Hello Alessio, ChimeraX does not have a ribbon style editor tool. You can change the ribbon (cartoon) width, height, etc. with the "cartoon style" command, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> There are also a few different ribbon presets in the Presets menu. <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#presets> 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 Jul 22, 2024, at 6:38 AM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I have been an academic user of chimera for years. I have just downloaded chimerax but I cannot find the ribbon style editor. Can you please help?

Best regards

Alessio

See <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> for full explanation of each parameter, but here are some examples: cartoon style helix width 1 thickness 0.5 cartoon style strand width 1 thickness 0.5 cartoon style arrowScale 3 cartoon style coil thickness 0.25 Also if you use the Presets menu to apply the cartoon styles it will show all the commands in the Log, so that is a way to see more examples. Elaine

On Jul 22, 2024, at 1:13 PM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thank you. But I did not understand how to modify the width and thickness of the helix, sheet, coil and arrow sections. Can you help please?

Best

A

Il giorno lun 22 lug 2024 alle ore 17:59 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Hello Alessio, ChimeraX does not have a ribbon style editor tool. You can change the ribbon (cartoon) width, height, etc. with the "cartoon style" command, see:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

There are also a few different ribbon presets in the Presets menu.

<https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#presets>

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 Jul 22, 2024, at 6:38 AM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I have been an academic user of chimera for years. I have just downloaded chimerax but I cannot find the ribbon style editor. Can you please help?

Best regards

Alessio

-- Dr. Alessio Nocentini Ricercatore Legge 240/10 a tempo determinato - Tipo B UNIVERSITÀ DEGLI STUDI DI FIRENZE Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) ECCELLENZA 2023-2027 Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Hi Alessio, It is another option of the "cartoon" command, "suppressBackboneDisplay false", which you can shorten when you enter, for example: cartoon suppress false There are lots of options in each command that we don't want to explain one by one, so you should really take a look at the help pages: <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> Best, Elaine

On Jul 22, 2024, at 3:00 PM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Ok thanks. It worked! Moreover, I would like to show both ribbon and backbone. In the old Chimera I was using "ribbackbone", but here it is not working. Can you help please?

Best

A

Il giorno lun 22 lug 2024 alle ore 23:15 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: See <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> for full explanation of each parameter, but here are some examples:

cartoon style helix width 1 thickness 0.5 cartoon style strand width 1 thickness 0.5 cartoon style arrowScale 3 cartoon style coil thickness 0.25

Also if you use the Presets menu to apply the cartoon styles it will show all the commands in the Log, so that is a way to see more examples.

Elaine

...

On Jul 22, 2024, at 1:13 PM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thank you. But I did not understand how to modify the width and thickness of the helix, sheet, coil and arrow sections. Can you help please?

Best

A

Il giorno lun 22 lug 2024 alle ore 17:59 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Hello Alessio, ChimeraX does not have a ribbon style editor tool. You can change the ribbon (cartoon) width, height, etc. with the "cartoon style" command, see:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

There are also a few different ribbon presets in the Presets menu.

<https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#presets>

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 Jul 22, 2024, at 6:38 AM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I have been an academic user of chimera for years. I have just downloaded chimerax but I cannot find the ribbon style editor. Can you please help?

Best regards

Alessio

-- Dr. Alessio Nocentini Ricercatore Legge 240/10 a tempo determinato - Tipo B UNIVERSITÀ DEGLI STUDI DI FIRENZE Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) ECCELLENZA 2023-2027 Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

-- Dr. Alessio Nocentini Ricercatore Legge 240/10 a tempo determinato - Tipo B UNIVERSITÀ DEGLI STUDI DI FIRENZE Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) ECCELLENZA 2023-2027 Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Hello Alessio, If you mean a session file, where you can open this file later in ChimeraX to restore your work, that file type is .cxs --- although Chimera had a .py session file, ChimeraX does not, it has .cxs instead. E.g. command save myfile.cxs ...or use menu: File... Save and choose Files of type: ChimeraX session. Later you can start ChimeraX and then open the .cxs file to restore your work, with the "open" command or menu: File... Open. Session file information: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> 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 12, 2024, at 6:29 AM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine,

I need your support, as I do not understand how to save a project .py file in chimeraX. I tried to follow the instructions, but did not find it.

Thank you

Best

A

Hi Alessio, ChimeraX does not read Chimera session files (.py). However, if you start from Chimera, you can save your project as a file to open ChimeraX. In Chimera, choose menu File... Export Scene, then choose file type: ChimeraX (also .py but is different than a Chimera session). See Chimera help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html> Then you can exit Chimera, start ChimeraX, and open the file you just saved (ChimeraX "open" command or menu: File... Open). This export does not include every type of data, though -- from the help link above: "includes atomic models, molecular surfaces, volume models (surface, mesh, image, plane/orthoplane, and box renderings), per-model clipping, sequences and sequence alignments, 2D labels and arrows, and color key. Not supported: per-vertex colorings of surfaces (e.g., by value, distance, or zone), nucleotide representations, worms, other types of surface models, etc." So if you had nucleotide representations, worms, or special surface colorings, you may have to regenerate them in ChimeraX. 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 27, 2024, at 8:26 AM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine,

I have another doubt. How do I open a Chimera project in ChimeraX. Is it possible?

Thank you for the support

best

Alessio

Hi Alessio, You can hide any atoms that you want. Those backbone atoms are shown because you showed the atoms of the whole residue, and "cartoon suppress false" means to allow showing backbone atoms at the same time as cartoon. You can either just hide those atoms, or if you don't want to see any backbone atoms at the same time as ribbon, do not use "suppress false" with "cartoon". There is no reason to use that option unless you want to show some backbone atoms at the same time as cartoon. Even with "suppress false", however, you can just hide any/all of the atoms. If you showed the whole residue :35 in chain A, for example, that will include backbone atoms N and C and O. You can hide them with command: hide /A:35@N,C,O Or, if you don't want to figure out the residue numbers, you can Ctrl-click on the atoms to select them (selecting shows green outline) and use menu Actions... Atoms/Bonds... Hide. <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions> See explanation of the cartoon "suppress" option (suppressBackboneDisplay): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> 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 28, 2024, at 12:22 AM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thanks a lot Elaine.

I propose you an example. Here is the figure. When typing "cartoon suppress false" I got these segments in red: how can I unshow them? How can I show the backbone for some residues only? In fact, I do not want to show backbones of residues such as those in green.

Thank you again

Best

Alessio

<Example.jpg>

I don't know what you mean by "segments". You can hide any atoms that you want, as described in the previous message, which will also hide their bonds. You can also hide ribbon segments, e.g. hide /A:35 ribbons If you mean those cones drawn between atoms and ribbon, they are "tethers" which you can hide by (a) hiding the atoms, or (b) making the tethers transparent, e.g. for residue :35 in chain /A: cartoon tether /A:35 opacity 0 See "cartoon tether" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether <mhttps://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether>> I hope this helps, Elaine

On Aug 28, 2024, at 8:38 AM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Perfect. What about the segments circled red? I cannot click on them to unshow.

Thanks

A

Il giorno mer 28 ago 2024 alle ore 17:30 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Hi Alessio, You can hide any atoms that you want. Those backbone atoms are shown because you showed the atoms of the whole residue, and "cartoon suppress false" means to allow showing backbone atoms at the same time as cartoon. You can either just hide those atoms, or if you don't want to see any backbone atoms at the same time as ribbon, do not use "suppress false" with "cartoon". There is no reason to use that option unless you want to show some backbone atoms at the same time as cartoon.

Even with "suppress false", however, you can just hide any/all of the atoms. If you showed the whole residue :35 in chain A, for example, that will include backbone atoms N and C and O. You can hide them with command:

hide /A:35@N,C,O

Or, if you don't want to figure out the residue numbers, you can Ctrl-click on the atoms to select them (selecting shows green outline) and use menu Actions... Atoms/Bonds... Hide. <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions>

See explanation of the cartoon "suppress" option (suppressBackboneDisplay): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>

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 28, 2024, at 12:22 AM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thanks a lot Elaine.

I propose you an example. Here is the figure. When typing "cartoon suppress false" I got these segments in red: how can I unshow them? How can I show the backbone for some residues only? In fact, I do not want to show backbones of residues such as those in green.

Thank you again

Best

Alessio

<Example.jpg>

-- Dr. Alessio Nocentini Ricercatore Legge 240/10 a tempo determinato - Tipo B UNIVERSITÀ DEGLI STUDI DI FIRENZE Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) ECCELLENZA 2023-2027 Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Dear Elaine, sorry for asking again for your support, but I am having problems in passing from Chimera to ChimeraX. Although I checked thoroughly the guidelines, I did not find how to reduce the size of the Arrow Tips (as they were called in Chimera, ribbon style editor panel), to fit the size of the coil. Here you have my case. Thank you a lot Best Alessio [image: image.png] Il giorno mer 28 ago 2024 alle ore 17:48 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:

I don't know what you mean by "segments". You can hide any atoms that you want, as described in the previous message, which will also hide their bonds. You can also hide ribbon segments, e.g.

hide /A:35 ribbons

If you mean those cones drawn between atoms and ribbon, they are "tethers" which you can hide by (a) hiding the atoms, or (b) making the tethers transparent, e.g. for residue :35 in chain /A:

cartoon tether /A:35 opacity 0

See "cartoon tether" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether <mhttps://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether>>

I hope this helps, Elaine

...

On Aug 28, 2024, at 8:38 AM, Alessio Nocentini via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Perfect. What about the segments circled red? I cannot click on them to unshow.

Thanks

A

Il giorno mer 28 ago 2024 alle ore 17:30 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Hi Alessio, You can hide any atoms that you want. Those backbone atoms are shown because you showed the atoms of the whole residue, and "cartoon suppress false" means to allow showing backbone atoms at the same time as cartoon. You can either just hide those atoms, or if you don't want to see any backbone atoms at the same time as ribbon, do not use "suppress false" with "cartoon". There is no reason to use that option unless you want to show some backbone atoms at the same time as cartoon.

Even with "suppress false", however, you can just hide any/all of the atoms. If you showed the whole residue :35 in chain A, for example, that will include backbone atoms N and C and O. You can hide them with command:

hide /A:35@N,C,O

Or, if you don't want to figure out the residue numbers, you can Ctrl-click on the atoms to select them (selecting shows green outline) and use menu Actions... Atoms/Bonds... Hide. <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions>

See explanation of the cartoon "suppress" option (suppressBackboneDisplay): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>

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 28, 2024, at 12:22 AM, Alessio Nocentini via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Thanks a lot Elaine.

I propose you an example. Here is the figure. When typing "cartoon suppress false" I got these segments in red: how can I unshow them? How can I show the backbone for some residues only? In fact, I do not want to show backbones of residues such as those in green.

Thank you again

Best

Alessio

<Example.jpg>

-- Dr. Alessio Nocentini Ricercatore Legge 240/10 a tempo determinato - Tipo B UNIVERSITÀ DEGLI STUDI DI FIRENZE Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) ECCELLENZA 2023-2027 Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

-- Dr. Alessio Nocentini <https://cercachi.unifi.it/p-doc2-0-0-A-3f2b3c29372831.html> *Ricercatore Legge 240/10 a tempo determinato - Tipo B* *UNIVERSITÀ DEGLI STUDI DI FIRENZE* Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) *ECCELLENZA 2023-2027* Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685

Dear Elaine, just another quick question. I use silhouettes in my figures. Is it possible not to have them for bonds, contacts, distances? In Chimera these elements did not have silhouettes. Thanks Alessio Il giorno mer 28 ago 2024 alle ore 22:55 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:

Dear Alessio, (I changed the Subject line so that other people may be able to find this answer later.)

Unfortunately there is no specific option for arrow-tip width. Probably you have already been looking at the options of the "cartoon style" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

To minimize the difference between the arrow tip and coil segment, the only choices I can see are to use a smaller "arrowScale" value, although that will decrease the width of the whole arrowhead, not just the tip. For example,

cartoon style arrowScale 1.5

Another issue is that the arrow tip is still an oval rather than circular cross-section like the coil. To get it closer to a circle requires increasing the fineness of triangulations along the ribbon path with the "divisions" value, for example

cartoon style divisions 40

Using higher values increases number of triangles drawn and may slow responsiveness of the program. Cartoon style won't let you use >40, but if you want an even higher number you can use a different command to do it, for example

graphics quality ribbonDivisions 100

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality>

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 28, 2024, at 1:25 PM, Alessio Nocentini via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine, sorry for asking again for your support, but I am having problems in passing from Chimera to ChimeraX. Although I checked thoroughly the guidelines, I did not find how to reduce the size of the Arrow Tips (as they were called in Chimera, ribbon style editor panel), to fit the size of the coil. Here you have my case.

Thank you a lot Best

Alessio

<image.png>

I

-- Dr. Alessio Nocentini <https://cercachi.unifi.it/p-doc2-0-0-A-3f2b3c29372831.html> *Ricercatore Legge 240/10 a tempo determinato - Tipo B* *UNIVERSITÀ DEGLI STUDI DI FIRENZE* Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) *ECCELLENZA 2023-2027* Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685

Dear Elaine, is it possible to display a MD done with Desmond (Schrodinger) in Chimera or ChimeraX? If yes, how can I do? Thank you Best regards A Il giorno gio 29 ago 2024 alle ore 17:50 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:

Sorry no. In Chimera these pseudobonds were flat lines (wire), and covalent bonds could also be shown as wire, but ChimeraX uses 3-dimensional cylinders, and all the 3-dimensional items get silhouettes.

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 7:19 AM, Alessio Nocentini via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine,

just another quick question. I use silhouettes in my figures. Is it possible not to have them for bonds, contacts, distances? In Chimera these elements did not have silhouettes.

Thanks

Alessio

-- Dr. Alessio Nocentini <https://cercachi.unifi.it/p-doc2-0-0-A-3f2b3c29372831.html> *Ricercatore Legge 240/10 a tempo determinato - Tipo B* *UNIVERSITÀ DEGLI STUDI DI FIRENZE* Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) *ECCELLENZA 2023-2027* Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685

Dear Elaine, I would like to ask for your support again. I have a visual problem with this type of protein (see attached image). The coils in the red square should be b-sheets. I do not know why Chimera or ChimeraX show them as coils. Are there settings to change to show them correctly? Thank you Best regards A Il giorno mar 3 set 2024 alle ore 17:16 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:

Hi Alessio, I don't know. It depends what format(s) the trajectory is in. Or, if Desmond does not write a format that Chimera or ChimeraX understands, maybe you can convert it with some other program.

Here are the trajectory formats ChimeraX can read <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory>

Here are the trajectory formats Chimera can read < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie....

...

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 Sep 3, 2024, at 1:36 AM, Alessio Nocentini via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine,

is it possible to display a MD done with Desmond (Schrodinger) in Chimera or ChimeraX? If yes, how can I do?

Thank you

Best regards

A

-- Dr. Alessio Nocentini <https://cercachi.unifi.it/p-doc2-0-0-A-3f2b3c29372831.html> *Ricercatore Legge 240/10 a tempo determinato - Tipo B* *UNIVERSITÀ DEGLI STUDI DI FIRENZE* Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) *ECCELLENZA 2023-2027* Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685

Dear Alessio, There are two possible reasons: (1) your input file (PDB or mmCIF) has helix and sheet information, but that information does not list these residues in sheet - OR - (2) your input does not have helix and sheet information, so ChimeraX tries to guess it -- this should be mentioned in the Log when you open the file Either way, however, how to fix it is the same. You can manually assign the secondary structure type as helix, strand, or coil. (A) One way is to use the "setattr" command to assign values of the residue attribute named "ss_type" as 1 (helix) or 2 (strand) instead of 0 (coil): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue> For example, to assign residues 10-15 of chain A as strand, command: setattr /A:10-15 r ss_type 2 Here is a previous post with more details about setting secondary structure with commands: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/IFC76NKUME5YWJCRQWSXMFMT3ICH3NQ7/> (B) Another way if you prefer using the graphical interface is to select the residue (e.g. Ctrl-click on residue) so that it has a green outline, then open the Selection Inspector (green magnifying glass icon in toolbar across top, or menu: Actions... Inspect). In the Selection Inspector tool, change from Inspect: "Atoms" to Inspect: "Residues", then set Secondary structure type to "strand" 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 Sep 9, 2024, at 1:16 AM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

<Senza titolo.png>

Il giorno lun 9 set 2024 alle ore 10:16 Alessio Nocentini <alessio.nocentini@unifi.it> ha scritto: Dear Elaine,

I would like to ask for your support again. I have a visual problem with this type of protein (see attached image). The coils in the red square should be b-sheets. I do not know why Chimera or ChimeraX show them as coils. Are there settings to change to show them correctly?

Thank you Best regards

A