January 2024 - ChimeraX-users - RBVI Mailing Lists

Question about Cylinder Representation
by Bi, Maxine 09 Jan '24

09 Jan '24

Hi there, I've been stuck trying to make my cylinder representation straight instead of curved as the default. I've tried many commands that I can find in the documentation. Could you please guide me if there is a way to just make the cylinders straight? There is a command like that in Pymol as an example (see link: https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense.com_v3_-5F-… ). Thank you so much, Maxine

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retrieve the sequence of an atom selection
by Engeholm, Maik 09 Jan '24

09 Jan '24

Hi there, I'm looking for a neat way to retrieve the sequence of an atom selection (in this case part of a double-stranded DNA molecule) from within a python script. I've been playing around with: selection = run (session, 'select #1/A:2-4|#1/B:6-9') for a in selection.atoms.unique_residues: print(a) which gives me: 151 atoms, 169 bonds, 7 residues, 1 model selected /A DG 2 /A DG 3 /A DG 4 /B G 6 /B G 7 /B A 8 /B T 9 This is a good start, but ideally I'd like to get back a contiguous sequence string for each chain (like (('A', 'GGG'), ('B', GGAT'))). Also, I do not really understand, why residue names are reported as 'DG' for strand A, but 'G' for strand B, which makes extracting a sequence string from the above output quite difficult. I've also tried: selection = run (session, 'select #1/A:2-4|#1/B:6-9') for a in selection.atoms.by_chain: print(a[1]) print(a[2].unique_residues.unique_sequences[0][1]) which gives me: 151 atoms, 169 bonds, 7 residues, 1 model selected A AGGGAGTAATCCCCTTG B CAAGGGGATTACTCCCT This is obviously also not what I want since it returns the entire sequence of each chain. I guess I could take the residue numbers from the first command and use those to slice the strings returned by the second, but that feels a little awkward, and so I was wondering if there was a better, more direct way to achieve this seemingly simple task. Your help would be much appreciated. Cheers, Maik

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ChimeraX : Cannot recommend to my class until minimization with vital cofactors such as FAD, NADH is built in. Returning to Chimera.
by Anne-Frances Miller 09 Jan '24

09 Jan '24

Dear Sir or Madam, After devoting several days to updating three weeks of my course to use ChimeraX instead of Chimera, I am returning to Chimera. ChimeraX may be a great cutting-edge tool, but it is not ready for a wider audience until it can make ‘common’ tasks easy. Please do not distance research from science. We desperately need science to be exciting and accessible to a wide audience. Chimera does that. ChimeraX does the opposite, sending the clear message that only an elite few are deemed worthy. Please please please, open the door to wider use, for the sake of science, and for the sake of the citizens of our country (who fund your agencies via taxes). Very Helpful - To make images with transparent backgrounds, members of my class as not going to type out ’transparentbackground true’ (even my emailer wants to spell the first string as two words). CRUCIAL - in-program minimization that includes critical cofactors (present in >40% of all enzymes and the actual source of their activities often!!) FAD, FMN, NAD(H), how is this anything more than structural biology if the sources of activity are not included? (‘biology’ implies life. Life REQUIRES chemical reactivity.) CRUCIAL - in-program trajectory analysis that can tabulate (for example) a distance, frame-by-frame and allow export in tabular form. Very Helpful - worms with thicknesses that can represent an attribute. These provide a critical orthogonal way to add a second attribute when color is already in use for a first. Very Helpful - Lighting/effects/side view GUI that allows easy optimization of figure reflectivity, special effects, all in one place and does not require users to remember what Cartesian coordinates they gave their first light. It is so much faster and delivers much better results than ChimeraX. This email records the current worst applicability gaps only, I see others have reported more. I would like to like ChimeraX, but as a person trying to bring science to wide audiences, ChimeraX is the best argument for Pymol I have seen in a while. Do not stop supporting Chimera until ChimeraX can serve real humans, please! Sincerely, and thanks to the team, Anne-Frances Novel Meritorious Research (and teaching) —•—•—•—•—•—•—•—•—•—•—•—•—•— A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

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Depth cueing
by Paul Miller 09 Jan '24

09 Jan '24

Hi How do I depth cue in ChimeraX? In Chimera I used to be able to precisely control this from the side view window but I cannot find any way of controlling depth cueing in ChimeraX. Thank you. Cheers, Paul Paul Miller (he/him), PhD University Lecturer in Pharmacology Department of Pharmacology University of Cambridge Tennis Court Road Cambridge CB2 1PD +44 1223 761267 https://www.phar.cam.ac.uk/research/miller

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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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