- Chimera-users - RBVI Mailing Lists

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 14 Nov '19

14 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 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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Can mouse preferences by set to specific UCSF Chimera function (ex. "Undo Move" under Movement Mouse Mode) ?
by Jun Ha Song 30 Oct '19

30 Oct '19

Dear RBVI, My current project involves modifying market set to better-fit the density map, and I use "*Undo Move*" function of "*Movement Mouse Mode*" window all the time (at least 100 times every hour). Although the "*Undo Move*" is already a godsend for my current project, I have to confess that I find moving my mouse all the way to "*Movement Mouse Mode*" window, then clicking "*Undo Move*" little bit tiring (especially after looking for "Movement Mouse Mode" Window over 10,000 times, at least). I have learned that there is also a way to use Undo Move via Toolbar, but the fact that I need to move my mouse from my model to click the Undo Move button remains the same. I want to ask the following question : "*Can Mouse button (ex. MMB), or a specific custom keyboard key (ex. Pause/Break), be assigned to activate a UCSF Chimera function that requires its button to be physically pressed?*" This is such a minor wish, as it would likely only benefit 1 person, I already feel guilty for asking this. That is why I want to know if mouse button can be assigned to actiavte UCSF Chimera function in general. Best, Junha Song.

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molecular dynamics simulation manual
by AYMAN NAEEM 29 Oct '19

29 Oct '19

Hello I want to use molecular dynamics simulation guideline by using chimera. I will be grateful for your attention. Best regards Ayman Naeem

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electron scattering factors
by Thomas Bick 29 Oct '19

29 Oct '19

Is it possible to create a density map based on a pdb using electron scattering factors rather then a sole gaussian distribution? The molmap command apparently doesn`t have a argument to include scattering factors? Are there maybe different possibilities do that in Chimera? Thanks for the help in advance! Best Thomas Bick

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Pov-Ray functionality
by Brown, Jeffrey 28 Oct '19

28 Oct '19

Hello, I like a lot about ChimeraX; however, I can’t figure out how to export to POV-RAY format. Has this functionality been removed? Although there is a pseudo ray trace function in Chimera X - it is impossible to add scenes like I did in this publication https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009406 In which I used Chimera to render all of the proteins and then moved them around and added membrane etc. Also there is a lot more control in POV-RAY as it is code that you can’t accidentally rotate with your mouse. Cheers, JWB Jeffrey Wade Brown, M.D., Ph.D. Instructor in Medicine Washington University School of Medicine Department of Gastroenterology 660 South Euclid, Campus Box 8124 St. Louis, MO 63110 Facsimile: (314) 362-3643 Office: (314) 454-8204 Pager: (314) 253-1585 E-Mail: brownjw(a)wustl.edu<mailto:brownjw@wustl.edu> http://independent.academia.edu/JeffreyWadeBrown ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Chimera-users] Creating movies with alpha channel / transparent background
by Tom Goddard 28 Oct '19

28 Oct '19

Hi Martin, It is possible that some Chimera movie encode command format option will put the transparency channel into the movie -- it all depends on what ffmpeg does and what those formats support. I don't know what ffmpeg supports nor what formats support transparency -- you could try to look that up online, or you could simply try each of the Chimera formats and see if it produces a movie with transparency. Chimera simply hands the sequence of PNG images to ffmpeg (which is bundled with Chimera, ffmpeg version 2.1). From what I saw in ffmpeg docs there is not a special include transparency option -- it is simply a matter of having a transparency channel in the images and having ffmpeg support for the specific output format. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#encode-op… Tom > On Oct 28, 2019, at 2:04 PM, Martin Textor <martin_textor(a)gmx.de> wrote: > > Hi Tom, > > thank you. I'm aware that Chimera can output a series of images with a transparent background, I have done this already (using png). As this is possible, and the "movie encode" command supports, besides other formats, .avi and .mov, both of which definitely support an alpha channel, I had hoped there might be some option for "movie encode" that's just not described in the documentation which allows obtaining a video with transparent background and spares me from having to use a third-party tool. > > With regards to Elaine's reply, I want to use the video overlaid to another one, so a static background image is not an option in this specific case, but thanks for the suggestion. > > Best, > Martin > > Am Mo., 28. Okt. 2019 um 20:05 Uhr schrieb Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>: > Hi Martin, > > You can have Chimera save a series of transparent background images using the movie command, for example, > > set bgtransp > movie record dir ~/Desktop/test format png ; turn y 1 90 ; wait 90 ; movie stop > > Then you would need to encode the PNG images in ~/Desktop/test into a movie using some encoding program. I doubt the Chimera "movie encode" command supports any video format that can handle transparent background. Chimera uses ffmpeg to encode movies and apparently ffmpeg can encode some video formats with transparency, for example, as described here the motion PNG format in .mov can handle transparency > > https://stackoverflow.com/questions/644684/turn-image-sequence-into-video-w… <https://stackoverflow.com/questions/644684/turn-image-sequence-into-video-w…> > > Tom > > > > >> On Oct 28, 2019, at 10:06 AM, Martin Textor wrote: >> >> Hello, >> >> I was wondering if it is possible to create movies with a transparent background? I know that it's possible to create images with a transparent background and that the video formats supported by Chimera to encode movies include avi and mov, both of which support an alpha channel as far as I know. >> >> Kind regards, >> Martin Textor >> >> _______________________________________________ >> 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> > > > > -- > Martin Textor > 20 Elmer Mews, > Leatherhead, Surrey, > KT22 9DN, UK > > Fon: +49(0)178 3993650 <> > Mail: martin_textor(a)gmx.de <mailto:martin_textor@gmx.de>

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Creating movies with alpha channel / transparent background
by Martin Textor 28 Oct '19

28 Oct '19

Hello, I was wondering if it is possible to create movies with a transparent background? I know that it's possible to create images with a transparent background and that the video formats supported by Chimera to encode movies include avi and mov, both of which support an alpha channel as far as I know. Kind regards, Martin Textor

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Fit list behavior query
by Oliver Clarke 28 Oct '19

28 Oct '19

Hi, I often use fitmap with the “search” flag to find the orientation of a fragment (e.g. a single domain of a larger protein) in a cryoEM map - something like “fitmap #1 #0 search 100 radius 5”. Normally, a fit list table will appear and the model will reorient to match the highest scoring entry in the fit list. One thing I have noticed is that if I run a second such command after the first (e.g. to try a different radius or number of trials), the fit list is not updated - all the entries are identical, and the model is again reoriented to match the highest entry in the first list. I find I need to first manually clear all the fits from the first trial in order for it to correctly update with the results of the second run. I wonder if it would be possible to alter this behavior such that the fits from the first run are automatically cleared if a second fitmap command is issued? Cheers Oli

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Using Chimera on IOS devices
by Lytle, Ayren 23 Oct '19

23 Oct '19

Good afternoon, I've reviewed the list of supported operating systems<http://www.rbvi.ucsf.edu/chimera/download.html> on your website and did not see IOS listed. Do you have any experience using Chimera on iPads and if so do you recommend it for College Biology students? Our instructors have referenced some Galaxy Tab A (2019) Android tablets, but we would prefer to support IOS devices over Android due to our existing central support manage systems. I've included a link below to the Andriod tablet they are considering as well. I appreciate your time. Thanks. https://www.cdwg.com/product/samsung-galaxy-tab-a-2019-tablet-android-9.0-p… Best regards, Ayren Lytle Manager, User Services College of Southern Nevada | Department of Office of Technology Services 3200 E. Cheyenne | North Las Vegas, NV. 89030 Office: (702)-651-4450<a%20href=%22tel:%20(702)-651-4450%22%3e123-456-7890%3c/a> | ayren.lytle(a)csn.edu<mailto:ayren.lytle@csn.edu> www.csn.edu/ots<https://at.csn.edu/otsservices> [ConfidentialSignatureLine]

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50 chains structure numbering errors
by Ahmad Khalifa 23 Oct '19

23 Oct '19

Hello, I'm trying to deposit a PDB with 50 chains. My PDB has a lot of HETATM records and at some point it switches from HETATM"number" to HETATM*****. The PDB throws an error regarding HETATM*****. If you any suggestions regarding the error and / or processing the .pdb to make the deposition easier, please let me know. I also wonder if I can save my file as a cif by Chimera. Regards.

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could not access chimera webpage
by Sirin Theerawatanasirikul 23 Oct '19

23 Oct '19

Dear Chimera UCSF developers I am Sirin Theerawatanasirikul from Thailand. I am working on protein structures and use chimera every day. In a couple days, I tried to access your website via safari run in Mac Os Mojave ; https://www.cgl.ucsf.edu › chimera I could not access any topic or any feature. Could you please give me a suggestion? Sincerely yours, Sirin -- Sirin Theerawatanasirikul DVM (Hon.),PhD.(Pathobiology) Assistant Professor, Department of Anatomy Faculty of Veterinary Medicine, Kasetsart University THAILAND e-mail: fvetsrth(a)ku.ac.th, sirin.t(a)ku.ac.th, numilo(a)hotmail.com office phone: +66(0)2 942 8954

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Reassign chain ID letters
by Ahmad Khalifa 21 Oct '19

21 Oct '19

Hello, I have a structure with multiple chain IDs, some of them include number chain IDs and same letter small case and capital case chain IDs. I want to reassign the chain ID's randomly so that they are letters first then numbers, capital case then small case. How can I do that?! Best regards.

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