Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video. Regards Waiting for a quick response Asma Tariq
Hi Asmi Tariq, This is not a bug, so please do not send mail to the bugs address. There is no such PDF or video, sorry. However, I do know that lots of people use Chimera to prep many ligands. Here are some tips: (1) You didn’t say what docking program you are using. Different programs take different input formats. Chimera would be used to prepare ligands and write them in mol2 format. If your docking program doesn’t take mol2, then Chimera is less useful for you. (2) My guess is that it wouldn’t be practical/feasible to read one giant SDF file with all those ligands for prepping. If using Chimera, it would probably work better if you had individual files for the individual ligands instead, e.g. lig00001.sdf, lig00002.sdf, etc. Also the SDF needs to be 3D coordinates. if you have SDFs with 2D chemical diagrams, Chimera will NOT be able to prep them into reasonable 3D molecules. (3) then you would have to manually figure out which command(s) to use to prep a single ligand. Probably you would need to use “open” (open ligand file), “addh”, “addcharge” and “write” (output mol2 file). There is usually some trial and error for you to figure out what command options you want. See the individual command help pages here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> (4) After you have figured out which commands you want to use, then you would write a script to loop through your many ligands as discussed here in the programmer’s guide. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> P.S. I changed the subject line to something useful. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 21, 2019, at 7:10 AM, Asmi Mahmood <asmi_mahmood@yahoo.com> wrote:
Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video. Regards Waiting for a quick response Asma Tariq
Thanks for your response. If i need to dock more than 50k ligands then preparaing and assigning charge to each ligand one by one is not practically feasible. I'm have a single file of 3D SDF format having all the ligands and split them into individual ligand files by using vina split. Plz guide me if it is possible to upload and prepare all ligands as a single step in chimera. Thanax Regards If possible plz give me an email of chimera resource person who can give me help in my queries. Sent from Yahoo Mail on Android On Mon, Dec 23, 2019 at 10:46 PM, Elaine Meng<meng@cgl.ucsf.edu> wrote: Hi Asmi Tariq, This is not a bug, so please do not send mail to the bugs address. There is no such PDF or video, sorry. However, I do know that lots of people use Chimera to prep many ligands. Here are some tips: (1) You didn’t say what docking program you are using. Different programs take different input formats. Chimera would be used to prepare ligands and write them in mol2 format. If your docking program doesn’t take mol2, then Chimera is less useful for you. (2) My guess is that it wouldn’t be practical/feasible to read one giant SDF file with all those ligands for prepping. If using Chimera, it would probably work better if you had individual files for the individual ligands instead, e.g. lig00001.sdf, lig00002.sdf, etc. Also the SDF needs to be 3D coordinates. if you have SDFs with 2D chemical diagrams, Chimera will NOT be able to prep them into reasonable 3D molecules. (3) then you would have to manually figure out which command(s) to use to prep a single ligand. Probably you would need to use “open” (open ligand file), “addh”, “addcharge” and “write” (output mol2 file). There is usually some trial and error for you to figure out what command options you want. See the individual command help pages here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> (4) After you have figured out which commands you want to use, then you would write a script to loop through your many ligands as discussed here in the programmer’s guide. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> P.S. I changed the subject line to something useful. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 21, 2019, at 7:10 AM, Asmi Mahmood <asmi_mahmood@yahoo.com> wrote:
Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video. Regards Waiting for a quick response Asma Tariq
Hi Asmi, This is the correct e-mail address for questions. However, we do not have the resources to provide free detailed consulting on individual research projects. You will have to spend the time learning and experimenting with the program yourself. How many you can open at the same time depends on the memory of your computer, but I’m sure that 50K would be far too many. That is why I suggested in my previous message splitting the file into smaller subsets or individual ligand files. Then you would just open one, process it, close it, and then go on to the next, as mentioned in #4 of the previous message. It should be feasible if there is a script to do the looping, as I said in #4 of the previous message. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 27, 2019, at 10:20 PM, Asmi Mahmood <asmi_mahmood@yahoo.com> wrote:
Thanks for your response. If i need to dock more than 50k ligands then preparaing and assigning charge to each ligand one by one is not practically feasible. I'm have a single file of 3D SDF format having all the ligands and split them into individual ligand files by using vina split. Plz guide me if it is possible to upload and prepare all ligands as a single step in chimera.
Thanax
Regards
If possible plz give me an email of chimera resource person who can give me help in my queries.
Sent from Yahoo Mail on Android
On Mon, Dec 23, 2019 at 10:46 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Asmi Tariq, This is not a bug, so please do not send mail to the bugs address.
There is no such PDF or video, sorry. However, I do know that lots of people use Chimera to prep many ligands. Here are some tips:
(1) You didn’t say what docking program you are using. Different programs take different input formats. Chimera would be used to prepare ligands and write them in mol2 format. If your docking program doesn’t take mol2, then Chimera is less useful for you.
(2) My guess is that it wouldn’t be practical/feasible to read one giant SDF file with all those ligands for prepping. If using Chimera, it would probably work better if you had individual files for the individual ligands instead, e.g. lig00001.sdf, lig00002.sdf, etc. Also the SDF needs to be 3D coordinates. if you have SDFs with 2D chemical diagrams, Chimera will NOT be able to prep them into reasonable 3D molecules.
(3) then you would have to manually figure out which command(s) to use to prep a single ligand. Probably you would need to use “open” (open ligand file), “addh”, “addcharge” and “write” (output mol2 file). There is usually some trial and error for you to figure out what command options you want. See the individual command help pages here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
(4) After you have figured out which commands you want to use, then you would write a script to loop through your many ligands as discussed here in the programmer’s guide. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
P.S. I changed the subject line to something useful.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 21, 2019, at 7:10 AM, Asmi Mahmood <asmi_mahmood@yahoo.com> wrote:
Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video. Regards Waiting for a quick response Asma Tariq
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Check this out: https://github.com/tevang/tutorials/tree/master/dockprep
participants (3)
-
Asmi Mahmood -
Elaine Meng -
Thomas Evangelidis