- Chimera-users - RBVI Mailing Lists

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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