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Re: [Chimera-users] THANKS! Chimera question
by Mike de la Flor 06 Jun '19

06 Jun '19

Hello, Thank you to all of you for getting back to me so fast. Thanks for the help. I am looking forward to ChimeraX Best, Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston From: Greg Couch [mailto:gregc@cgl.ucsf.edu] Sent: Thursday, June 06, 2019 1:28 AM To: Mike de la Flor; UCSF Chimera users mailing list Subject: Re: [Chimera-users] Chimera question 1f16 is a NMR structure and as such has 20 different variations of the structure. Using the command line, you can hide all except for the first structure with the command: ~modeldisplay #0.2-20. To do that graphically, bring up the Model Panel, then click on the group/ungroup button to show controls for the individual structures. Then select the structures you don't want (click, drag, control-click, and shift-click as appropriate), and click on the hide button to leave the one you want. HTH, Greg On 6/5/2019 8:44 PM, Mike de la Flor wrote: Hello Mr. Pettersen, I apologize for bothering you but I had a Chimera question that is best explained by the screenshot attached. For some reason Chimera is importing multiple copies of 1f16.pdb. PyMol does not do this, but I prefer to use Chimera. Do you have any suggestions as to how to fix this? Thank you in advance. Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston _______________________________________________ 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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Chimera question
by Mike de la Flor 06 Jun '19

06 Jun '19

Hello Mr. Pettersen, I apologize for bothering you but I had a Chimera question that is best explained by the screenshot attached. For some reason Chimera is importing multiple copies of 1f16.pdb. PyMol does not do this, but I prefer to use Chimera. Do you have any suggestions as to how to fix this? Thank you in advance. Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston

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split map based on resolution or surface color
by Shu-Hao Liou 03 Jun '19

03 Jun '19

Hi Chimera User, Is that possible to split a density map base on its resolution? That means I have a surface color file contained all local resolution distribution through a density map. Best, Shu-hao

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