- ChimeraX-users - RBVI Mailing Lists

Re: [Chimera-users] Finding SASA for individual residues
by Elaine Meng 29 Aug '24

29 Aug '24

Hi Ale, In the future please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd here) for ChimeraX questions. This chimera-users@cgl address is for Chimera, which is a different program, and I don't want to confuse the other users. Everybody, this answer is for ChimeraX: I believe you are misunderstanding how "measure sasa" works. It will actually enclose the specified atoms in a surface, so if you say "measure sasa :12" that surface will only be around residue 12 and ignore all the other atoms. I am guessing that you really want the SASA of the aromatic rings in the context of the surface that goes around the whole protein, not for a bunch of individual bubbles drawn around each aromatic ring. In that case, your commands are wrong. Instead you want something like: measure sasa protein sum :trp,tyr,phe & aromatic-ring See "measure sasa" help for description of how it works: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> I hope this helps, 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 Aug 29, 2024, at 4:16 AM, alessandro.strofaldi--- via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > I'll reply to this post for my question cause the title seems appropriate. > I've a one-chain protein and I simply want to calculate the SASA of the aromatic-ring of all TRP,TYR and PHE of the protein using ChimeraX. > > This is the log: > measure sasa /A > Solvent accessible area for /A = 22276 > measure sasa /A:trp & aromatic-ring > Solvent accessible area for /A:trp & aromatic-ring = 1824.9 > measure sasa /A:phe & aromatic-ring > Solvent accessible area for /A:phe & aromatic-ring = 3339.6 > measure sasa /A:tyr & aromatic-ring > Solvent accessible area for /A:tyr & aromatic-ring = 3977.3 > > But the I tried to get the sum: > > measure sasa /A:trp,tyr,phe & aromatic-ring sum :trp,tyr,phe > Solvent accessible area for /A:trp,tyr,phe & aromatic-ring = 7683.3 > Solvent accessible area for :trp,tyr,phe (285 atoms) of /A:trp,tyr,phe & aromatic-ring = 7683.3 > > Which is different from the sum of the values I got before. I think I'm missing something basic on SASA calculations... > Also, from your answer to Prathvi, those numbers should be squared Agstrom. Do these number make sense? For a single residue (measure sasa:263, which is a surface-exposed Tyrosine) I got 331.95. Those values are similar to what Prathvi got so am I doing the same mistake? I was expecting, for a single residue something like two order of magnitude less. > You said ".. then it will make a surface that only encloses that one residue, with area 292 as you said. I'm pretty sure that is NOT what you want. Instead you want tthe surface of the whole protein (or maybe one chain) and then the area of the residue given that larger surface. " Does this means that with the commands I typed ChimeraX "Isolates" the residue and calculate the SASA as if it was not included in the protein? > Anyway, I think it is clear I'm an unexpert user so If there is any tutorial about SASA on ChimeraX (could not find those, only for Chimera), please, feel free to suggest. > > Thank you!! > Best, > Ale

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Re: Command line interface saving
by Mark Rosenberg 26 Aug '24

26 Aug '24

Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk<mailto:mark.rosenberg@manchester.ac.uk> mjfssmr mark.rosenberg(a)manchester.ac.uk<mailto:mark.rosenberg@manchester.ac.uk>mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:46, mjfssmr <http://mark.rosenberg@manchester.ac.uk> wrote: Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:31, Guillaume Gaullier <http://guillaume.gaullier@KEMI.UU.SE> wrote: Hello, The log of your saved session should be there, but it is hidden at the top of the log window when you re-open the session file. There should be a black triangle that you can click to open the log contents from the previous session. I hope this helps, Guillaume ________________________________ From: Mark Rosenberg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Monday, August 26, 2024 1:26:25 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Command line interface saving Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. 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/ [http://uu.se<https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifte…> 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 [http://uu.se<https://urldefense.com/v3/__http://www.uu.se/en/about-uu/data-protection-po…>

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Re: Command line interface saving
by Guillaume Gaullier 26 Aug '24

26 Aug '24

Not that I know, sorry. But maybe somebody else knows, so it is better to keep the list in CC. 😊 Cheers, Guillaume ________________________________ From: Mark Rosenberg <mark.rosenberg(a)manchester.ac.uk> Sent: Monday, August 26, 2024 1:46:29 PM To: Guillaume Gaullier Subject: Re: Command line interface saving Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:31, Guillaume Gaullier <guillaume.gaullier(a)KEMI.UU.SE> wrote: Hello, The log of your saved session should be there, but it is hidden at the top of the log window when you re-open the session file. There should be a black triangle that you can click to open the log contents from the previous session. I hope this helps, Guillaume ________________________________ From: Mark Rosenberg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Monday, August 26, 2024 1:26:25 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Command line interface saving Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. 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/ [uu.se]<https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifte…> 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 [uu.se]<https://urldefense.com/v3/__http://www.uu.se/en/about-uu/data-protection-po…> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

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Command line interface saving
by Mark Rosenberg 26 Aug '24

26 Aug '24

Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark

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molmap command question
by Grigory Mechetin, Ph.D. 23 Aug '24

23 Aug '24

Dear ChimeraX developers, when I use the molmap command on grid ('molmap #1 10 onGrid #2', grid2 was created with' vop new size 256,256,256 gridSpacing 0.74' command ) I get half-map. How to get the full one? When I use molmap without onGrid it generates the volume with non-equal grid size, but I need square 256^3 grid. [cid:3853c8fe-0ccd-4133-ba08-4732e3be8905] Best regards, Grigory Mechetin, PhD, MEMS, Duke University.

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Data handling / privacy policy information?
by Frumolt, Brian 23 Aug '24

23 Aug '24

Hi, We are looking at ChimeraX for commercial use. I was looking on the site for information related to data use and privacy policies. I understand the app runs locally, but was wondering whether it leverages any web services, or passes any data outside the local installation? We have strict data handling policies in place for our clients, so would need to be aware. If there is a policy document I missed, that would be ideal. Thanks! Brian This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto.

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Morphing two GPCR conformations
by Enrico Martinez 23 Aug '24

23 Aug '24

Dear Chimera-X users! I try to use the morph command to model the conformational change of GPCR related to its activation. Having two superimposed conformations of the receptor, which are different in the position of the internal part of the transmembrane helix VI, I try to visualize the displacement of this helix using morph #2,1 frames 250 Unfortunately the produced trajectory looks very unnatural (one helix overlaps with another one). Would it be possible to improve the accuracy of such morphing e.g. providing some restraints? Many thanks in advance ! Enrico

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Mol 2.0 desktop version
by Nicholas Koylass 22 Aug '24

22 Aug '24

Good day, I am trying to interface ChimeraX with a XML file that was converted to json to perform MOLE Channel Coloring by Property. However, I did not use the mole server. I used the desktop version since the server was unavailable. Thus, I received this error : molepore-7sqf.json does not look like Mole Online json file, does not contain Channels. Can anyone assist me with this? Thanks, Respectfully, Nicholas Nicholas Koylass Ph.D. Candidate, Department of Physiology, Qiu Lab XDBio Graduate Program Johns Hopkins School of Medicine nkoylas1(a)jh.edu

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Restoration of missing helical fragments of the structure
by Enrico Martinez 22 Aug '24

22 Aug '24

Dear Chimera-X users ! Suppose I have a pdb structure with a missed C-terminal fragment corresponding to the transmembrane helical part that should anchor the protein in the membrane. Is it possible to use some built-in utilities (modeller?) to predict this missing fragment based on the full length sequence of the entire construct? Many thanks in advance Enrico

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results swiss dock
by Aurélie Hoeffel 21 Aug '24

21 Aug '24

Dear Chimeras members, I obtained some docking results from swiss dock, unfortunately my result.dock4 document is not readable in chimerax, I did not achieve to open it. Is it something special I have to do? Because, on the website it is written that we can directly upload it and it will work but for me chimerax did not recognize my .dock4 document. What should I do? Thank for the answer, Aurelie Hoeffel

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