- Chimera-users - RBVI Mailing Lists

Problem with swapaa
by Dan Kool 20 Nov '19

20 Nov '19

I am having problems mutating some residues with the 'swapaa' command. How do I mutate to 'A' or 'G' or 'I' for example? I always get an error that the rotamer library doesn't support it. Is there a workaround or is it actually not possible to simply mutate a residue to one of those? I tried changing the rotamer library, but I get the same error. Best, Dan ---------------------------------------------------- Daniel Kool Graduate Assistant, Jernigan Lab, 335 Kildee Bioinformatics and Computational Biology Iowa State University kool(a)iastate.edu

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Programmatic trimming of PDB files based on alignment with reference structure
by Zachariah Schuurs 19 Nov '19

19 Nov '19

Dear Chimera Team, I have a reference protein domain and then a series of PDB files which all contain the same domain. I have programmatically been able to script an alignment of the reference to the same domain in the other files whereby he domain in the proteins of interest are isolated using the zone select method. This however leaves me with fragments and often misses some of the domain features of the interest proteins that occur outside of the specified zone. I am wondering if it is possible to write a python script that selects the area on the protein of interest by selecting the residues in the sequence alignment after MatchMaker is conducted. For instance - protein #0 is my reference protein, which is 150 residues long. My protein of interest contains the same domain as the reference, but is 500 residues long. Upon conducting MatchMaker and getting an output sequence alignment, the 150 residues of #0 (the reference) are selected, along with the aligned residues in the protein of interest. It is possible to select the residues in the sequence alignment window (as in the picture) but I wish to be able to script it. The selected 150 residues (or so) in the protein of interest are then saved as their own trimmed file. I have been able to write a python script for completing the MatchMaker etc, but I am not sure how to achieve the selection of residues in #1 based of the alignment with #0, or if it is even possible. Thanks Zachariah Schuurs | PhD Candidate CARP - Cancer & Ageing Research Program Institute of Health and Biomedical Innovation | Queensland University of Technology Level 6 | Translational Research Institute | 37 Kent St | Woolloongabba QLD 4102 T: +61 7 3443 7296 | E: zachariah.schuurs(a)hdr.qut.edu.au | Web: www.carp.org.au<http://www.carp.org.au/> [email] I acknowledge the Turrbal and Yugara, as the First Nations owners of the lands where QUT now stands. I pay respect to their Elders, lores, customs and creation spirits. I recognise that these lands have always been places of teaching, research and learning. This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email. [cid:image004.png@01D59AF3.602278E0]

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Re: [Chimera-users] setting zoom with a specific window size.
by Elaine Meng 19 Nov '19

19 Nov '19

> On Nov 19, 2019, at 5:56 AM, JOHN FLANAGAN <jmf27(a)psu.edu> wrote: > > Hi > I am trying to compare several negative stain em maps to make a figure. For what I want to do its easier not to have all of the maps loaded at the same time. However, I am having trouble keeping everything on the same scale. I am able to set the windowsize, center the maps but the zoom is not always the same. I searched the web and found that there used to be zoom and setzoom commands that should do the trick, but neither is recognized in my version of chimera (commands I mean). All of the maps have the same starting A/px but what I want to do is take the map with the largest extent and set that and whatever its being aligned too to fill the window then for every other session have the same windowsize and effective zoom. Pardon my inelegant description but I hope that provides sufficient explanation for what I am trying to do. > > Cheers > John Hi John, Sending this to chimera-users(a)cgl.ucsf.edu, the recommended address for Chimera questions. That way, whoever has the expertise can answer, and others can benefit. This previous post may answer your question. It says you have to download the setzoom command code separately and provides a link. <http://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013091.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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exit code -1073741819 + debug
by Fatemeh Haghighi 18 Nov '19

18 Nov '19

Hi I have tried to make a movie of MD simulation by Chimera. I could be done one time, then for other MD’s it exits abnormally with the code -1073741819. Even I have decreased the size of .xtc file, it exits abnormally yet. I have reinstalled chimera, but the problem did not resolve. The debug report was: Cannot execute 'gzip': no automatic decompression of .Z files Best Regards

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Elliptical cylinders
by John Hackett 15 Nov '19

15 Nov '19

Good morning, is to possible to draw capped elliptical cylinders in Chimera? I would like to render elliptical cylinder representations of nanodiscs together with a membrane protein to visualize results from small-angle scattering experiments. Thanks, -jch ________________________________ John C Hackett, PhD, RPh Associate Professor, Physiology & Biophysics VCU School of Medicine Goodwin Research Laboratory Rm. 165 Massey Cancer Center 401 College St. Richmond, Virginia 23298-0035 Telephone: +1.804.828.5679 ________________________________

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problem picking atoms in graphic window
by Wartell, Roger M 15 Nov '19

15 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 14 Nov '19

14 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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