October 2024 - ChimeraX-users - RBVI Mailing Lists

placing a model at points defined in a CMM file
by Pranav Shah 22 Oct '24

22 Oct '24

hi Team, In addition to my previous question, is there a chimeraX function I could leverage to translate a pdb model to a point defined in a CMM file? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Viewing ccp4 volume data - Hiding outline box volume outside surface
by Stylianos Iliadis 22 Oct '24

22 Oct '24

Hello, I want to visualise a surface (isosurface) loaded from a ccp4 file on top of a protein binding site. When I load the volume and adjust the level properly, I can see the “correct” surface (visualised usually on Pymol), but this is only possible when I view slices of the volume=cube box. If I don’t use the sliced view, I only see a cube. Essentially, my question is how can someone hide the “negative” volume inside the cube box that is not part of the depicted isosurface? Thanks, Best, Stel Iliadis

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Named selection problem
by Patrick Moynihan 22 Oct '24

22 Oct '24

Hi, I was hoping someone could help me with a persistent problem I am having. I am running ChimeraX version 1.8 (2024-06-10) on OSX. This problem has persisted for quite a while through several versions. If I work in ChimeraX and save a group of atoms as a named selection, it generally works as expected for the first group. After that, if I use the command “name XXXX” or define a selection via the GUI, it seems to take the input and reserve the name. However, when I return and select that named selection, the entire protein gets selected. I cannot for the life of me figure out why. I’ve tried low numbers of atoms and high, short names and long, the problem persists. Any advice would be appreciated. Thanks, Patrick

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Set transparency of multiple models
by Ioannis Skalidis 22 Oct '24

22 Oct '24

Dear ChimeraX mailing list, I was wondering if there is a command to set the alpha (transparency) of multiple models (not maps). So far, I know that this is possible for maps through the transparency command, but the only way I know of to make a model transparent is to set each model alpha value individually in its color panel. Thanks for your help! Cheers, Dr. Ioannis Skalidis | Structural Biochemist | Twitter: @imjohnskal <https://twitter.com/imjohnskal> | johnskalidis(a)gmail.com

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Query regarding Chimerax capablities
by Joseph Clifford 21 Oct '24

21 Oct '24

Hi Team, I hope this email reaches you well. I am a R&D scientist at Randox Laboratories and was wondering if possible could you model the nicked free form of PSA with the additional 7 amino acids at the N-term. I am exploring the capabilities of chimerax and want to put a business case together to my manager regarding this software application. [cid:54b7fcba-418a-438f-a6b0-5358e796c896] Many thanks in advance, Joseph Clifford This e-mail and any attachments are confidential and intended solely for the addressee and may also be privileged or exempt from disclosure under applicable law. If you are not the addressee, or have received this e-mail in error, please notify the sender immediately, delete it from your system and do not copy, disclose or otherwise act upon any part of this e-mail or its attachments. E-mail communications are not guaranteed to be secure or virus-free. Therefore Randox does not accept responsibility for any loss arising from unauthorised access to, or interference with, any e-mail communications by any third party, or from the transmission of any viruses. Randox does not accept liability for any errors or omissions in the contents of this message which arise as a result of e-mail transmission. Replies to this e-mail may be monitored by Randox for business and operational purposes. Any opinion or other information in this e-mail or its attachments that does not relate to the business of Randox is personal to the sender and is not given or endorsed by Randox.

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Inquiry on Setting Clipping Caps for Helix in Cylinder Visualization
by youngxiaolin 18 Oct '24

18 Oct '24

Dear Sir/Madam, I am currently working on a cross-sectional visualization of a transmembrane helix bundle shown as cylindrical cartoon. I notice that, unlike in surface visualizations, my helices are not capped, leaving the ends exposed. Are there specific parameters or settings within ChimeraX that I should adjust to customize the appearance of the helix caps? Thank you in advance for your assistance. I am looking forward to your expert advice. Best regards, Xiaolin Yang National clinical research center for Infectious diseases

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Issues accessing your websites
by Karp Mike (External) 18 Oct '24

18 Oct '24

Hi, We've been trying to install a chimerax plugin over the last few weeks and noticed we were unable to access the webpage the application tries to open (ChimeraX Toolshed). We checked and found this wasn't accessible from multiple internet connections. I've since noticed we are also unable to access any content on https://cgl.ucsf.edu Are you aware of an issue with your web sites? Regards, Mike. ________________________________ Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail. (Ref: #*UG1107) [Ref-UG1107] ________________________________

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Fwd: 3d glasses free monitors from acer....
by Tom Goddard 18 Oct '24

18 Oct '24

Hi Krish, Ok. I fixed the first error which was caused by the Acer display OpenXR saying it did not have valid position and orientation data for the viewer. ChimeraX did not handle that correctly since VR headsets never have that problem. It might mean that eye tracking of the Acer display did not see your eyes so it did not know your viewing position. Or it could mean the Acer display never provides both position and orientation. If it never provides position and orientation of the viewer then the fixed code still won't render anything and we'll have to do more work to figure out how you are are supposed to get the view direction. The fixed XR code will be in daily builds dated October 17, 2024 or newer. Tom > > >> On Oct 16, 2024, at 2:53 PM, Krishnan Raman <RKrishnan(a)BIOCRYST.com> wrote: >> >> Hi Tom, >> I am willing it work with it till it gets resolved. It might open the display for other applications as well. >> Thanks again for your prompt responses. >> krish >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Wednesday, October 16, 2024 4:14 PM >> To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> >> Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... >> >> [EXTERNAL] >> >> Hi Krish, >> >> That is some progress. I see why ChimeraX gives that error. It is looking for if the OpenXR connected device does both position and orientation tracking (for VR headsets) and your display says it doesn't do at least one of those and then the ChimeraX code breaks. I may be able to fix that and see if you get further. I say "may" because the ChimeraX code is designed for VR where the headset has a position and orientation in space that is reported. If the Acer display doesn't give a position and orientation for the person's head using its eye tracking then the ChimeraX code would need to do something different to decide the view point. If I had a display I could explore it, but without one it will be hard to figure out. If you want to replace some ChimeraX Python code I can give you some that will help figure out the issues, but it may take a lot of back and forth of you trying code to get anywhere. >> >> Tom >> >> >> >> On Oct 16, 2024, at 1:40 PM, Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> wrote: >> >> SpatialLabs User Guide (acer.com) <https://link.edgepilot.com/s/e6a7c1ed/uvnt1Jd_IECk7VUP7-Ti6Q?u=https://spat…> >> >> <image001.png> >> >> Also, >> Tried XR on. The display froze but did go into the 3D mode. Chimerax is recognizing the driver and the monitor. I got an error while reporting this bug. So pasting it here. >> >> >> An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. >> >> 'XR' object has no attribute '_eye_view_states' >> >> Traceback (most recent call last): >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\core\updateloop.py", line 84, in draw_new_frame >> view.draw(check_for_changes = False) >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\graphics\view.py", line 188, in draw >> self._draw_scene(camera, drawings) >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\graphics\view.py", line 231, in _draw_scene >> camera.set_render_target(vnum, r) >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\xr.py", line 941, in set_render_target >> self._start_rendering() >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\xr.py", line 796, in _start_rendering >> if not xr.start_frame(): >> ^^^^^^^^^^^^^^^^ >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\openxr.py", line 372, in start_frame >> self._end_xr_frame() >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\openxr.py", line 446, in _end_xr_frame >> eye_view = self._eye_view_states[eye_index] >> ^^^^^^^^^^^^^^^^^^^^^ >> AttributeError: 'XR' object has no attribute '_eye_view_states' >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Wednesday, October 16, 2024 12:10 PM >> To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> >> Cc: Greg Couch <gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>>; ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... >> >> [EXTERNAL] >> >> Hi Krish, >> >> I would hope the Acer SpatialLabs 3D display could render with the standard sequential stereo used with old LCD shutter glasses or polarized glasses systems. ChimeraX can output that using command "camera stereo". But I didn't seen any indication in searching online that they support that. Nor did I see any mention of them supporting the standard side-by-side stereo format which ChimeraX can also output (camera sbs). I would think the display would handle these format because 3D games use those. How could they not make it work with 3D games? What I did see online is that it works with OpenXR which is what virtual reality headsets use. That makes sense because the display offers eye tracking and the sequential or side-by-side stereo methods would not be able to use the eye tracking to change the viewing angle as you moved your head, while software that uses OpenXR will allow that. ChimeraX can uses OpenXR, command "xr on". I did not see online what software you use with the display to work with OpenXR. It would need some SpatialLabs OpenXR display control software running on your computer. Here is a bit of discussion about trying to use this display with another 3D app called Slicer >> >> https://link.edgepilot.com/s/cad1c1c9/DC6RKYZmHE2WohxUaEbXfw?u=https://disc… >> >> where the poster did get Slicer's OpenXR to show 3D with the display. >> >> Let me know what you figure out. If you find some technical reference for the display online that explains the types of 3D input it accepts or how to set it up to work with applications that use OpenXR, I'd be interested in seeing that documentation. If it works well my lab might get a display. >> >> Tom >> >> >> >> >> On Oct 16, 2024, at 7:35 AM, Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> wrote: >> >> Hi Tom, >> I got a new 3d glasses free monitor. >> Acer 27" SpatialLabs View Pro Stereoscopic 3D Monitor - Black - FF.R2CAA.002 - Computer Monitors - CDW.com <https://link.edgepilot.com/s/f5cca637/LqUzzf13mUCbZBJiJkeIJQ?u=https://www.…> >> I used the spatiallabs (GO app) software to see stereoscopic 3d images from Chimerax, coot(mapfitting) amd MOE. Seemd to work fine. >> The Go app converts any 2d to 3d stereo when the program displaying is set to fullscreen. >> The Spatiallabs software from acer has plugins for unity , blender and a few other software suites. >> The Go app is compatible with *.obj and Gitf 3d formats. I tried those from chimerax and the result is spectacular. >> Is there any possibility of getting a chimerax plugin? >> Regards >> Krish >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Friday, July 12, 2024 1:22 PM >> To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> >> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... >> >> [EXTERNAL] >> >> Hi Krishnan, >> >> We do not have any of the new 3D laptops to try ChimeraX. Let us know if it works. You will probably use the ChimeraX command "camera stereo" to put it into 3D model on one of these 3D laptops. >> >> Samsung also showed a 3D monitor at January's Consumer Electronics Show with rumors that it may come out this summer. Also don't know if ChimeraX will work on that display. >> >> While I think ChimeraX stereo is likely to work on these displays a problem with past stereo that used shutter glasses was that only workstation graphics cards could do stereo in a window, meaning that part of the display is showing 3D (e.g. the ChimeraX graphics pane) while the rest is showing 2D. This required special graphics driver support only offered in the workstation cards (like Nvidia Quadro) and not in the consumer cards. Full screen stereo where everything is rendered in 3D was available on consumer cards mostly for video games where everything is in 3D including user interface elements. >> >> Let us know if you get something working. >> >> Tom >> >> >> >> >> >> On Jul 12, 2024, at 8:56 AM, Krishnan Raman via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> https://link.edgepilot.com/s/22d26e4a/CHuCkVzwKkGj1oPV_qX5bQ?u=https://www.… >> >> maybe we can see chimerax😊 in 3d in these… they do have a plugin for unity.. Iam trying get one of these to try things out. >> >> Krishnan Raman >> Executive Director, Structural Biology >> BioCryst Pharmaceuticals >> >> >> >> >> CONFIDENTIALITY NOTICE >> >> This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> Archives: https://link.edgepilot.com/s/bb15c3bf/yEg7mgqw30m5lBrfcz6VNQ?u=https://mail… >> >> >> >> Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. >> >> >> >> CONFIDENTIALITY NOTICE >> >> This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >> >> >> >> >> Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. >> >> >> >> CONFIDENTIALITY NOTICE >> >> This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >> >> >> >> >> Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. >> >> >> >> CONFIDENTIALITY NOTICE >> >> This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >> >

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Question about creation of splines for alpha helix models
by Shriya Sivakumar 18 Oct '24

18 Oct '24

Dear Sir/Madam, My name is Shriya and I am an undergraduate research assistant at the Microsystems and Mechanobiology Lab at Carnegie Mellon University. I was wondering if you could help me with regard to how ChimeraX creates splines when modeling alpha helices. In particular, which atoms from the protein backbone are used as the points through which the spline is calculated? Thank you! Sincerely, Shriya Sivakumar

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Re: 3d glasses free monitors from acer....
by Tom Goddard 18 Oct '24

18 Oct '24

Hi Krish, I would hope the Acer SpatialLabs 3D display could render with the standard sequential stereo used with old LCD shutter glasses or polarized glasses systems. ChimeraX can output that using command "camera stereo". But I didn't seen any indication in searching online that they support that. Nor did I see any mention of them supporting the standard side-by-side stereo format which ChimeraX can also output (camera sbs). I would think the display would handle these format because 3D games use those. How could they not make it work with 3D games? What I did see online is that it works with OpenXR which is what virtual reality headsets use. That makes sense because the display offers eye tracking and the sequential or side-by-side stereo methods would not be able to use the eye tracking to change the viewing angle as you moved your head, while software that uses OpenXR will allow that. ChimeraX can uses OpenXR, command "xr on". I did not see online what software you use with the display to work with OpenXR. It would need some SpatialLabs OpenXR display control software running on your computer. Here is a bit of discussion about trying to use this display with another 3D app called Slicer https://discourse.slicer.org/t/spatiallabs-stereoscopic-display/34800 where the poster did get Slicer's OpenXR to show 3D with the display. Let me know what you figure out. If you find some technical reference for the display online that explains the types of 3D input it accepts or how to set it up to work with applications that use OpenXR, I'd be interested in seeing that documentation. If it works well my lab might get a display. Tom > On Oct 16, 2024, at 7:35 AM, Krishnan Raman <RKrishnan(a)BIOCRYST.com> wrote: > > Hi Tom, > I got a new 3d glasses free monitor. > Acer 27" SpatialLabs View Pro Stereoscopic 3D Monitor - Black - FF.R2CAA.002 - Computer Monitors - CDW.com <https://www.cdw.com/product/acer-27-spatiallabs-view-pro-stereoscopic-3d-mo…> > I used the spatiallabs (GO app) software to see stereoscopic 3d images from Chimerax, coot(mapfitting) amd MOE. Seemd to work fine. > The Go app converts any 2d to 3d stereo when the program displaying is set to fullscreen. > The Spatiallabs software from acer has plugins for unity , blender and a few other software suites. > The Go app is compatible with *.obj and Gitf 3d formats. I tried those from chimerax and the result is spectacular. > Is there any possibility of getting a chimerax plugin? > Regards > Krish > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Friday, July 12, 2024 1:22 PM > To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... > > [EXTERNAL] > > Hi Krishnan, > > We do not have any of the new 3D laptops to try ChimeraX. Let us know if it works. You will probably use the ChimeraX command "camera stereo" to put it into 3D model on one of these 3D laptops. > > Samsung also showed a 3D monitor at January's Consumer Electronics Show with rumors that it may come out this summer. Also don't know if ChimeraX will work on that display. > > While I think ChimeraX stereo is likely to work on these displays a problem with past stereo that used shutter glasses was that only workstation graphics cards could do stereo in a window, meaning that part of the display is showing 3D (e.g. the ChimeraX graphics pane) while the rest is showing 2D. This required special graphics driver support only offered in the workstation cards (like Nvidia Quadro) and not in the consumer cards. Full screen stereo where everything is rendered in 3D was available on consumer cards mostly for video games where everything is in 3D including user interface elements. > > Let us know if you get something working. > > Tom > > > > On Jul 12, 2024, at 8:56 AM, Krishnan Raman via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > https://link.edgepilot.com/s/22d26e4a/CHuCkVzwKkGj1oPV_qX5bQ?u=https://www.… > > maybe we can see chimerax😊 in 3d in these… they do have a plugin for unity.. Iam trying get one of these to try things out. > > Krishnan Raman > Executive Director, Structural Biology > BioCryst Pharmaceuticals > > > > > CONFIDENTIALITY NOTICE > > This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> > Archives: https://link.edgepilot.com/s/bb15c3bf/yEg7mgqw30m5lBrfcz6VNQ?u=https://mail… > > > > Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. > > > > CONFIDENTIALITY NOTICE > > This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >

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Chimerax Download
by Michael Gerber 18 Oct '24

18 Oct '24

To whom this may concern, Would it be possible to get the Chimerax zip download file for Windows? I have a school project I need to do it for and my presentation is coming up. Please and thank you! Best Michael

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Odp.: problems with accessing server
by Leszek Wawiórka 18 Oct '24

18 Oct '24

I have just found information (https://x.com/ucsfchimerax) that the server is down for several days so the problem seems to be resolved 😉. Best regards Leszek ________________________________ Od: Leszek Wawiórka Wysłane: środa, 16 października 2024 08:20:32 Do: chimerax-users(a)cgl.ucsf.edu Temat: problems with accessing server Hallo there, I'm contacting You because I encounter permanent problem with my connection with your server. I would like to re-install both chimera and chimeraX packages but I can't get to your home webpage. There is error just saying ERR_CONNECTION_TIMED_OUT. I have checked the connection with ping www.cgl.ucsf.edu<http://www.cgl.ucsf.edu> saying that there is no delay. It seems that I can't connect with UCSF server through port 443. The port works for other servers. I have checked it for several different internet connections. Please advise me why its like that? and what is more important, is there any way to fix it somehow. I'd really appreciate your help. I look forward to hearing from you. All the best Leszek Wawiórka Department of Molecular Biologu University of Maria Curie-Sklodowska in Lublin, Poland dr Leszek Wawiórka<https://www.umcs.pl/pl/addres-book-employee,2923,pl.html> Uniwersytet Marii Curie-Skłodowskiej w Lublinie www.umcs.pl UMCS dba o środowisko. Jeśli nie musisz, nie drukuj tego dokumentu. Mejl może zawierać informację poufne, objęte prawem własności intelektualnej lub tajemnicą Uniwersytetu Marii Curie-Skłodowskiej w Lublinie. Jeśli nie jesteś jego adresatem, powiadom o tym nadawcę i usuń wiadomość. Wykorzystanie treści mejla lub załączników jest zakazane. Dziękujemy!

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Question regarding licensing, when publishing data.
by Russ, Peter 14 Oct '24

14 Oct '24

Hi, I used your software for parts in an article where I also cited your requested quotes. The publisher wanted to confirm our licensing. In my understanding licensing is not a problem, as I am with the university for Stuttgart and don't earn money with this article. It would be nice if you could confirm this. Sincerely Peter Russ

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Interface Residue Plot
by Reza Khayat 13 Oct '24

13 Oct '24

Hi, I'm hoping this question wasn't asked before. Is there a way to draw a dotted line between interacting residues? This would be similar to the Chain Interface graph that shows interaction between chains. Thanks. Best wishes, Reza Reza Khayat, PhD City College of New York Associate Professor Department of Chemistry and Biochemistry Co-Director NIH G-RISE program

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saving a multi-model pdb with the subset of frames
by Enrico Martinez 11 Oct '24

11 Oct '24

Dear Chimera-X users! I am dealing with the visualization of a trajectory provided as the multi-model pdb contanained 3000 frames in multi-model format. How can I extract every 5th frame from a multi-model PDB file and save the reduced set of frames into a new PDB file, such that the new file contains five times fewer frames ? I've tried to do it like I did with the netcdf files but it does not work open ./my.pdb structureModel #1 step 5 Many thanks in advance Enriico

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Support for _ma_qa_metric_local_pairwise to display PAE matrices stored in ModelArchive
by Gerardo Tauriello 11 Oct '24

11 Oct '24

Dear ChimeraX developers, Following up on discussions in https://github.com/chaidiscovery/chai-lab/issues/52 and the large amounts of models which have been deposited in ModelArchive (MA; https://modelarchive.org/) in the meantime, I would propose to support loading PAE (or other local-pairwise scores) values from ModelCIF files as used by MA. Here I link some examples which should capture most use cases: 1. ma-bak-cepc-0944<https://www.modelarchive.org/doi/10.5452/ma-bak-cepc-0944> includes 2 local-pairwise scores (PAE and "contact probability") and only stores scores for inter-chain residue-pairs. 2. ma-dm-hisrep-003<https://www.modelarchive.org/doi/10.5452/ma-dm-hisrep-003> includes a full PAE matrix. 3. In all cases in MA, entries contain a single accompanying zip file which also contains the local pairwise scores which are extracted into a separate file to keep the main ModelCIF file at a manageable size. The linked modelcif_examples_for_chimerax.zip<https://sibcloud-my.sharepoint.com/:u:/g/personal/gerardo_tauriello_sib_swi…> package includes pae_associated_file where the pairwise scores are directly in a separate file instead of being in a zip file and pae_in_main_file which includes the pairwise scores directly in the main ModelCIF file. Already now ChimeraX is able to parse the ma_qa_metric_local category in ModelCIF to do per-residue coloring for pLDDT etc which is awesome. To make sense of ma_qa_metric_local_pairwise one needs the following (I try to be detailed to simplify the implementation): 1. Parse ma_qa_metric and keep the IDs (_ma_qa_metric.id) for rows with ma_qa_metric.mode == "local-pairwise". If we want to restrict this to PAE matrices, one would additionally check that _ma_qa_metric.type == "PAE". 2. Look for the _ma_qa_metric_local_pairwise category. There are 3 options on where to find it: * Directly in the main ModelCIF file (as in pae_in_main_file/003-Spombe_H3-H4_tetramer_DPB3.cif). * In a separate file via _ma_entry_associated_files (as in pae_associated_file/003-Spombe_H3-H4_tetramer_DPB3.cif). You can find the file via _ma_entry_associated_files.file_url for the _ma_entry_associated_files row with file_content == "local pairwise QA scores". * In a separate file via _ma_associated_archive_file_details (as in all MA entries such as ma-bak-cepc-0944 and ma-dm-hisrep-003). Procedure to get it: * Find row in _ma_associated_archive_file_details with file_content == "local pairwise QA scores" and keep archive_file_id and file_path. * Find zip file in _ma_entry_associated_files with id == archive_file_id and download via file_url. * Fetch file named file_path from that zip file. 3. Within the _ma_qa_metric_local_pairwise extract scores for all given residue pairs for metric_id matching the desired IDs from step 1. Each residue is identified with model_id, label_asym_id, label_seq_id, and (redundantly) label_comp_id. There are no guarantees on the order of the data or completeness of the data but each referenced residue is guaranteed to exist in the atom_site category. Here is the current list of model sets in MA which include PAE matrices: ma-bak-cepc<https://modelarchive.org/doi/10.5452/ma-bak-cepc>, ma-coffe-slac<https://modelarchive.org/doi/10.5452/ma-coffe-slac>, ma-tbvar3d<https://modelarchive.org/doi/10.5452/ma-tbvar3d>, ma-ornl-sphdiv<https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv>, ma-t3vr3<https://modelarchive.org/doi/10.5452/ma-t3vr3>, ma-low-csi<https://modelarchive.org/doi/10.5452/ma-low-csi>, ma-ombbaf2<https://modelarchive.org/doi/10.5452/ma-ombbaf2>, ma-rap-bacsu<https://modelarchive.org/doi/10.5452/ma-rap-bacsu>, ma-nmpfamsdb<https://modelarchive.org/doi/10.5452/ma-nmpfamsdb>, ma-jd-viral<https://modelarchive.org/doi/10.5452/ma-jd-viral>, ma-dm-prc<https://modelarchive.org/doi/10.5452/ma-dm-prc>, ma-dm-hisrep<https://modelarchive.org/doi/10.5452/ma-dm-hisrep>, ma-osf-ppp2r2a<https://modelarchive.org/doi/10.5452/ma-osf-ppp2r2a>. All together MA has over 200'000 models with PAE matrices which all supplement the AFDB in some way (e.g. protein complexes, viral proteins and other proteins not covered in UniProt). It would be great to include support for ModelArchive's ModelCIF files in ChimeraX and I am happy to provide further information and help as needed. Regards, Gerardo

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Re: [Chimera-users] Center and Orient
by Tom Goddard 10 Oct '24

10 Oct '24

You want sym #3 H,8,120,10,-5 as indicated in the documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html Tom > On Oct 9, 2024, at 2:50 PM, Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> wrote: > > Also when tryng to give the symetry explicitly I get an error. Perhaps I am using the wrong syntax (??) > > sym #3 sym-type H,8,120,10,-5 > Expected a keyword > > Thanks > > > H. > > > ___________________________________ > Hernando Sosa, PhD. > Dept. of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu > ___________________________________ > > > > From: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> > Sent: Wednesday, October 9, 2024 5:41 PM > To: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [Chimera-users] Center and Orient > > I need to explicitly give the symmetry (helical) because the command > > > measure symmetry #1 set true (#1 is my map) > > reports: > > No symmetry found for my_map.mrc > > > H. > > > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Wednesday, October 9, 2024 12:32 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> > Cc: chimera-users(a)cgl.ucsf.edu List <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Center and Orient > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > Hi Hernando, > > Here is how to apply symmetry to one copy of an atomic model in a symmetric cryoEM map in ChimeraX. First use the "measure symmetry" command to determine the map symmetry, then use the "sym" command to make the symmetric copies of the atomic model. Here is an example > > open 8ofx > open 16862 from emdb > measure symmetry #2 set true > sym #1 symmetry #2 > > Tom > > > On Oct 9, 2024, at 7:52 AM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks Elaine, > > I will try to do this with ChimeraX. What I am trying to to do is to generate symetry related copies of a model fitted into a density map using the sym command. I noticed that the only way to define the center of symetry to be centered on the density volume was using the option center #n (where n is the id of the voume density) but only after doing center and orient by pressing the buttons in the volume viewer. > > Although chimeraX is much more prowerful I still find hard to find the the equivalent in ChimeraX of some operations that I use often in Chimera. 😉 > > Thanks again, > > Best > > H. > > _ > From: Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> > Sent: Tuesday, October 8, 2024 5:04 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> > Cc: chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: Re: [Chimera-users] Center and Orient > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > > In Chimera, there may not be commands that do exactly the same thing as some button. You might look at "focus <model-number>" and "reset" (maybe only if one model is open, or they haven't been moved relative to one another?) but in my tests, they did not do exactly the same thing as those buttons. > > That's one reason ChimeraX is way better than Chimera! You can use the GUI and it shows the command that it used in the Log. > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Resource for Biocomputing, Visualization, and Informatics > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Oct 8, 2024, at 1:38 PM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: > > > > Dear Chimera, > > > > What would be the equivalent commands to the Center and Orient buttons at the bottom of the Volume Viewer menu tab? > > > > Thanks > > > > H. > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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Oct 14-20 Chimera(X) website downtime
by Elaine Meng 10 Oct '24

10 Oct '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable starting Monday, October 14, 10 AM PDT and continuing for several days, potentially through the following weekend (October 14-20). Apologies for the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Configuring ChimeraX AlphaFold “Fetch” and “Search” features
by Jim Thorpe 10 Oct '24

10 Oct '24

Hi ChimeraX Team In our commercial lab we are unable to access public domain AlphaFold databases, and instead have our own copy on-premises. Is there a mechanism to reconfigure the ChimeraX AlphaFold “Fetch” and “Search” features to query our in-house copy? ChimeraX error reported is: Fetching url https://alphafold.ebi.ac.uk/files/AF-Q5STB3-F1-model_v4.cif failed: HTTP Error 403: Forbidden Many Thanks for advising me Best Regards Jim [cid:image001.png@01DB1A36.151649E0] Jim Thorpe Scientific Investigator Protein, Cellular & Structural Sciences Target Discovery GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK james.h.thorpe(a)gsk.com [cid:image002.png@01DB1A36.151649E0]<https://www.gsk.com/> [cid:image003.png@01DB1A36.151649E0]<https://www.facebook.com/GSK> [cid:image004.png@01DB1A36.151649E0]<https://twitter.com/GSK> [cid:image005.png@01DB1A36.151649E0]<https://www.linkedin.com/company/glaxosmithkline> GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.

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Changing dihedral angle
by Prathvi Singh 09 Oct '24

09 Oct '24

Hi Elaine, Is it possible to change the dihedral angle between any given four sets of atoms, say CA,CB,CG, HG2 of a Lysine residue using command line in either chimera/chmeraX? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [Chimera-users] Center and Orient
by Tom Goddard 09 Oct '24

09 Oct '24

The documentation explains how to measure symmetry for a helical map https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry You have to use the helix option to give it some clue about the rise and twist angle per asymmetric unit step. Tom > On Oct 9, 2024, at 2:41 PM, Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> wrote: > > I need to explicitly give the symmetry (helical) because the command > > > measure symmetry #1 set true (#1 is my map) > > reports: > > No symmetry found for my_map.mrc > > > H. > > > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Wednesday, October 9, 2024 12:32 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> List <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: Re: [Chimera-users] Center and Orient > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > Hi Hernando, > > Here is how to apply symmetry to one copy of an atomic model in a symmetric cryoEM map in ChimeraX. First use the "measure symmetry" command to determine the map symmetry, then use the "sym" command to make the symmetric copies of the atomic model. Here is an example > > open 8ofx > open 16862 from emdb > measure symmetry #2 set true > sym #1 symmetry #2 > > Tom > > > On Oct 9, 2024, at 7:52 AM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks Elaine, > > I will try to do this with ChimeraX. What I am trying to to do is to generate symetry related copies of a model fitted into a density map using the sym command. I noticed that the only way to define the center of symetry to be centered on the density volume was using the option center #n (where n is the id of the voume density) but only after doing center and orient by pressing the buttons in the volume viewer. > > Although chimeraX is much more prowerful I still find hard to find the the equivalent in ChimeraX of some operations that I use often in Chimera. 😉 > > Thanks again, > > Best > > H. > > _ > From: Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> > Sent: Tuesday, October 8, 2024 5:04 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> > Cc: chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: Re: [Chimera-users] Center and Orient > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > > In Chimera, there may not be commands that do exactly the same thing as some button. You might look at "focus <model-number>" and "reset" (maybe only if one model is open, or they haven't been moved relative to one another?) but in my tests, they did not do exactly the same thing as those buttons. > > That's one reason ChimeraX is way better than Chimera! You can use the GUI and it shows the command that it used in the Log. > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Resource for Biocomputing, Visualization, and Informatics > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Oct 8, 2024, at 1:38 PM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: > > > > Dear Chimera, > > > > What would be the equivalent commands to the Center and Orient buttons at the bottom of the Volume Viewer menu tab? > > > > Thanks > > > > H. > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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How to remove a biological assembly from an atomic model
by Guillaume Gaullier 09 Oct '24

09 Oct '24

Hello, I am using the asymmetric unit of a PDB entry to define my own biological assembly based on a symmetric cryoEM map. Using the sym command, I can store the new biological assembly in the cif file. However, it seems I can't remove the biological assembly that came with the PDB entry's annotation, but that is now completely irrelevant because I moved the coordinates into my map (when I apply it, I get new chains completely outside the map). Is there a way to do this without needing to edit the cif file with a text editor? Thank you, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Images in background
by Enrico Martinez 08 Oct '24

08 Oct '24

Dear ChimeraX Development Team, I would like to extend my appreciation for your continuous work on ChimeraX and the powerful capabilities it offers for molecular visualization. I previously inquired about the possibility of using static images as backgrounds, similar to what is available in UCSF Chimera. Together, we discovered a workaround by loading an image as a model, adjusting its orientation, and setting it as a static background. However, there is still a significant limitation: when rotating a molecular model (defined in a separate model), the entire scene—including the background—rotates. This compromises the visual experience, as it disrupts the intended static nature of the background image. I would like to formally request the introduction of a more robust solution that allows for the following: - The ability to set static images as true background elements that remain fixed when manipulating other models (e.g., rotating or zooming in on molecular structures). - Support for short background animations, allowing users to load video or animated files that can play while the molecular models are rotated and manipulated independently. These features would greatly enhance the flexibility and presentation capabilities of ChimeraX, making it easier to create high-quality visualizations and presentations. I believe many users would benefit from these enhancements. Thank you for considering this request, and I look forward to any updates on the possibility of implementing these features. Yours sincerely Enrico

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Buried SAS Area selection
by Fernando Villa 07 Oct '24

07 Oct '24

Dear Chimera users I have been trying to select the atoms involved in the interface of a receptor/ligand complex in ChimeraX without success. In UCSF Chimera e.g. open 4RSC del solvent sel #0:.b del sel select ligand zr>10 del sel focus measure buriedArea protein ligand sel @/buriedSASArea “Only atoms at the interface are selected” = OK **The interface buried area calculation was performed and the atoms involved in the buried area were selected. However, I wish to do the same in ChimeraX, for surface area calculations: e.g. open 4RSC del solvent del /B select ::name="A3V" view sel measure buriedarea protein withAtoms2 ligand sel t list t cutoff 0 “All atoms in the interface are selected per residue” = KO The results of the calculations are the following: UCSF Chimera = 719.643 ChimeraX = 719.65 = OK I have difficulties to select only the atoms in the interface, not all atoms of the residues, I have tried several ways to do this but it has been complicated, I even tried to insert the command “sel @/buriedSASArea” of UCSF Chimera in ChimeraX without success. Sincerely. Fer <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus.www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Color Zone
by Mark Rosenberg 07 Oct '24

07 Oct '24

Using an atomic model and map, when I colour a different zone, I "lose" the colour from the previous zone I coloured. Is this a bug? This is in Windows 11. Thanks in advance.

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