November 2019 - Chimera-users - RBVI Mailing Lists

problem picking atoms in graphic window
by Wartell, Roger M 14 Nov '19

14 Nov '19

Hi, I have a peculiar but simple problem using Chimera [version 1.13.1(build 41965)] on a Windows 10 PC-computer]. Using it to model docking of small molecules to an RNA using autodock vina. This has worked fine. Recently wanted to measure distances by control-click on atom 1 and control-shift-click on atom 2 (picking the atoms in graphic window). Nothing came up in 'Structure Measurement' box when I 'picked' the atoms and clicked on Create except for it telling me I had to pick atom 1 and atom 2. If I hold the 'control' key of the keyboard down and move the mouse's hand symbol around an atom, the green outlined shape does not remain when I lift my finger from the mouse. On the right side of the bottom bar of the screen it says 'selection cleared' which disappears in a few seconds. When one holds both control and shift keys down and encircle the green shape around an atom, the outline remains. Control click in an empty area removes it, as it should. A postdoc in an adjacent lab who uses Chimera took a look and was puzzled since her downloaded version on her computer works fine in picking atoms etc. She also was puzzled since my mouse arrow when moved over an atom/residue did not show what residue it was, which apparently it should. We tried several pdb files (proteins and an RNA) and they all behave the same. We checked under Preferences that the matrix of radio buttons for my mouse's actions were set the same as hers. Is there some other preference setting I do not have set properly? Everything the mouse should be doing with regard to moving/rotating molecules is as expected, and the program otherwise appears to work fine. Any/all suggestions on solving this 'picking' atoms problem are most welcome. Thank you and the others at UCSF who have developed Chimera. Best Roger

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Support for Chimera1.13.1
by Mr 13 Nov '19

13 Nov '19

HI Developer I am about to purchase and use the software of Chimera1.13.1 . I need to configure a workstation for processing. I have a long-term plan. Do you have a recommended computer hardware configuration here? I will also use the following program in this workstation: Software: Discovery studio (version 2.5); MOE (version 2015); PyMOL (version 2.3); Amber (version 14); Schrodinger (version 2018-4x64); RStudio (3.5), etc.; Database: Microarry; TCGA; NCBI; RNA-seq; RCSB PDB; NONCODE, etc.; Which operating system can run these software perfectly and let them not conflict with your company's software. Sorry to ask so many questions, I hope you can reply to me. Thank you!

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Shiny cilnders
by Luca Pellegrini 13 Nov '19

13 Nov '19

Hello, I have prepared a ribbons drawing for my structure, with axes for the helices in it (Tools -> Structure Analysis -> Axes/Planes/Centroids). When I try to reduce the shininess of the figure, I can change it for the ribbons (Viewing -> Lightning -> Shininess) but not for the axes, that remain unchanged (very shiny). Is there a way to change the shininess for all objects, ribbons and axes? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Re: [Chimera-users] images from ChimeraX
by Tom Goddard 12 Nov '19

12 Nov '19

Hi Mike, Neither Chimera nor ChimeraX can output CMYK images. Your computer screen is RGB and the CMYK color space and RGB color space includes colors that the CMYK color space of a specific printer cannot duplicate as shown in this wikipedia color space image https://en.wikipedia.org/wiki/Color_space#/media/File:CIE1931xy_gamut_compa… <https://en.wikipedia.org/wiki/Color_space#/media/File:CIE1931xy_gamut_compa…> The colors can be quite different as shown in the the comparison below also from wikipedia color space. So you should convert the image yourself in Photoshop or Gimp or other photo-editor so you can see what it will look like. It would be helpful if ChimeraX was able to show you what your image would look like when limited to CMYK and help you pick colors that can be exactly represented in CMYK that most printers will handle, but we don't have that capability. Tom > On Nov 12, 2019, at 10:20 AM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu> wrote: > > Hi- > Another last thought… > The company I sent the left and right eye views to said there was a problem converting the .png RGB files to CMYK for printing. Is there a way (ChimeraX) to output CMYK, or do I have to find someone with Photoshop or something to convert it? > This is their email: > > Hello and thank you for your business. We are happy to help you. Our production department is stating that the artwork we received was submitted in RGB color format. > When we convert your file to the required CMYK color book we use for printing. There is a drastic change in color. > > We would suggest converting your artwork to CMYK then color adjusting your artwork so that your order prints accurately. > > Please revise and resend us your artwork saved in CMYK color format. Once we receive your updated artwork, we will review and respond to you right away. > > We are here to review and answer any questions you have. Please let us know anything we may help you with. > > Thanks. > > From: Tom Goddard <goddard(a)sonic.net> > Date: Thursday, November 7, 2019 at 2:57 PM > To: "Schmid, Michael F." <m-schmid(a)slac.stanford.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] images from ChimeraX > > Hi Mike, > > One last thought (I hope it is the last!). ChimeraX has a camera mode called side by side, enabled with command "camera sbs". This shows left and right eye images and is for recording videos that use SBS format. It behaves just like wall eye stereo. There is a parameter that controls the depth of field (which adjust the angle of rotation between the left/right views), "camera sbs eyeSeparation 10". Here the number 10 is in Angstroms, the separation of the left and right cameras in the scene. You can preview this cross-eye but the depth will be inverted because the left and right eye images need swapping from cross eye. If it worked you could swap left and right panels by just cutting each out in a photo editing program. Alternatively you could use negative eye separation, then it seems to work as cross-eye but the image separation is bit weird. > > There were errors when I used ChimeraX camera sbs and resized the window. I fixed those today. The errors are harmless -- just warning that OpenGL resources were not deleted. But tonight's ChimeraX won't have those errors. > > Tom > > > > On Nov 7, 2019, at 1:59 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > > Hi Mike, > > I just noticed the subject of your message said ChimeraX. All my answer was about Chimera, not ChimeraX. (There is a separate ChimeraX mailing list chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>). > > Here are ChimeraX tips. So in ChimeraX there is no cross-eye stereo mode (yet). So I would suggest using the two side-by-side ChimeraX windows. There is an icon in the lower right corner that hides all the tool panels at the right edge so the graphics is the full window width. Use the windowsize command to get the right aspect ratio (e.g. windowsize 900 1200). Use a saved session. Rotate one image with "turn y 6". Use the File / Save... dialog and choose PNG image and set pixel size to be 300 times desired print width in inches. One thing that could be a bit weird is if you use full lighting then it casts a direct shadow and the left and right eye direct shadows won't match since the light direction is fixed to the view direction (ie the light does not rotate 6 degrees, so the left and right eye won't see the same lighting). Soft lighting only has isotropic shadows so won't have that problem. If the direct shadow is a problem you could rotate the light using the "lighting" command. Use lighting with no options to show the current direction vector for the light, then calculate a rotated direction 6 degrees and set it with the "lighting direction x,y,z" command. > > Tom > > > > On Nov 7, 2019, at 1:47 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > > You might also set "supersample 1x1". The default 3x3 setting makes the image 3 times bigger on each axis and then bins down by a factor of 3. Making it 3 times larger make cause the graphics to fail on such a large image. And at 300 dots per inch the 3x3 supersample won't have a visible effect. > > Tom > > > > On Nov 7, 2019, at 1:45 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > > Hi Mike, > > The panel shown by File / Save Image... says pixels "Units pixels". > > Tom > > <Screen Shot 2019-11-07 at 1.44.52 PM.png> > > On Nov 7, 2019, at 1:34 PM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu <mailto:m-schmid@slac.stanford.edu>> wrote: > > Hi- > Thanks. That really helps! So the “width” and “height”, if just given as 5400 and 7200, respectively, will be understood as pixels, or do you have to say “5400 pixels”? > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Date: Thursday, November 7, 2019 at 1:28 PM > To: "Schmid, Michael F." <m-schmid(a)slac.stanford.edu <mailto:m-schmid@slac.stanford.edu>> > Cc: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: Re: [Chimera-users] images from ChimeraX > > Hi Mike, > > To avoid pixelation make sure to save the left and right eye images at high resolution. Using Chimera File / Save Image... you would set the image size in pixels to be maybe 300 times the number of inches wide you will make the image (so if one eye image is 18 inches wide that use image width 5400 pixels). > > For surface rendering of the tomogram make sure step is 1 in volume viewer so it is using the full resolution data. > > For getting the right angle of rotation between the two images I would suggest that you display it on a large flat panel screen (e.g. 50" TV) if you have one at the size you want to print at and check visually how well the cross-eye stereo pair is working. Make the Chimera window aspect ratio exactly match what you will print (e.g. 36 x 24n inches would be 3 to 2), for example use Chimera command "windowsize 1800 1200". In Chimera you can use the "cross-eye stereo" camera in the side view (menu Favorites / Side View) Camera tab in the "camera mode" menu. Then you can fiddle a bit with the focal plane by going to the Side View tab, choose "Side: top" and drag the vertical dashed yellow line left or right. It represents the focal plane. I'm not sure what that means for cross-eyed stereo but it effects the angle of rotation between left and right images. I tried this on my 24 inch wide screen (so not as big as you will print) and I really have to stand far back (5 or 6 feet) to comfortably look at it, otherwise the floating image is too close to my face and I think my eyes don't like to converge that close while still focusing 5 feet away. If this cross-eye stereo mode works for you, you can use File / Save Image... and it will save the two eyes as a single image. > > If that cross-eye stereo mode isn't working well for you you could open two copies of Chimera side by side and rotate the image of one relative to the other with the command "turn y 6" to rotate one view by 6 degrees. You might first save a session in the desired orientation that you open in both Chimera copies then rotate just one of them. > > I think the key here is to try it on a screen to see if it is giving you what you want before you print. > > Tom > > > > > > > On Nov 7, 2019, at 9:48 AM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu <mailto:m-schmid@slac.stanford.edu>> wrote: > > Hi- > I am trying to make a high resolution image of a surface rendering of a tomogram. The final size of the image(s) will be 18 in x 24 in. It is for a wall display. How do I do it for the best (minimally pixelated) result? I presume I will have to adjust the triangle rendering of the maps to be included, and also the rendering of the final images (for a stereo pair). Also, I assume I have to render them at ~6 degrees total tilt with respect to each other. > Thanks, > Mike > _______________________________________________ > 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> > > > > _______________________________________________ > 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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Fetch by EMDB via GUI downloads first where before uncompressing in users downloads directory
by Ryan Harlich 08 Nov '19

08 Nov '19

Hi Chimera, If I fetch by EMDB via GUI and it downloads then decompresses and freezes where did it go? I know when it is done it goes to my download directory, but where does the gz get downloaded to and where does the partial uncompressed file end up. I cannot find ~5-~10 GB of this lost file. It was ~5 GB gz file so I think the gz is still on my computer. I searched for it to and my computer said no results found so I am not sure if it is named something else when you fetch by EMDB. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Re: [Chimera-users] images from ChimeraX
by Tom Goddard 07 Nov '19

07 Nov '19

Hi Mike, The panel shown by File / Save Image... says pixels "Units pixels". Tom > On Nov 7, 2019, at 1:34 PM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu> wrote: > > Hi- > Thanks. That really helps! So the “width” and “height”, if just given as 5400 and 7200, respectively, will be understood as pixels, or do you have to say “5400 pixels”? > > From: Tom Goddard <goddard(a)sonic.net> > Date: Thursday, November 7, 2019 at 1:28 PM > To: "Schmid, Michael F." <m-schmid(a)slac.stanford.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] images from ChimeraX > > Hi Mike, > > To avoid pixelation make sure to save the left and right eye images at high resolution. Using Chimera File / Save Image... you would set the image size in pixels to be maybe 300 times the number of inches wide you will make the image (so if one eye image is 18 inches wide that use image width 5400 pixels). > > For surface rendering of the tomogram make sure step is 1 in volume viewer so it is using the full resolution data. > > For getting the right angle of rotation between the two images I would suggest that you display it on a large flat panel screen (e.g. 50" TV) if you have one at the size you want to print at and check visually how well the cross-eye stereo pair is working. Make the Chimera window aspect ratio exactly match what you will print (e.g. 36 x 24n inches would be 3 to 2), for example use Chimera command "windowsize 1800 1200". In Chimera you can use the "cross-eye stereo" camera in the side view (menu Favorites / Side View) Camera tab in the "camera mode" menu. Then you can fiddle a bit with the focal plane by going to the Side View tab, choose "Side: top" and drag the vertical dashed yellow line left or right. It represents the focal plane. I'm not sure what that means for cross-eyed stereo but it effects the angle of rotation between left and right images. I tried this on my 24 inch wide screen (so not as big as you will print) and I really have to stand far back (5 or 6 feet) to comfortably look at it, otherwise the floating image is too close to my face and I think my eyes don't like to converge that close while still focusing 5 feet away. If this cross-eye stereo mode works for you, you can use File / Save Image... and it will save the two eyes as a single image. > > If that cross-eye stereo mode isn't working well for you you could open two copies of Chimera side by side and rotate the image of one relative to the other with the command "turn y 6" to rotate one view by 6 degrees. You might first save a session in the desired orientation that you open in both Chimera copies then rotate just one of them. > > I think the key here is to try it on a screen to see if it is giving you what you want before you print. > > Tom > > > > > > On Nov 7, 2019, at 9:48 AM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu <mailto:m-schmid@slac.stanford.edu>> wrote: > > Hi- > I am trying to make a high resolution image of a surface rendering of a tomogram. The final size of the image(s) will be 18 in x 24 in. It is for a wall display. How do I do it for the best (minimally pixelated) result? I presume I will have to adjust the triangle rendering of the maps to be included, and also the rendering of the final images (for a stereo pair). Also, I assume I have to render them at ~6 degrees total tilt with respect to each other. > Thanks, > Mike > _______________________________________________ > 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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images from ChimeraX
by Schmid, Michael F. 07 Nov '19

07 Nov '19

Hi- I am trying to make a high resolution image of a surface rendering of a tomogram. The final size of the image(s) will be 18 in x 24 in. It is for a wall display. How do I do it for the best (minimally pixelated) result? I presume I will have to adjust the triangle rendering of the maps to be included, and also the rendering of the final images (for a stereo pair). Also, I assume I have to render them at ~6 degrees total tilt with respect to each other. Thanks, Mike

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UCSF Chimera on Arm processors
by Dr. Santanu Roy 04 Nov '19

04 Nov '19

Dear Sir/Madam, I just wanted to know if there is any version of UCSF Chimera that can be run on Arm v8 based Single Board Computers like the Raspberry Pi 4 with 4 GB RAM. Thanks and Regards, S Roy Dr. Santanu Roy Department of Microbiology, Acharya Prafulla Chandra College, New Barrackpore, Kolkata - 700 131

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Atom box
by MARIA CLARA BLANES MIRA 04 Nov '19

04 Nov '19

Dear Chimera experts, I have been measuring surface volumes by using the atom box option in order to obtain a surface slice volume and then the volume measure. But how could I use the atom box in the command line? Thank you! clara import chimera import os from chimera import runCommand runCommand(’sel :2.A,19.A,25.A, 5.B, 23.B, 26.B’) # to define the box runCommand(‘atomBox ????’) runCommand('measure volume #0') runCommand('close all')

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Re: [Chimera-users] Coloring map by curvature
by Tom Goddard 03 Nov '19

03 Nov '19

Hi Shengyou, The curvature.py script was attached to the Chimera mailing list message you found. http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009580.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009580.html> It got renamed with a ".bin" suffix, so after you download you should change the file name to curvature.py. A similar capability is in ChimeraX, the "measure convexity" command https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#convexity <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#convexity> Here's an example image using "measure convexity #1" on EMDB 0074. Tom > On Oct 6, 2019, at 7:15 AM, huangsy(a)hust.edu.cn wrote: > > Hi Tom, > > > > I just noticed that you had helped a user about "Coloring EM map by curvature" in UCSF Chimera through some scripts like the following > > open 1grl > > molmap #0 15 grid 2 model #1 > select #1 > open ~/Desktop/curvature.py > Could you please send me the "curvature.py" file or tell me where to download it? > > > Thank you very much for your help! > > Best regards, > > > > Shengyou > > -- > > Shengyou Huang, PhD > > Professor of Biophysics > School of Physics > Huazhong University of Science and Technology > Email: huangsy(a)hust.edu.cn <mailto:huangsy@hust.edu.cn> > Lab web: http://huanglab.phys.hust.edu.cn/ <http://huanglab.phys.hust.edu.cn/>

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Chimera-users November 2019