AFTER DOCKING I AM SAVING THE PDB FILES, BUT IN THAT PDB FILE THE LIGAND AND RECEPTOR ARE HAVING THE SAME NAME
For analysis, I want to have a PDB file of let's say with the first docked ligand in chimera which I did with autodock vina. I was able to save and open it in chimera. But the receptor and the ligand are both having the same name which I am using to save my PDB file. How can I change the names of receptor and ligand in the PDB file so that it is considered as different molecules in that particular PDB file. I want to give two different names to the receptor and the ligand in that particluar PDB file. This I need for my project. Please help me with this. Thank you. -- Shinjini Ghosh. Student of Master of Science, Biophysics and Molecular Biology' Rajabazar Science College, University of Calcutta. <https://mailtrack.io/?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> Sender notified by Mailtrack <https://mailtrack.io/?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> 08/07/20, 08:02:34 PM <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <x-msg://5/#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
Hi Shinjini, It is unclear what name you are talking about. There is a "model name", maybe the ligand and receptor are together in one model. There is a "file name" of the saved PDB file. There are "residue names," many different amino acids in the receptor, each one with its own name, and probably the ligand also has another different residue name. Each atom also has an "atom name." If you want separate files, just select the atoms you want in one file, use menu: File ... Save PDB and choose the option to "save selected atoms only". Then select the atoms you want in the other file, and use the same process to save another PDB file. You can name each file whatever you want. Selecting atoms: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Saving PDB files: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> If you want to change residue names or atom names, maybe you just want to text-edit the PDB file directly (not using Chimera). Here is some explanation of PDB file format so you can understand how to edit the text. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 7, 2020, at 7:37 AM, Shinjini Ghosh <shinjinighosh2014@gmail.com> wrote:
For analysis, I want to have a PDB file of let's say with the first docked ligand in chimera which I did with autodock vina. I was able to save and open it in chimera. But the receptor and the ligand are both having the same name which I am using to save my PDB file. How can I change the names of receptor and ligand in the PDB file so that it is considered as different molecules in that particular PDB file. I want to give two different names to the receptor and the ligand in that particluar PDB file. This I need for my project. Please help me with this. Thank you.
I am sorry, but the above links did not help me. Yes they are together in one model. But if suppose a receptor has NAD in it , it shows in the residue region. But after docking the ligand name becomes the same as the receptor. So it is difficult for me to show which ligand I have used to dock. I have attached an example pdb file. Here both the ligand and receptor are in chain A and have the same name : dock.pdb and under "residue" my docked ligand is not coming. How to save a pdb file (docked file) which considers the receptor and ligand separately in the same PDB, like for example in the 3U31 file which I have attached (PDB file downloaded from PDB) has NAD, gol, etc under residues. and when I am using another software to check the interaction, it is showing the interactions with all the residues. But this "dock" PDB file which I made (after docking) there is difficult to understand the interaction as it is showing no ligand bound, since both of them are saved under the same name. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> 08/07/20, 09:56:05 PM On Fri, Aug 7, 2020 at 9:48 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Shinjini, It is unclear what name you are talking about. There is a "model name", maybe the ligand and receptor are together in one model. There is a "file name" of the saved PDB file. There are "residue names," many different amino acids in the receptor, each one with its own name, and probably the ligand also has another different residue name. Each atom also has an "atom name."
If you want separate files, just select the atoms you want in one file, use menu: File ... Save PDB and choose the option to "save selected atoms only". Then select the atoms you want in the other file, and use the same process to save another PDB file. You can name each file whatever you want.
Selecting atoms: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
Saving PDB files: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
If you want to change residue names or atom names, maybe you just want to text-edit the PDB file directly (not using Chimera). Here is some explanation of PDB file format so you can understand how to edit the text. < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.htm...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 7, 2020, at 7:37 AM, Shinjini Ghosh <shinjinighosh2014@gmail.com> wrote:
For analysis, I want to have a PDB file of let's say with the first docked ligand in chimera which I did with autodock vina. I was able to save and open it in chimera. But the receptor and the ligand are both having the same name which I am using to save my PDB file. How can I change the names of receptor and ligand in the PDB file so that it is considered as different molecules in that particular PDB file. I want to give two different names to the receptor and the ligand in that particluar PDB file. This I need for my project. Please help me with this. Thank you.
-- Shinjini Ghosh. Student of Master of Science, Biophysics and Molecular Biology' Rajabazar Science College, University of Calcutta. <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
Hi Shinjini, In your dock.pdb file, there are two different models in one file, one for the ligand and one for the receptor, and both have the same model name because they came from one file. The other PDB file has the ligand and receptor in the same model, and there is only one model with one name. However, the model name is not important, you can still select the ligand by its residue name, UNK. For example, menu: Select... Residue... UNK. Maybe you didn't see it in the menu because it is listed in the menu together with the amino acids. It is listed there because UNK is not supposed to be used for ligands, but I guess it had that name in your docking input and output. Again I don't think it matters at all, but if you really wanted to combine the two models in your dock.pdb file into one model, you could do it with the Model Panel function "copy/combine" or the command "combine" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 7, 2020, at 9:36 AM, Shinjini Ghosh <shinjinighosh2014@gmail.com> wrote:
I am sorry, but the above links did not help me. Yes they are together in one model. But if suppose a receptor has NAD in it , it shows in the residue region. But after docking the ligand name becomes the same as the receptor. So it is difficult for me to show which ligand I have used to dock.
I have attached an example pdb file. Here both the ligand and receptor are in chain A and have the same name : dock.pdb and under "residue" my docked ligand is not coming. How to save a pdb file (docked file) which considers the receptor and ligand separately in the same PDB, like for example in the 3U31 file which I have attached (PDB file downloaded from PDB) has NAD, gol, etc under residues. and when I am using another software to check the interaction, it is showing the interactions with all the residues. But this "dock" PDB file which I made (after docking) there is difficult to understand the interaction as it is showing no ligand bound, since both of them are saved under the same name.
Sender notified by Mailtrack 08/07/20, 09:56:05 PM
On Fri, Aug 7, 2020 at 9:48 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Shinjini, It is unclear what name you are talking about. There is a "model name", maybe the ligand and receptor are together in one model. There is a "file name" of the saved PDB file. There are "residue names," many different amino acids in the receptor, each one with its own name, and probably the ligand also has another different residue name. Each atom also has an "atom name."
If you want separate files, just select the atoms you want in one file, use menu: File ... Save PDB and choose the option to "save selected atoms only". Then select the atoms you want in the other file, and use the same process to save another PDB file. You can name each file whatever you want.
Selecting atoms: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
Saving PDB files: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
If you want to change residue names or atom names, maybe you just want to text-edit the PDB file directly (not using Chimera). Here is some explanation of PDB file format so you can understand how to edit the text. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 7, 2020, at 7:37 AM, Shinjini Ghosh <shinjinighosh2014@gmail.com> wrote:
For analysis, I want to have a PDB file of let's say with the first docked ligand in chimera which I did with autodock vina. I was able to save and open it in chimera. But the receptor and the ligand are both having the same name which I am using to save my PDB file. How can I change the names of receptor and ligand in the PDB file so that it is considered as different molecules in that particular PDB file. I want to give two different names to the receptor and the ligand in that particluar PDB file. This I need for my project. Please help me with this. Thank you.
-- Shinjini Ghosh. Student of Master of Science, Biophysics and Molecular Biology' Rajabazar Science College, University of Calcutta.
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