January 2024 - ChimeraX-users - RBVI Mailing Lists

Hydrophobic comparison
by M.J. 09 Jan '24

09 Jan '24

Hi Dear ChimeraX developers, I met a problem and cannot find a solution on the website. I have a protein that has two conformations, in those two conformations the hydrophobic character is different, I can show them clearly by the command of mlp in Chimerax, super convenient! My question is that is there a way to show the difference quantitatively? or can be shown in one molecule and color the different on one molecule? (What I means is, for conformation A each residue has a parameter for hydrophobic, so as conformation B, can I get the numbers and do a subtraction correspondingly and know which conformation is more hydrophobic quantitatively, and even I can color one of the conformation by the subtraction). Thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171

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Subscribe
by Hernando J Sosa 05 Jan '24

05 Jan '24

How do I subscribe to this (ChimeraX users) list? When I click the subscribe link in: file:///C:/Program Files/ChimeraX/bin/share/docs/contact.html I get an error message (Page not found). Thanks Hernando ___________________________________ 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: chimerax-users-bounces(a)cgl.ucsf.edu <chimerax-users-bounces(a)cgl.ucsf.edu> Sent: Friday, January 5, 2024 12:42 PM To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> Subject: Your message to chimerax-users(a)cgl.ucsf.edu awaits moderator approval 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. Your mail to 'chimerax-users(a)cgl.ucsf.edu' with the subject Python IDE Is being held until the list moderator can review it for approval. The message is being held because: The message is not from a list member Either the message will get posted to the list, or you will receive notification of the moderator's decision.

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Re: Python IDE
by sette＠uniroma2.it 05 Jan '24

05 Jan '24

Yes. Tools --> General -- Shell Best regards, Marco Il 05/01/2024 18:42, Hernando J Sosa via ChimeraX-users ha scritto: > Dear ChimeraX, > > Does chimera-X come with an IDE to edit and run python scripts?, > something like IDLE in Chimera? > > Thanks > Hernando > > ___________________________________ > 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 > ___________________________________ > > > > _______________________________________________ > ChimeraX-users mailing list --chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email tochimerax-users-leave(a)cgl.ucsf.edu > Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl… -- Dr Marco Sette, PhD. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it Tel.: +39-0672594424

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Python IDE
by Hernando J Sosa 05 Jan '24

05 Jan '24

Dear ChimeraX, Does chimera-X come with an IDE to edit and run python scripts?, something like IDLE in Chimera? Thanks Hernando ___________________________________ 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 ___________________________________

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Re: [Chimera-users] Changing threshold value of attributes
by Eric Pettersen 05 Jan '24

05 Jan '24

Hi Abril, There are separate mailing list for Chimera and ChimeraX, so you should send ChimeraX questions to chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> . The problem you ran into has been fixed and the fix is in the 1.7 release candidate, so if you use that then things will work. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Nov 28, 2023, at 10:25 AM, Abril Gijsbers via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear community, > > I want to render my model by attribute and change the thresholds (up and bottom limits). I want to change the 0.3 to 0.1 and the 2.6 to 2.7 (see the figure), this way I can compare the colour intensity with other conditions. > <image.png> > > When I do that, I get the following error. My ignorance in command use limits my understanding. Could someone help me out to understand this? I have a colleague that changes the up and bottom limit with no problem. Why? :( > > ui tool show <> "Render By Attribute" > Traceback (most recent call last): > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 759, in _set_value_cb > self._redraw_cb() > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 646, in _redraw_cb > self._bins = left + filled_bins + right > ValueError: operands could not be broadcast together with shapes (0,) (157,) > > ValueError: operands could not be broadcast together with shapes (0,) (157,) > > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 646, in _redraw_cb > self._bins = left + filled_bins + right > > See log for complete Python traceback. > > Traceback (most recent call last): > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 760, in _set_value_cb > self._move_cur_marker(v) > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 570, in _move_cur_marker > self._active_markers._update_plot() > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 1222, in _update_plot > self._update_marker_coordinates() > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 1207, in _update_marker_coordinates > x, y = self._scene_xy(m.xy) > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 1090, in _scene_xy > return self.histogram._scene_xy(abs_xy) > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 512, in _scene_xy > num_bins = len(self._bins) > TypeError: object of type 'function' has no len() > > TypeError: object of type 'function' has no len() > > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 512, in _scene_xy > num_bins = len(self._bins) > > See log for complete Python traceback. > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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volume amount estimation
by Jesse Hansen 05 Jan '24

05 Jan '24

dear ChimeraX users, We have a tomogram volume (.mrc) which we have segmented different components (stl files; surfaces). Is there any tool available to estimate the volume within each of the cellular components (within each surface)? Either some approximation of the cubic Angstrom/nanometers, or as a percentage of the total tomogram volume. thanks in advance! best Jesse Hansen

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looking glass technology for chimerax,
by Krishnan Raman 05 Jan '24

05 Jan '24

Hi guys, Happy new year. I came across this https://www.schrodinger.com/3d-visualization-looking-glass-holographic-disp… . Can we look forward to having this compatible for chimerax since we are having difficulty finding 3D stereo displays for structural biology. Regards Krish 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.

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Tile behavior in Chimera vs ChimeraX - different behavior of independent rotation?
by Oliver Clarke 04 Jan '24

04 Jan '24

Hi all, Happy new year! I have some observations/queries regarding the "tile models" command in Chimera vs ChimeraX. In Chimera, the rotation mode is not linked to a specific mouse mode - so if I change it from "front center" to "independent", this will affect rotation of models regardless of how I do it - whether using the mouse, the trackpad, or using the rock, roll or turn commands on the command line. In ChimeraX, independent rotation is now a separate mousemode - so it only applies to whatever mouse mode (e.g. left mouse) one has it applied to, and does not apply to the trackpad or command line. Is there any prospect of altering this behavior, or mimicking the old behavior? When tiling many models (or maps) for comparison, I like to view them with a rocking motion to give better 3D perception, but now I can't do this (it just rocks the entire "plane" of dispersed models, rather than each independently). Cheers Oli

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Error when trying to run previously working script
by Alexander Hung Lee 04 Jan '24

04 Jan '24

I have a .py script that successfully works on 400 pdb's. I tried using the same script to open a single pdb containing several thousand models. ChimeraX quit and sent me this error message in terminal "Release of profile requested but webenginepage still not deleted" Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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ChimeraX Inquiry
by ‍강유은[학생](대학원 생명공학원) 03 Jan '24

03 Jan '24

Hello I would like to purchase the premium GPU A100 to predict large proteins. How can I get access to the purchasing page? Regards, Yoo Kang

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