Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.
Greetings, Chimera's ViewDock tool does not read .crd format. The help page for that tool lists the formats it can use: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html> However, the SwissDock website may also give you other files that you could open in Chimera. The "old" SwissDock website would give you an output file for Chimera (not .crd). See their old website including a video with instructions of how to view the results in Chimera: <http://old.swissdock.ch/> But maybe you tried the "new" website: <https://www.swissdock.ch/> I have not tried the new website but their own help page explains their output files: <https://www.swissdock.ch/FAQ.php> See answer to #2," What can I find in the results folder?" "Once you untar the results.tar.gz file you obtain a results folder, in which you can find, for Attracting Cavities: • parameters: the file containing your query parameters • result.dock4: the result file containing ligand poses • extra.par: the parameter file for the ligand and small molecules present • ligand.pdb: the ligand coordinate file • extra.rtf: the topology file for the ligand and small molecules present • receptor.crd: the receptor coordinate file • receptor.pdb: the receptor PDB file • receptor.psf: the receptor protein structure file For AutoDock Vina: • parameters: the file containing your query parameters • ligand.pdbqt: the pdbqt file of your ligand used for Vina • system.pdbqt: the pdbqt file of your target used for Vina • vina_out.pdb: the result file containing different ligand poses • vina_out.pdbqt: the result file in pdbqt format containing different ligand poses • and your query files" So there is no reason to open .crd anyway, since you could open receptor.pdb instead of receptor.crd if you need to show it. Also that is not even the results anyway, it is only the receptor. If you were using the AutoDock Vina option, you can view the vina_out.pdbqt file with Chimera's ViewDock tool. If you were using the Attracting Cavities option, it seems like the output is "result.dock4" ... I don't know what format that is, so I don't know if you can view that in Chimera or not. 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 2, 2024, at 3:09 AM, safi ch via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.
Greetings, hope you are doing great. Thank you for your detailed guidance; Respected Elaine Meng! I explored the UCSF Chimera and realized that .crd format is not available here. But there are 2 videos on YouTube where they could easily open .crd file from SwissDock on UCSF Chimera. So I thought perhaps there is a way to open it and I don't have the package installed. The SwissDock tool themselves have an attachment of installation file named 'open.chimerax' and I tried my best to incorporate it in Chimera (by copying that file to every folder in UCSF Chimera directory in C Disk) but could not succeed. I actually used both, new and old version of Swiss Dock, even used both docking options available in new interface; Docking with Attractive Cavities and Docking with AutoDock Vina. You are right that the files in newer version don't seem to have ligand bonded with target protein (hence why I went for older version as it has a folder name "clusters.zip" where seeds are given which are actually the protein-ligand complexes where you select a seed that has most favourable DDG value). The "result.dock4" file you are talking about is the sum of all seeds that the server came up with, so I cannot use it. I have to go for Molecular Dynamics Simulations so I was taking a shortcut but now I guess I would have to take a long route for doing so :). Regardless, have a bright day Miss/Ma'am or Sir, Thank you again! On Sat, Aug 3, 2024 at 12:14 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Greetings, Chimera's ViewDock tool does not read .crd format. The help page for that tool lists the formats it can use: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd....
However, the SwissDock website may also give you other files that you could open in Chimera.
The "old" SwissDock website would give you an output file for Chimera (not .crd). See their old website including a video with instructions of how to view the results in Chimera: <http://old.swissdock.ch/>
But maybe you tried the "new" website: <https://www.swissdock.ch/>
I have not tried the new website but their own help page explains their output files: <https://www.swissdock.ch/FAQ.php>
See answer to #2," What can I find in the results folder?"
"Once you untar the results.tar.gz file you obtain a results folder, in which you can find, for Attracting Cavities:
• parameters: the file containing your query parameters • result.dock4: the result file containing ligand poses • extra.par: the parameter file for the ligand and small molecules present • ligand.pdb: the ligand coordinate file • extra.rtf: the topology file for the ligand and small molecules present • receptor.crd: the receptor coordinate file • receptor.pdb: the receptor PDB file • receptor.psf: the receptor protein structure file
For AutoDock Vina: • parameters: the file containing your query parameters • ligand.pdbqt: the pdbqt file of your ligand used for Vina • system.pdbqt: the pdbqt file of your target used for Vina • vina_out.pdb: the result file containing different ligand poses • vina_out.pdbqt: the result file in pdbqt format containing different ligand poses • and your query files"
So there is no reason to open .crd anyway, since you could open receptor.pdb instead of receptor.crd if you need to show it. Also that is not even the results anyway, it is only the receptor. If you were using the AutoDock Vina option, you can view the vina_out.pdbqt file with Chimera's ViewDock tool. If you were using the Attracting Cavities option, it seems like the output is "result.dock4" ... I don't know what format that is, so I don't know if you can view that in Chimera or not.
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 2, 2024, at 3:09 AM, safi ch via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.
Hello Safi, This video shows opening swissdock results in Chimera, but you have to skip ahead to time 23-25 minutes: <https://www.youtube.com/watch?v=KcZ1EV_FcK8> That video is showing the old swissdock website. You just click some link on the web browser to automatically start Chimera. I don't think it uses the .crd file. You don't have to install any package. Just make sure you are using UCSF Chimera, not UCSF ChimeraX. Otherwise, I don't have any other suggestions. Elaine
On Aug 3, 2024, at 5:00 AM, safi ch via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing great. Thank you for your detailed guidance; Respected Elaine Meng!
I explored the UCSF Chimera and realized that .crd format is not available here. But there are 2 videos on YouTube where they could easily open .crd file from SwissDock on UCSF Chimera. So I thought perhaps there is a way to open it and I don't have the package installed. The SwissDock tool themselves have an attachment of installation file named 'open.chimerax' and I tried my best to incorporate it in Chimera (by copying that file to every folder in UCSF Chimera directory in C Disk) but could not succeed.
I actually used both, new and old version of Swiss Dock, even used both docking options available in new interface; Docking with Attractive Cavities and Docking with AutoDock Vina. You are right that the files in newer version don't seem to have ligand bonded with target protein (hence why I went for older version as it has a folder name "clusters.zip" where seeds are given which are actually the protein-ligand complexes where you select a seed that has most favourable DDG value). The "result.dock4" file you are talking about is the sum of all seeds that the server came up with, so I cannot use it.
I have to go for Molecular Dynamics Simulations so I was taking a shortcut but now I guess I would have to take a long route for doing so :). Regardless, have a bright day Miss/Ma'am or Sir, Thank you again!
On Sat, Aug 3, 2024 at 12:14 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Greetings, Chimera's ViewDock tool does not read .crd format. The help page for that tool lists the formats it can use: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>
However, the SwissDock website may also give you other files that you could open in Chimera.
The "old" SwissDock website would give you an output file for Chimera (not .crd). See their old website including a video with instructions of how to view the results in Chimera: <http://old.swissdock.ch/>
But maybe you tried the "new" website: <https://www.swissdock.ch/>
I have not tried the new website but their own help page explains their output files: <https://www.swissdock.ch/FAQ.php>
See answer to #2," What can I find in the results folder?"
"Once you untar the results.tar.gz file you obtain a results folder, in which you can find, for Attracting Cavities:
• parameters: the file containing your query parameters • result.dock4: the result file containing ligand poses • extra.par: the parameter file for the ligand and small molecules present • ligand.pdb: the ligand coordinate file • extra.rtf: the topology file for the ligand and small molecules present • receptor.crd: the receptor coordinate file • receptor.pdb: the receptor PDB file • receptor.psf: the receptor protein structure file
For AutoDock Vina: • parameters: the file containing your query parameters • ligand.pdbqt: the pdbqt file of your ligand used for Vina • system.pdbqt: the pdbqt file of your target used for Vina • vina_out.pdb: the result file containing different ligand poses • vina_out.pdbqt: the result file in pdbqt format containing different ligand poses • and your query files"
So there is no reason to open .crd anyway, since you could open receptor.pdb instead of receptor.crd if you need to show it. Also that is not even the results anyway, it is only the receptor. If you were using the AutoDock Vina option, you can view the vina_out.pdbqt file with Chimera's ViewDock tool. If you were using the Attracting Cavities option, it seems like the output is "result.dock4" ... I don't know what format that is, so I don't know if you can view that in Chimera or not.
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 2, 2024, at 3:09 AM, safi ch via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
I haven't used the swissdock website myself, but my guess is that when you click the "Launch UCSF Chimera" link on the "old SwissDock" website as shown in the video at time 23:30, it will download a Chimera web data file:
Chimera web data files are named something.chimerax (maybe your open.chimerax file??) and in the video, the download of such a file automatically starts Chimera to show it. Maybe you did not already configure Chimera to show .chimerax files and so it just got downloaded but nothing happened. Anyway you should be able to open that file in Chimera simply by using Chimera menu: File... Open, or you can configure your browser to make Chimera start automatically when that type of file is downloaded from a website. Please see the help for description of Chimera web data files: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> Elaine
On Aug 4, 2024, at 8:47 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello Safi, This video shows opening swissdock results in Chimera, but you have to skip ahead to time 23-25 minutes: <https://www.youtube.com/watch?v=KcZ1EV_FcK8>
That video is showing the old swissdock website. You just click some link on the web browser to automatically start Chimera. I don't think it uses the .crd file. You don't have to install any package. Just make sure you are using UCSF Chimera, not UCSF ChimeraX.
Otherwise, I don't have any other suggestions. Elaine
On Aug 3, 2024, at 5:00 AM, safi ch via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing great. Thank you for your detailed guidance; Respected Elaine Meng!
I explored the UCSF Chimera and realized that .crd format is not available here. But there are 2 videos on YouTube where they could easily open .crd file from SwissDock on UCSF Chimera. So I thought perhaps there is a way to open it and I don't have the package installed. The SwissDock tool themselves have an attachment of installation file named 'open.chimerax' and I tried my best to incorporate it in Chimera (by copying that file to every folder in UCSF Chimera directory in C Disk) but could not succeed.
I actually used both, new and old version of Swiss Dock, even used both docking options available in new interface; Docking with Attractive Cavities and Docking with AutoDock Vina. You are right that the files in newer version don't seem to have ligand bonded with target protein (hence why I went for older version as it has a folder name "clusters.zip" where seeds are given which are actually the protein-ligand complexes where you select a seed that has most favourable DDG value). The "result.dock4" file you are talking about is the sum of all seeds that the server came up with, so I cannot use it.
I have to go for Molecular Dynamics Simulations so I was taking a shortcut but now I guess I would have to take a long route for doing so :). Regardless, have a bright day Miss/Ma'am or Sir, Thank you again!
On Sat, Aug 3, 2024 at 12:14 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Greetings, Chimera's ViewDock tool does not read .crd format. The help page for that tool lists the formats it can use: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>
However, the SwissDock website may also give you other files that you could open in Chimera.
The "old" SwissDock website would give you an output file for Chimera (not .crd). See their old website including a video with instructions of how to view the results in Chimera: <http://old.swissdock.ch/>
But maybe you tried the "new" website: <https://www.swissdock.ch/>
I have not tried the new website but their own help page explains their output files: <https://www.swissdock.ch/FAQ.php>
See answer to #2," What can I find in the results folder?"
"Once you untar the results.tar.gz file you obtain a results folder, in which you can find, for Attracting Cavities:
• parameters: the file containing your query parameters • result.dock4: the result file containing ligand poses • extra.par: the parameter file for the ligand and small molecules present • ligand.pdb: the ligand coordinate file • extra.rtf: the topology file for the ligand and small molecules present • receptor.crd: the receptor coordinate file • receptor.pdb: the receptor PDB file • receptor.psf: the receptor protein structure file
For AutoDock Vina: • parameters: the file containing your query parameters • ligand.pdbqt: the pdbqt file of your ligand used for Vina • system.pdbqt: the pdbqt file of your target used for Vina • vina_out.pdb: the result file containing different ligand poses • vina_out.pdbqt: the result file in pdbqt format containing different ligand poses • and your query files"
So there is no reason to open .crd anyway, since you could open receptor.pdb instead of receptor.crd if you need to show it. Also that is not even the results anyway, it is only the receptor. If you were using the AutoDock Vina option, you can view the vina_out.pdbqt file with Chimera's ViewDock tool. If you were using the Attracting Cavities option, it seems like the output is "result.dock4" ... I don't know what format that is, so I don't know if you can view that in Chimera or not.
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 2, 2024, at 3:09 AM, safi ch via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
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Greetings, hope you are healthy. Thank you so much for your kind response and valuable information; Respected Elaine Meng! Yes sure please, big thanks for your detailed guidance and the video link. I will ensure to follow the steps you instructed. Thank you for your time! Regardless, have a bright day ahead. You helped me a lot in this regard, thanks again Dear Professor :) On Sun, Aug 4, 2024 at 8:47 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Safi, This video shows opening swissdock results in Chimera, but you have to skip ahead to time 23-25 minutes: <https://www.youtube.com/watch?v=KcZ1EV_FcK8>
That video is showing the old swissdock website. You just click some link on the web browser to automatically start Chimera. I don't think it uses the .crd file. You don't have to install any package. Just make sure you are using UCSF Chimera, not UCSF ChimeraX.
Otherwise, I don't have any other suggestions. Elaine
On Aug 3, 2024, at 5:00 AM, safi ch via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing great. Thank you for your detailed guidance; Respected Elaine Meng!
I explored the UCSF Chimera and realized that .crd format is not available here. But there are 2 videos on YouTube where they could easily open .crd file from SwissDock on UCSF Chimera. So I thought perhaps there is a way to open it and I don't have the package installed. The SwissDock tool themselves have an attachment of installation file named 'open.chimerax' and I tried my best to incorporate it in Chimera (by copying that file to every folder in UCSF Chimera directory in C Disk) but could not succeed.
I actually used both, new and old version of Swiss Dock, even used both docking options available in new interface; Docking with Attractive Cavities and Docking with AutoDock Vina. You are right that the files in newer version don't seem to have ligand bonded with target protein (hence why I went for older version as it has a folder name "clusters.zip" where seeds are given which are actually the protein-ligand complexes where you select a seed that has most favourable DDG value). The "result.dock4" file you are talking about is the sum of all seeds that the server came up with, so I cannot use it.
I have to go for Molecular Dynamics Simulations so I was taking a shortcut but now I guess I would have to take a long route for doing so :). Regardless, have a bright day Miss/Ma'am or Sir, Thank you again!
On Sat, Aug 3, 2024 at 12:14 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Greetings, Chimera's ViewDock tool does not read .crd format. The help page for that tool lists the formats it can use: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd....
However, the SwissDock website may also give you other files that you could open in Chimera.
The "old" SwissDock website would give you an output file for Chimera (not .crd). See their old website including a video with instructions of how to view the results in Chimera: <http://old.swissdock.ch/>
But maybe you tried the "new" website: <https://www.swissdock.ch/>
I have not tried the new website but their own help page explains their output files: <https://www.swissdock.ch/FAQ.php>
See answer to #2," What can I find in the results folder?"
"Once you untar the results.tar.gz file you obtain a results folder, in which you can find, for Attracting Cavities:
• parameters: the file containing your query parameters • result.dock4: the result file containing ligand poses • extra.par: the parameter file for the ligand and small molecules present • ligand.pdb: the ligand coordinate file • extra.rtf: the topology file for the ligand and small molecules present • receptor.crd: the receptor coordinate file • receptor.pdb: the receptor PDB file • receptor.psf: the receptor protein structure file
For AutoDock Vina: • parameters: the file containing your query parameters • ligand.pdbqt: the pdbqt file of your ligand used for Vina • system.pdbqt: the pdbqt file of your target used for Vina • vina_out.pdb: the result file containing different ligand poses • vina_out.pdbqt: the result file in pdbqt format containing different ligand poses • and your query files"
So there is no reason to open .crd anyway, since you could open receptor.pdb instead of receptor.crd if you need to show it. Also that is not even the results anyway, it is only the receptor. If you were using the AutoDock Vina option, you can view the vina_out.pdbqt file with Chimera's ViewDock tool. If you were using the Attracting Cavities option, it seems like the output is "result.dock4" ... I don't know what format that is, so I don't know if you can view that in Chimera or not.
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 2, 2024, at 3:09 AM, safi ch via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Greetings, Thanks for your continuous guidance; Respected Elaine Meng! I watched the video, I tried my best to workout the things on my computer as well as on Chimera, I am sorry to disappoint you that nothing worked. I guess I get stuck at "Configuration of Browser" as I am not able to create "new file type" from where all commands regarding execution of chimerax folder starts. I downloaded chimera again to ensure if something would happen but nothing happened again. Whenever I click on "Launch Chimera to view file (on the old Swiss DOCK server)", it again downloads that chimerax file. I found another tool named "CB-Dock 2.0" for the docking purpose and it provides ligand-receptor complexes in pdb format :) I would love to come up with a solution to this problem, as I saw numerous comments on YouTube from other fellows who had the same problem too. Again Thank you so much for being so kind, thanks for your time and thanks for your detailed assistance. I really wish I could solve this problem and tell you that we got this, but I am sorry I couldn't. By the way, I am Asfiya Moqaddas (I am a girl and Safi is the boyish version of my name 'Asfiya' as they have the same meaning; "Pure"). I have recently completed my M.Phil in Biochemistry and Molecular Biology (CGPA= 3.91/4, although I am hopeful of being a Gold Medalist but am still waiting for confirmation :)). In my original research, I performed site directed mutagenesis on Lumbrokinase for increased stability and luckily I got results for two mutations, but there was my senior in PhD who was working on same protein but faced challenges and could not get any result on Lumbrokinase (She was working on two proteins, the Lumbrokinase was difficult to work with), so my supervisor integrated my mutations work to her work and asked me to write only the Bioinformatics part of research article as it would be more than enough. So I started to add additional research efforts to my research work to make it more competitive. I am writing to express my interest for a PhD Scholarship at the University of Barcelona (UB), Spain and seek your guidance and support. I would be honored to contribute to a research project under your supervision please. I am very capable and would just need your little guidance and validation throughout my research project. Your invaluable assistance would be very valuable for strengthening my CV and would increase my chance in availing the Scholarship at the UB. If you can give me just this much time (well the amount of time you already extended me is way more than I thought, I was not expecting it, thanks Dear Professor), If you could consider providing me with your kind guidance and support, I would be able to write another research article that would significantly impact my academic journey please! Regardless, I wish you happiness and good health. Thank you very much for your time and consideration, Respected Professor :) On Sun, Aug 4, 2024 at 11:07 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
I haven't used the swissdock website myself, but my guess is that when you click the "Launch UCSF Chimera" link on the "old SwissDock" website as shown in the video at time 23:30, it will download a Chimera web data file:
Chimera web data files are named something.chimerax (maybe your open.chimerax file??) and in the video, the download of such a file automatically starts Chimera to show it. Maybe you did not already configure Chimera to show .chimerax files and so it just got downloaded but nothing happened. Anyway you should be able to open that file in Chimera simply by using Chimera menu: File... Open, or you can configure your browser to make Chimera start automatically when that type of file is downloaded from a website. Please see the help for description of Chimera web data files:
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.h...
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax....
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
Elaine
On Aug 4, 2024, at 8:47 AM, Elaine Meng via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hello Safi, This video shows opening swissdock results in Chimera, but you have to skip ahead to time 23-25 minutes: <https://www.youtube.com/watch?v=KcZ1EV_FcK8>
That video is showing the old swissdock website. You just click some link on the web browser to automatically start Chimera. I don't think it uses the .crd file. You don't have to install any package. Just make sure you are using UCSF Chimera, not UCSF ChimeraX.
Otherwise, I don't have any other suggestions. Elaine
On Aug 3, 2024, at 5:00 AM, safi ch via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing great. Thank you for your detailed guidance; Respected Elaine Meng!
I explored the UCSF Chimera and realized that .crd format is not available here. But there are 2 videos on YouTube where they could easily open .crd file from SwissDock on UCSF Chimera. So I thought perhaps there is a way to open it and I don't have the package installed. The SwissDock tool themselves have an attachment of installation file named 'open.chimerax' and I tried my best to incorporate it in Chimera (by copying that file to every folder in UCSF Chimera directory in C Disk) but could not succeed.
I actually used both, new and old version of Swiss Dock, even used both docking options available in new interface; Docking with Attractive Cavities and Docking with AutoDock Vina. You are right that the files in newer version don't seem to have ligand bonded with target protein (hence why I went for older version as it has a folder name "clusters.zip" where seeds are given which are actually the protein-ligand complexes where you select a seed that has most favourable DDG value). The "result.dock4" file you are talking about is the sum of all seeds that the server came up with, so I cannot use it.
I have to go for Molecular Dynamics Simulations so I was taking a shortcut but now I guess I would have to take a long route for doing so :). Regardless, have a bright day Miss/Ma'am or Sir, Thank you again!
On Sat, Aug 3, 2024 at 12:14 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Greetings, Chimera's ViewDock tool does not read .crd format. The help page for that tool lists the formats it can use: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd....
However, the SwissDock website may also give you other files that you
could open in Chimera.
The "old" SwissDock website would give you an output file for Chimera
(not .crd). See their old website including a video with instructions of how to view the results in Chimera:
But maybe you tried the "new" website: <https://www.swissdock.ch/>
I have not tried the new website but their own help page explains their output files: <https://www.swissdock.ch/FAQ.php>
See answer to #2," What can I find in the results folder?"
"Once you untar the results.tar.gz file you obtain a results folder, in which you can find, for Attracting Cavities:
• parameters: the file containing your query parameters • result.dock4: the result file containing ligand poses • extra.par: the parameter file for the ligand and small molecules present • ligand.pdb: the ligand coordinate file • extra.rtf: the topology file for the ligand and small molecules present • receptor.crd: the receptor coordinate file • receptor.pdb: the receptor PDB file • receptor.psf: the receptor protein structure file
For AutoDock Vina: • parameters: the file containing your query parameters • ligand.pdbqt: the pdbqt file of your ligand used for Vina • system.pdbqt: the pdbqt file of your target used for Vina • vina_out.pdb: the result file containing different ligand poses • vina_out.pdbqt: the result file in pdbqt format containing different ligand poses • and your query files"
So there is no reason to open .crd anyway, since you could open receptor.pdb instead of receptor.crd if you need to show it. Also that is not even the results anyway, it is only the receptor. If you were using the AutoDock Vina option, you can view the vina_out.pdbqt file with Chimera's ViewDock tool. If you were using the Attracting Cavities option, it seems like the output is "result.dock4" ... I don't know what format that is, so I don't know if you can view that in Chimera or not.
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 2, 2024, at 3:09 AM, safi ch via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.
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You can skip the browser configuration. It is only needed for automatically starting Chimera when you click the link on the SwissDock website. If you don't do browser configuration, then Chimera won't start automatically. However, you can still start Chimera yourself manually and then open the "open.chimerax" file that was downloaded when you clicked the link on the SwissDock website. I mentioned this in the previous reply but maybe it was not clear. You can just use Chimera menu: File... Open to open the open.chimerax file. You don't have to do anything else. Elaine
On Aug 4, 2024, at 11:07 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I haven't used the swissdock website myself, but my guess is that when you click the "Launch UCSF Chimera" link on the "old SwissDock" website as shown in the video at time 23:30, it will download a Chimera web data file:
Chimera web data files are named something.chimerax (maybe your open.chimerax file??) and in the video, the download of such a file automatically starts Chimera to show it. Maybe you did not already configure Chimera to show .chimerax files and so it just got downloaded but nothing happened. Anyway you should be able to open that file in Chimera simply by using Chimera menu: File... Open, or you can configure your browser to make Chimera start automatically when that type of file is downloaded from a website. Please see the help for description of Chimera web data files:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
Elaine
On Aug 4, 2024, at 8:47 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello Safi, This video shows opening swissdock results in Chimera, but you have to skip ahead to time 23-25 minutes: <https://www.youtube.com/watch?v=KcZ1EV_FcK8>
That video is showing the old swissdock website. You just click some link on the web browser to automatically start Chimera. I don't think it uses the .crd file. You don't have to install any package. Just make sure you are using UCSF Chimera, not UCSF ChimeraX.
Otherwise, I don't have any other suggestions. Elaine
On Aug 3, 2024, at 5:00 AM, safi ch via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing great. Thank you for your detailed guidance; Respected Elaine Meng!
I explored the UCSF Chimera and realized that .crd format is not available here. But there are 2 videos on YouTube where they could easily open .crd file from SwissDock on UCSF Chimera. So I thought perhaps there is a way to open it and I don't have the package installed. The SwissDock tool themselves have an attachment of installation file named 'open.chimerax' and I tried my best to incorporate it in Chimera (by copying that file to every folder in UCSF Chimera directory in C Disk) but could not succeed.
I actually used both, new and old version of Swiss Dock, even used both docking options available in new interface; Docking with Attractive Cavities and Docking with AutoDock Vina. You are right that the files in newer version don't seem to have ligand bonded with target protein (hence why I went for older version as it has a folder name "clusters.zip" where seeds are given which are actually the protein-ligand complexes where you select a seed that has most favourable DDG value). The "result.dock4" file you are talking about is the sum of all seeds that the server came up with, so I cannot use it.
I have to go for Molecular Dynamics Simulations so I was taking a shortcut but now I guess I would have to take a long route for doing so :). Regardless, have a bright day Miss/Ma'am or Sir, Thank you again!
On Sat, Aug 3, 2024 at 12:14 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Greetings, Chimera's ViewDock tool does not read .crd format. The help page for that tool lists the formats it can use: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>
However, the SwissDock website may also give you other files that you could open in Chimera.
The "old" SwissDock website would give you an output file for Chimera (not .crd). See their old website including a video with instructions of how to view the results in Chimera: <http://old.swissdock.ch/>
But maybe you tried the "new" website: <https://www.swissdock.ch/>
I have not tried the new website but their own help page explains their output files: <https://www.swissdock.ch/FAQ.php>
See answer to #2," What can I find in the results folder?"
"Once you untar the results.tar.gz file you obtain a results folder, in which you can find, for Attracting Cavities:
• parameters: the file containing your query parameters • result.dock4: the result file containing ligand poses • extra.par: the parameter file for the ligand and small molecules present • ligand.pdb: the ligand coordinate file • extra.rtf: the topology file for the ligand and small molecules present • receptor.crd: the receptor coordinate file • receptor.pdb: the receptor PDB file • receptor.psf: the receptor protein structure file
For AutoDock Vina: • parameters: the file containing your query parameters • ligand.pdbqt: the pdbqt file of your ligand used for Vina • system.pdbqt: the pdbqt file of your target used for Vina • vina_out.pdb: the result file containing different ligand poses • vina_out.pdbqt: the result file in pdbqt format containing different ligand poses • and your query files"
So there is no reason to open .crd anyway, since you could open receptor.pdb instead of receptor.crd if you need to show it. Also that is not even the results anyway, it is only the receptor. If you were using the AutoDock Vina option, you can view the vina_out.pdbqt file with Chimera's ViewDock tool. If you were using the Attracting Cavities option, it seems like the output is "result.dock4" ... I don't know what format that is, so I don't know if you can view that in Chimera or not.
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 2, 2024, at 3:09 AM, safi ch via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
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Greetings, hope you are great, thank you again for your guidance: Respected Elaine Meng! I am glad to share that I can visualize my .crd file. Thank you, and wow, it was so simple, thanks a lot, Dear Professor. Stay blessed and healthy, thanks for all your help throughout this problem, I will share it with everyone who needs it, I am so happy : ) Thank you again! On Mon, Aug 5, 2024 at 8:26 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
You can skip the browser configuration. It is only needed for automatically starting Chimera when you click the link on the SwissDock website.
If you don't do browser configuration, then Chimera won't start automatically. However, you can still start Chimera yourself manually and then open the "open.chimerax" file that was downloaded when you clicked the link on the SwissDock website. I mentioned this in the previous reply but maybe it was not clear.
You can just use Chimera menu: File... Open to open the open.chimerax file. You don't have to do anything else.
Elaine
On Aug 4, 2024, at 11:07 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I haven't used the swissdock website myself, but my guess is that when you click the "Launch UCSF Chimera" link on the "old SwissDock" website as shown in the video at time 23:30, it will download a Chimera web data file:
Chimera web data files are named something.chimerax (maybe your open.chimerax file??) and in the video, the download of such a file automatically starts Chimera to show it. Maybe you did not already configure Chimera to show .chimerax files and so it just got downloaded but nothing happened. Anyway you should be able to open that file in Chimera simply by using Chimera menu: File... Open, or you can configure your browser to make Chimera start automatically when that type of file is downloaded from a website. Please see the help for description of Chimera web data files:
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.h...
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax....
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
Elaine
On Aug 4, 2024, at 8:47 AM, Elaine Meng via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hello Safi, This video shows opening swissdock results in Chimera, but you have to skip ahead to time 23-25 minutes: <https://www.youtube.com/watch?v=KcZ1EV_FcK8>
That video is showing the old swissdock website. You just click some link on the web browser to automatically start Chimera. I don't think it uses the .crd file. You don't have to install any package. Just make sure you are using UCSF Chimera, not UCSF ChimeraX.
Otherwise, I don't have any other suggestions. Elaine
On Aug 3, 2024, at 5:00 AM, safi ch via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing great. Thank you for your detailed guidance; Respected Elaine Meng!
I explored the UCSF Chimera and realized that .crd format is not available here. But there are 2 videos on YouTube where they could easily open .crd file from SwissDock on UCSF Chimera. So I thought perhaps there is a way to open it and I don't have the package installed. The SwissDock tool themselves have an attachment of installation file named 'open.chimerax' and I tried my best to incorporate it in Chimera (by copying that file to every folder in UCSF Chimera directory in C Disk) but could not succeed.
I actually used both, new and old version of Swiss Dock, even used both docking options available in new interface; Docking with Attractive Cavities and Docking with AutoDock Vina. You are right that the files in newer version don't seem to have ligand bonded with target protein (hence why I went for older version as it has a folder name "clusters.zip" where seeds are given which are actually the protein-ligand complexes where you select a seed that has most favourable DDG value). The "result.dock4" file you are talking about is the sum of all seeds that the server came up with, so I cannot use it.
I have to go for Molecular Dynamics Simulations so I was taking a shortcut but now I guess I would have to take a long route for doing so :). Regardless, have a bright day Miss/Ma'am or Sir, Thank you again!
On Sat, Aug 3, 2024 at 12:14 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Greetings, Chimera's ViewDock tool does not read .crd format. The help page for that tool lists the formats it can use: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd....
However, the SwissDock website may also give you other files that you
could open in Chimera.
The "old" SwissDock website would give you an output file for Chimera
(not .crd). See their old website including a video with instructions of how to view the results in Chimera:
But maybe you tried the "new" website: <https://www.swissdock.ch/>
I have not tried the new website but their own help page explains their output files: <https://www.swissdock.ch/FAQ.php>
See answer to #2," What can I find in the results folder?"
"Once you untar the results.tar.gz file you obtain a results folder, in which you can find, for Attracting Cavities:
• parameters: the file containing your query parameters • result.dock4: the result file containing ligand poses • extra.par: the parameter file for the ligand and small molecules present • ligand.pdb: the ligand coordinate file • extra.rtf: the topology file for the ligand and small molecules present • receptor.crd: the receptor coordinate file • receptor.pdb: the receptor PDB file • receptor.psf: the receptor protein structure file
For AutoDock Vina: • parameters: the file containing your query parameters • ligand.pdbqt: the pdbqt file of your ligand used for Vina • system.pdbqt: the pdbqt file of your target used for Vina • vina_out.pdb: the result file containing different ligand poses • vina_out.pdbqt: the result file in pdbqt format containing different ligand poses • and your query files"
So there is no reason to open .crd anyway, since you could open receptor.pdb instead of receptor.crd if you need to show it. Also that is not even the results anyway, it is only the receptor. If you were using the AutoDock Vina option, you can view the vina_out.pdbqt file with Chimera's ViewDock tool. If you were using the Attracting Cavities option, it seems like the output is "result.dock4" ... I don't know what format that is, so I don't know if you can view that in Chimera or not.
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 2, 2024, at 3:09 AM, safi ch via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
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participants (2)
-
Elaine Meng -
safi ch