attributes from viewdockx.
Hi guys, * Make ViewDockX table information available as model attributes<https://rbvi.github.io/chimerax-recipes/vdx_attrs/vdx_attrs.html>. December 17, 2021 Used this Py to register my attributes into chimerax. Is there a way to display the attributes next to the model of the ligand? Thanks 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.
Hi Krish, See the "label" command and its "attribute" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html#options> There are several examples in the explanation of the option, .e.g.: label /A:1 residues attr structure.name height 5 offset 1,1,1 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 May 28, 2024, at 1:21 PM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi guys, • Make ViewDockX table information available as model attributes. December 17, 2021 Used this Py to register my attributes into chimerax. Is there a way to display the attributes next to the model of the ligand? Thanks Krish
Hi guys, label #1:1 attr structure.vdx_Registration_Number offset -10,-10,1 height 2. I have this working after a I read in a *.mol2 file and attached the attributes to each structure. Can I have additional attributes displayed alongside from the same attribute list? Thanks Krish -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, May 28, 2024 3:35 PM To: Krishnan Raman <RKrishnan@BIOCRYST.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] attributes from viewdockx. [EXTERNAL] Hi Krish, See the "label" command and its "attribute" option: <https://link.edgepilot.com/s/1dea9e8c/lZKXJdUqZECgkgm0ow-M2w?u=https://rbvi....> <https://link.edgepilot.com/s/47edf4aa/QQV5o3jY1k_07gWSHFARAA?u=https://rbvi....> There are several examples in the explanation of the option, .e.g.: label /A:1 residues attr structure.name height 5 offset 1,1,1 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 May 28, 2024, at 1:21 PM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi guys, • Make ViewDockX table information available as model attributes. December 17, 2021 Used this Py to register my attributes into chimerax. Is there a way to display the attributes next to the model of the ligand? Thanks Krish
Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. 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.
Hi Krish, Yes, you can put multiple attribute values in the same label, but in that case you would need to use the "text" option instead, see for example the phi,psi and name/number examples in the "label" command option examples: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html#options> 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 May 30, 2024, at 1:50 PM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi guys, label #1:1 attr structure.vdx_Registration_Number offset -10,-10,1 height 2. I have this working after a I read in a *.mol2 file and attached the attributes to each structure. Can I have additional attributes displayed alongside from the same attribute list? Thanks Krish
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, May 28, 2024 3:35 PM To: Krishnan Raman <RKrishnan@BIOCRYST.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] attributes from viewdockx.
[EXTERNAL]
Hi Krish, See the "label" command and its "attribute" option:
<https://link.edgepilot.com/s/1dea9e8c/lZKXJdUqZECgkgm0ow-M2w?u=https://rbvi....> <https://link.edgepilot.com/s/47edf4aa/QQV5o3jY1k_07gWSHFARAA?u=https://rbvi....>
There are several examples in the explanation of the option, .e.g.:
label /A:1 residues attr structure.name height 5 offset 1,1,1
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 May 28, 2024, at 1:21 PM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi guys, • Make ViewDockX table information available as model attributes. December 17, 2021 Used this Py to register my attributes into chimerax. Is there a way to display the attributes next to the model of the ligand? Thanks Krish
[cid:image001.png@01DAB34D.7A85BE50] Elaine, I am stuck with this command . can you please help me out? Thanks. Krish -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Sent: Tuesday, May 28, 2024 3:35 PM To: Krishnan Raman <RKrishnan@BIOCRYST.com<mailto:RKrishnan@BIOCRYST.com>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] attributes from viewdockx. [EXTERNAL] Hi Krish, See the "label" command and its "attribute" option: <https://link.edgepilot.com/s/1dea9e8c/lZKXJdUqZECgkgm0ow-M2w?u=https://rbvi....> <https://link.edgepilot.com/s/47edf4aa/QQV5o3jY1k_07gWSHFARAA?u=https://rbvi....> There are several examples in the explanation of the option, .e.g.: label /A:1 residues attr structure.name height 5 offset 1,1,1 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 May 28, 2024, at 1:21 PM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi guys,
• Make ViewDockX table information available as model attributes. December 17, 2021
Used this Py to register my attributes into chimerax.
Is there a way to display the attributes next to the model of the ligand?
Thanks
Krish
Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. 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.
Hi Krish, Did you look at the examples in the link I sent before? <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html#options> You need a space after the word text. You should not have #1.1 or the words "residues attributes" inside the stuff in the quotes. These are separate arguments to the command, not the value of the "text" option which specifies what is inside the label. Also the "attribute" option is for labeling with only a single attribute, but you are not using that, instead you are using "text" so that you can label with multiple attributes. I don't know what your attributes are or what exactly you expect the result to look like, so I can't give you the exact command that you need, but if you are trying to label residues with two attributes of the structures named attrname1 and attrname2 with a comma between them it would be more like this: label #1.1 residues text "{0.structure.attrname1},{0.structure.attrname2}" 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 May 31, 2024, at 9:27 AM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
<image001.png>
Elaine, I am stuck with this command . can you please help me out? Thanks. Krish
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, May 28, 2024 3:35 PM To: Krishnan Raman <RKrishnan@BIOCRYST.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] attributes from viewdockx.
[EXTERNAL]
Hi Krish, See the "label" command and its "attribute" option:
<https://link.edgepilot.com/s/1dea9e8c/lZKXJdUqZECgkgm0ow-M2w?u=https://rbvi....> <https://link.edgepilot.com/s/47edf4aa/QQV5o3jY1k_07gWSHFARAA?u=https://rbvi....>
There are several examples in the explanation of the option, .e.g.:
label /A:1 residues attr structure.name height 5 offset 1,1,1
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 May 28, 2024, at 1:21 PM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi guys, • Make ViewDockX table information available as model attributes. December 17, 2021 Used this Py to register my attributes into chimerax. Is there a way to display the attributes next to the model of the ligand? Thanks Krish
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