Hello - I would like to request two features in ChimeraX that we use a lot in Chimera:
1. Render by Attribute 2. Ability to read .poc files created by CASTp
Thanks, Ishwar
On Jan 14, 2022, at 4:06 PM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello - I would like to request two features in ChimeraX that we use a lot in Chimera:
Hi Ishwar, Thanks for letting us know what's missing that's important to you. It helps us prioritize.
- Render by Attribute
This is being worked on and might, maybe make the 1.4 release. Well, in some form. Initially probably only Render/Colors and Select. Not too much later Render/Radii, but probably much later Render/Worms, since that last one will require significant additions to the ribbon-depiction code. If Render/Worms is very important to you, pipe up! :-)
I'll add you to the recipient list for the ticket we have for this so that you will automatically be notified when progress occurs.
- Ability to read .poc files created by CASTp
This had been pretty low priority. Are we talking about structures that you've run CASTp on by hand rather than fetched from the database? The database doesn't seem to include any recent structures.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
Hello Eric - thank you so much for the quick turnaround! My responses are below. - ir
On 1/18/2022 8:39 PM, Eric Pettersen wrote:
On Jan 14, 2022, at 4:06 PM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello - I would like to request two features in ChimeraX that we use a lot in Chimera:
Hi Ishwar, Thanks for letting us know what's missing that's important to you. It helps us prioritize.
- Render by Attribute
This is being worked on and /might, maybe/ make the 1.4 release. Well, in some form. Initially probably only Render/Colors and Select. Not too much later Render/Radii, but probably much later Render/Worms, since that last one will require significant additions to the ribbon-depiction code. If Render/Worms is very important to you, pipe up! :-)
I'll add you to the recipient list for the ticket we have for this so that you will automatically be notified when progress occurs.
Render by Attribute/Colors is what we use the most to map NMR chemical shift perturbations on to a structure, so I'm glad that it's receiving the highest priority!
- Ability to read .poc files created by CASTp
This had been pretty low priority. Are we talking about structures that you've run CASTp on by hand rather than fetched from the database? The database doesn't seem to include any recent structures.
Yes, I'm talking about the ability to read .poc files for structures for which we have manually asked CASTp to calculate pockets on their webserver.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 19, 2022, at 6:59 AM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Eric - thank you so much for the quick turnaround! My responses are below. - ir
On 1/18/2022 8:39 PM, Eric Pettersen wrote:
On Jan 14, 2022, at 4:06 PM, Ishwar Radhakrishnan via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hello - I would like to request two features in ChimeraX that we use a lot in Chimera:
Hi Ishwar, Thanks for letting us know what's missing that's important to you. It helps us prioritize.
- Render by Attribute
This is being worked on and might, maybe make the 1.4 release. Well, in some form. Initially probably only Render/Colors and Select. Not too much later Render/Radii, but probably much later Render/Worms, since that last one will require significant additions to the ribbon-depiction code. If Render/Worms is very important to you, pipe up! :-)
I'll add you to the recipient list for the ticket we have for this so that you will automatically be notified when progress occurs.
Render by Attribute/Colors is what we use the most to map NMR chemical shift perturbations on to a structure, so I'm glad that it's receiving the highest priority!
Good to know.
- Ability to read .poc files created by CASTp
This had been pretty low priority. Are we talking about structures that you've run CASTp on by hand rather than fetched from the database? The database doesn't seem to include any recent structures.
Yes, I'm talking about the ability to read .poc files for structures for which we have manually asked CASTp to calculate pockets on their webserver.
Very doable. I'll open a ticket with you cc'ed so you'll know when something happens.
--Eric
Hi Ishwar, In case you didn't know already: in ChimeraX now, you can use the "color byattribute" command to do it. It's not as convenient as the Render by Attribute GUI, in that you can't see the histogram of values and interactively position the colors on the histogram, but if you already had a standard color-to-value mapping that you prefer, it is just specified directly in the command.
Example: open 2gbp color byattribute bfactor palette 0,blue:20,red:40,yellow key true
command details: https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute
To assign your custom attribute, ChimeraX also already reads the "attribute file" format like Chimera, and it has a Color Key tool.
The "key true" option in the example command above shows a color key and brings up the dialog for redrawing/sizing by hand and optionally changing any other color key parameters.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2022, at 11:46 AM, Eric Pettersen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jan 19, 2022, at 6:59 AM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Eric - thank you so much for the quick turnaround! My responses are below. - ir
On 1/18/2022 8:39 PM, Eric Pettersen wrote:
On Jan 14, 2022, at 4:06 PM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello - I would like to request two features in ChimeraX that we use a lot in Chimera:
Hi Ishwar, Thanks for letting us know what's missing that's important to you. It helps us prioritize.
- Render by Attribute
This is being worked on and might, maybe make the 1.4 release. Well, in some form. Initially probably only Render/Colors and Select. Not too much later Render/Radii, but probably much later Render/Worms, since that last one will require significant additions to the ribbon-depiction code. If Render/Worms is very important to you, pipe up! :-)
I'll add you to the recipient list for the ticket we have for this so that you will automatically be notified when progress occurs.
Render by Attribute/Colors is what we use the most to map NMR chemical shift perturbations on to a structure, so I'm glad that it's receiving the highest priority!
Good to know.
- Ability to read .poc files created by CASTp
This had been pretty low priority. Are we talking about structures that you've run CASTp on by hand rather than fetched from the database? The database doesn't seem to include any recent structures.
Yes, I'm talking about the ability to read .poc files for structures for which we have manually asked CASTp to calculate pockets on their webserver.
Very doable. I'll open a ticket with you cc'ed so you'll know when something happens.
--Eric
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks for the tip, Elaine. I gave it a go and it works very nicely if the attribute is already present in the PDB file (e.g., b-factor). But what about if we wished to display a custom attribute like chemical shift perturbation; we could do that in Chimera via the Define Attribute and Render Attribute features. Is there a way to define a custom attribute in ChimeraX?
Thanks much, Ishwar
On 1/19/2022 2:05 PM, Elaine Meng wrote:
Hi Ishwar, In case you didn't know already: in ChimeraX now, you can use the "color byattribute" command to do it. It's not as convenient as the Render by Attribute GUI, in that you can't see the histogram of values and interactively position the colors on the histogram, but if you already had a standard color-to-value mapping that you prefer, it is just specified directly in the command.
Example: open 2gbp color byattribute bfactor palette 0,blue:20,red:40,yellow key true
command details: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
To assign your custom attribute, ChimeraX also already reads the "attribute file" format like Chimera, and it has a Color Key tool.
The "key true" option in the example command above shows a color key and brings up the dialog for redrawing/sizing by hand and optionally changing any other color key parameters.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2022, at 11:46 AM, Eric Pettersen via ChimeraX-userschimerax-users@cgl.ucsf.edu wrote:
On Jan 19, 2022, at 6:59 AM, Ishwar Radhakrishnan via ChimeraX-userschimerax-users@cgl.ucsf.edu wrote:
Hello Eric - thank you so much for the quick turnaround! My responses are below. - ir
On 1/18/2022 8:39 PM, Eric Pettersen wrote:
On Jan 14, 2022, at 4:06 PM, Ishwar Radhakrishnan via ChimeraX-userschimerax-users@cgl.ucsf.edu wrote:
Hello - I would like to request two features in ChimeraX that we use a lot in Chimera:
Hi Ishwar, Thanks for letting us know what's missing that's important to you. It helps us prioritize.
- Render by Attribute
This is being worked on and might, maybe make the 1.4 release. Well, in some form. Initially probably only Render/Colors and Select. Not too much later Render/Radii, but probably much later Render/Worms, since that last one will require significant additions to the ribbon-depiction code. If Render/Worms is very important to you, pipe up! :-)
I'll add you to the recipient list for the ticket we have for this so that you will automatically be notified when progress occurs.
Render by Attribute/Colors is what we use the most to map NMR chemical shift perturbations on to a structure, so I'm glad that it's receiving the highest priority!
Good to know.
- Ability to read .poc files created by CASTp
This had been pretty low priority. Are we talking about structures that you've run CASTp on by hand rather than fetched from the database? The database doesn't seem to include any recent structures.
Yes, I'm talking about the ability to read .poc files for structures for which we have manually asked CASTp to calculate pockets on their webserver.
Very doable. I'll open a ticket with you cc'ed so you'll know when something happens.
--Eric
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
Hi Ishwar, How were you defining your custom attribute in Chimera? All of the same methods are available in ChimeraX.
I.e. ChimeraX reads the same attribute file format as Chimera (in ChimeraX you would just name the file ending in .defattr and use "open" to open it), or you can use the "setattr" command to set one value at a time.
See ChimeraX help links https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2022, at 12:41 PM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks for the tip, Elaine. I gave it a go and it works very nicely if the attribute is already present in the PDB file (e.g., b-factor). But what about if we wished to display a custom attribute like chemical shift perturbation; we could do that in Chimera via the Define Attribute and Render Attribute features. Is there a way to define a custom attribute in ChimeraX?
Thanks much, Ishwar
On 1/19/2022 2:05 PM, Elaine Meng wrote:
Hi Ishwar, In case you didn't know already: in ChimeraX now, you can use the "color byattribute" command to do it. It's not as convenient as the Render by Attribute GUI, in that you can't see the histogram of values and interactively position the colors on the histogram, but if you already had a standard color-to-value mapping that you prefer, it is just specified directly in the command.
Example: open 2gbp color byattribute bfactor palette 0,blue:20,red:40,yellow key true
command details:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
To assign your custom attribute, ChimeraX also already reads the "attribute file" format like Chimera, and it has a Color Key tool.
The "key true" option in the example command above shows a color key and brings up the dialog for redrawing/sizing by hand and optionally changing any other color key parameters.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2022, at 11:46 AM, Eric Pettersen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jan 19, 2022, at 6:59 AM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Eric - thank you so much for the quick turnaround! My responses are below. - ir
On 1/18/2022 8:39 PM, Eric Pettersen wrote:
On Jan 14, 2022, at 4:06 PM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello - I would like to request two features in ChimeraX that we use a lot in Chimera:
Hi Ishwar, Thanks for letting us know what's missing that's important to you. It helps us prioritize.
- Render by Attribute
This is being worked on and might, maybe make the 1.4 release. Well, in some form. Initially probably only Render/Colors and Select. Not too much later Render/Radii, but probably much later Render/Worms, since that last one will require significant additions to the ribbon-depiction code. If Render/Worms is very important to you, pipe up! :-)
I'll add you to the recipient list for the ticket we have for this so that you will automatically be notified when progress occurs.
Render by Attribute/Colors is what we use the most to map NMR chemical shift perturbations on to a structure, so I'm glad that it's receiving the highest priority!
Good to know.
- Ability to read .poc files created by CASTp
This had been pretty low priority. Are we talking about structures that you've run CASTp on by hand rather than fetched from the database? The database doesn't seem to include any recent structures.
Yes, I'm talking about the ability to read .poc files for structures for which we have manually asked CASTp to calculate pockets on their webserver.
Very doable. I'll open a ticket with you cc'ed so you'll know when something happens.
--Eric
ChimeraX-users mailing list
ChimeraX-users@cgl.ucsf.edu
Manage subscription:
https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
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Thanks, Elaine; we'll give it a try in ChimeraX. Below is the file format we import into Chimera (in this case the custom attribute is resonance peak intensity ratio but could be other things like chemical shift perturbation):
attribute: intensity recipient: residues :250 0 :251 9.977277803 :252 19.70945973 :253 23.07676553 :254 20.8434625
etc.
Best, Ishwar
On 1/19/2022 3:03 PM, Elaine Meng wrote:
Hi Ishwar, How were you defining your custom attribute in Chimera? All of the same methods are available in ChimeraX.
I.e. ChimeraX reads the same attribute file format as Chimera (in ChimeraX you would just name the file ending in .defattr and use "open" to open it), or you can use the "setattr" command to set one value at a time.
See ChimeraX help links <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/formats...
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2022, at 12:41 PM, Ishwar Radhakrishnan via ChimeraX-userschimerax-users@cgl.ucsf.edu wrote:
Thanks for the tip, Elaine. I gave it a go and it works very nicely if the attribute is already present in the PDB file (e.g., b-factor). But what about if we wished to display a custom attribute like chemical shift perturbation; we could do that in Chimera via the Define Attribute and Render Attribute features. Is there a way to define a custom attribute in ChimeraX?
Thanks much, Ishwar
On 1/19/2022 2:05 PM, Elaine Meng wrote:
Hi Ishwar, In case you didn't know already: in ChimeraX now, you can use the "color byattribute" command to do it. It's not as convenient as the Render by Attribute GUI, in that you can't see the histogram of values and interactively position the colors on the histogram, but if you already had a standard color-to-value mapping that you prefer, it is just specified directly in the command.
Example: open 2gbp color byattribute bfactor palette 0,blue:20,red:40,yellow key true
command details:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
To assign your custom attribute, ChimeraX also already reads the "attribute file" format like Chimera, and it has a Color Key tool.
The "key true" option in the example command above shows a color key and brings up the dialog for redrawing/sizing by hand and optionally changing any other color key parameters.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2022, at 11:46 AM, Eric Pettersen via ChimeraX-userschimerax-users@cgl.ucsf.edu wrote:
On Jan 19, 2022, at 6:59 AM, Ishwar Radhakrishnan via ChimeraX-userschimerax-users@cgl.ucsf.edu wrote:
Hello Eric - thank you so much for the quick turnaround! My responses are below. - ir
On 1/18/2022 8:39 PM, Eric Pettersen wrote:
> On Jan 14, 2022, at 4:06 PM, Ishwar Radhakrishnan via ChimeraX-userschimerax-users@cgl.ucsf.edu > wrote: > > Hello - I would like to request two features in ChimeraX that we use a lot in Chimera: > Hi Ishwar, Thanks for letting us know what's missing that's important to you. It helps us prioritize.
> 1. Render by Attribute > This is being worked on and might, maybe make the 1.4 release. Well, in some form. Initially probably only Render/Colors and Select. Not too much later Render/Radii, but probably much later Render/Worms, since that last one will require significant additions to the ribbon-depiction code. If Render/Worms is very important to you, pipe up! :-)
I'll add you to the recipient list for the ticket we have for this so that you will automatically be notified when progress occurs.
Render by Attribute/Colors is what we use the most to map NMR chemical shift perturbations on to a structure, so I'm glad that it's receiving the highest priority!
Good to know.
> 2. Ability to read .poc files created by CASTp > This had been pretty low priority. Are we talking about structures that you've run CASTp on by hand rather than fetched from the database? The database doesn't seem to include any recent structures.
Yes, I'm talking about the ability to read .poc files for structures for which we have manually asked CASTp to calculate pockets on their webserver.
Very doable. I'll open a ticket with you cc'ed so you'll know when something happens.
--Eric
ChimeraX-users mailing list
ChimeraX-users@cgl.ucsf.edu
Manage subscription:
https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
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Hi Ishwar,
Here is an example coloring a surface by NMR chemical shift perturbation value.
https://www.rbvi.ucsf.edu/chimerax/data/nanobody-feb2021/chemshift.html https://www.rbvi.ucsf.edu/chimerax/data/nanobody-feb2021/chemshift.html
Tom
On Jan 19, 2022, at 1:28 PM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks, Elaine; we'll give it a try in ChimeraX. Below is the file format we import into Chimera (in this case the custom attribute is resonance peak intensity ratio but could be other things like chemical shift perturbation):
attribute: intensity recipient: residues :250 0 :251 9.977277803 :252 19.70945973 :253 23.07676553 :254 20.8434625
etc.
Best, Ishwar
On 1/19/2022 3:03 PM, Elaine Meng wrote:
Hi Ishwar, How were you defining your custom attribute in Chimera? All of the same methods are available in ChimeraX.
I.e. ChimeraX reads the same attribute file format as Chimera (in ChimeraX you would just name the file ending in .defattr and use "open" to open it), or you can use the "setattr" command to set one value at a time.
See ChimeraX help links <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/formats... > https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!BITeDaDhhKKMpK7-YbQQ4gyRpHTNS2EfeJghadh1GtVdxRVddC0oc76JWNN3TZt7gPxHRK24Ofw$ <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... > https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!BITeDaDhhKKMpK7-YbQQ4gyRpHTNS2EfeJghadh1GtVdxRVddC0oc76JWNN3TZt7gPxH27hDLaU$
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2022, at 12:41 PM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu wrote:
Thanks for the tip, Elaine. I gave it a go and it works very nicely if the attribute is already present in the PDB file (e.g., b-factor). But what about if we wished to display a custom attribute like chemical shift perturbation; we could do that in Chimera via the Define Attribute and Render Attribute features. Is there a way to define a custom attribute in ChimeraX?
Thanks much, Ishwar
On 1/19/2022 2:05 PM, Elaine Meng wrote:
Hi Ishwar, In case you didn't know already: in ChimeraX now, you can use the "color byattribute" command to do it. It's not as convenient as the Render by Attribute GUI, in that you can't see the histogram of values and interactively position the colors on the histogram, but if you already had a standard color-to-value mapping that you prefer, it is just specified directly in the command.
Example: open 2gbp color byattribute bfactor palette 0,blue:20,red:40,yellow key true
command details:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... > https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html*byattribute__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!GAojFDIw0WEbNhxXklg8cYlrwx_rWN3jpgRQLGUVaJMGYDFHzpcBlenSJRdEc17nT-6J8ooYzcw$
To assign your custom attribute, ChimeraX also already reads the "attribute file" format like Chimera, and it has a Color Key tool.
The "key true" option in the example command above shows a color key and brings up the dialog for redrawing/sizing by hand and optionally changing any other color key parameters.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2022, at 11:46 AM, Eric Pettersen via ChimeraX-users chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu wrote:
On Jan 19, 2022, at 6:59 AM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu wrote:
Hello Eric - thank you so much for the quick turnaround! My responses are below. - ir
On 1/18/2022 8:39 PM, Eric Pettersen wrote:
>> On Jan 14, 2022, at 4:06 PM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu >> wrote: >> >> Hello - I would like to request two features in ChimeraX that we use a lot in Chimera: >> > Hi Ishwar, > Thanks for letting us know what's missing that's important to you. It helps us prioritize. > > >> 1. Render by Attribute >> > This is being worked on and might, maybe make the 1.4 release. Well, in some form. Initially probably only Render/Colors and Select. Not too much later Render/Radii, but probably much later Render/Worms, since that last one will require significant additions to the ribbon-depiction code. If Render/Worms is very important to you, pipe up! :-) > > I'll add you to the recipient list for the ticket we have for this so that you will automatically be notified when progress occurs. > > Render by Attribute/Colors is what we use the most to map NMR chemical shift perturbations on to a structure, so I'm glad that it's receiving the highest priority!
Good to know.
>> 2. Ability to read .poc files created by CASTp >> > This had been pretty low priority. Are we talking about structures that you've run CASTp on by hand rather than fetched from the database? The database doesn't seem to include any recent structures. > > Yes, I'm talking about the ability to read .poc files for structures for which we have manually asked CASTp to calculate pockets on their webserver.
Very doable. I'll open a ticket with you cc'ed so you'll know when something happens.
--Eric
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This will very handy; thank you, Tom.
Ishwar
On 1/19/2022 4:13 PM, Tom Goddard wrote:
Hi Ishwar,
Here is an example coloring a surface by NMR chemical shift perturbation value.
https://www.rbvi.ucsf.edu/chimerax/data/nanobody-feb2021/chemshift.html https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/data/nanobody-feb2021/chemshift.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!DMQP_xovEie4Fnv2AHX-MdxTqOmb07LBjFxghcncOHR6V3CgEsCzk_iz9w69jg-WxuinSu9mxbc$
Tom
On Jan 19, 2022, at 1:28 PM, Ishwar Radhakrishnan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks, Elaine; we'll give it a try in ChimeraX. Below is the file format we import into Chimera (in this case the custom attribute is resonance peak intensity ratio but could be other things like chemical shift perturbation):
attribute: intensity recipient: residues :250 0 :251 9.977277803 :252 19.70945973 :253 23.07676553 :254 20.8434625
etc.
Best, Ishwar
On 1/19/2022 3:03 PM, Elaine Meng wrote:
Hi Ishwar, How were you defining your custom attribute in Chimera? All of the same methods are available in ChimeraX.
I.e. ChimeraX reads the same attribute file format as Chimera (in ChimeraX you would just name the file ending in .defattr and use "open" to open it), or you can use the "setattr" command to set one value at a time.
See ChimeraX help links <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/formats...
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2022, at 12:41 PM, Ishwar Radhakrishnan via ChimeraX-userschimerax-users@cgl.ucsf.edu wrote:
Thanks for the tip, Elaine. I gave it a go and it works very nicely if the attribute is already present in the PDB file (e.g., b-factor). But what about if we wished to display a custom attribute like chemical shift perturbation; we could do that in Chimera via the Define Attribute and Render Attribute features. Is there a way to define a custom attribute in ChimeraX?
Thanks much, Ishwar
On 1/19/2022 2:05 PM, Elaine Meng wrote:
Hi Ishwar, In case you didn't know already: in ChimeraX now, you can use the "color byattribute" command to do it. It's not as convenient as the Render by Attribute GUI, in that you can't see the histogram of values and interactively position the colors on the histogram, but if you already had a standard color-to-value mapping that you prefer, it is just specified directly in the command.
Example: open 2gbp color byattribute bfactor palette 0,blue:20,red:40,yellow key true
command details:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
To assign your custom attribute, ChimeraX also already reads the "attribute file" format like Chimera, and it has a Color Key tool.
The "key true" option in the example command above shows a color key and brings up the dialog for redrawing/sizing by hand and optionally changing any other color key parameters.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2022, at 11:46 AM, Eric Pettersen via ChimeraX-userschimerax-users@cgl.ucsf.edu wrote:
> On Jan 19, 2022, at 6:59 AM, Ishwar Radhakrishnan via ChimeraX-userschimerax-users@cgl.ucsf.edu > wrote: > > Hello Eric - thank you so much for the quick turnaround! My responses are below. - ir > > On 1/18/2022 8:39 PM, Eric Pettersen wrote: > >>> On Jan 14, 2022, at 4:06 PM, Ishwar Radhakrishnan via ChimeraX-userschimerax-users@cgl.ucsf.edu >>> wrote: >>> >>> Hello - I would like to request two features in ChimeraX that we use a lot in Chimera: >>> >> Hi Ishwar, >> Thanks for letting us know what's missing that's important to you. It helps us prioritize. >> >> >>> 1. Render by Attribute >>> >> This is being worked on and might, maybe make the 1.4 release. Well, in some form. Initially probably only Render/Colors and Select. Not too much later Render/Radii, but probably much later Render/Worms, since that last one will require significant additions to the ribbon-depiction code. If Render/Worms is very important to you, pipe up! :-) >> >> I'll add you to the recipient list for the ticket we have for this so that you will automatically be notified when progress occurs. >> >> > Render by Attribute/Colors is what we use the most to map NMR chemical shift perturbations on to a structure, so I'm glad that it's receiving the highest priority! > Good to know.
>>> 2. Ability to read .poc files created by CASTp >>> >> This had been pretty low priority. Are we talking about structures that you've run CASTp on by hand rather than fetched from the database? The database doesn't seem to include any recent structures. >> >> > Yes, I'm talking about the ability to read .poc files for structures for which we have manually asked CASTp to calculate pockets on their webserver. > Very doable. I'll open a ticket with you cc'ed so you'll know when something happens.
--Eric
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participants (4)
-
Elaine Meng -
Eric Pettersen -
Ishwar Radhakrishnan -
Tom Goddard