- Chimera-users - RBVI Mailing Lists

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 26 Jun '19

26 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 13 Jun '19

13 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 10 Jun '19

10 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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