FW: chimera download
Here is another inquiry for user help. From: bushra TAJ <bushraistaj@gmail.com<mailto:bushraistaj@gmail.com>> Date: Thursday, May 18, 2017 at 10:53 PM To: Joanne Williams <Joanne.Williams@ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> Subject: Re: chimera download Hello Sir will you please guide me for one more thing, I got pdb of my protein and have Autodock installed in my PC. I have 6 derivatives that I synthesized myself, can I load chemdraw.cdx file in chimera to prepare it for docking and finally safe it in Mol2 format??? What format I can take of my ligand to load in Chimera?? On Fri, May 19, 2017 at 9:50 AM, bushra TAJ <bushraistaj@gmail.com<mailto:bushraistaj@gmail.com>> wrote: My full name is Maria Taj Muhammad and I am doing PhD at Karachi University Chemistry department in Karachi city of PAKISTAN. is that OK Regards On Thu, May 18, 2017 at 7:41 PM, Williams, Joanne <Joanne.Williams@ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> wrote: Hello, Apologies, I was waiting to hear back from you. Please send me the following information: 1. Full Name: 2. School Name or company name that you are affiliated with: Thank you, JoAnne From: bushra TAJ <bushraistaj@gmail.com<mailto:bushraistaj@gmail.com>> Date: Wednesday, May 17, 2017 at 10:35 PM To: "Williams, Joanne" <Joanne.Williams@ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> Subject: Re: FW: chimera download Hello Sir I know I am disturbing you, but I asked for Chimera free trial (if possible). waiting for your kind response On Thu, May 11, 2017 at 8:12 PM, Williams, Joanne <Joanne.Williams@ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> wrote: Ok, let me know which school you are affiliated with and I will see about getting you access. Thank you, JoAnne From: bushra TAJ <bushraistaj@gmail.com<mailto:bushraistaj@gmail.com>> Date: Thursday, May 11, 2017 at 2:28 AM To: "Williams, Joanne" <Joanne.Williams@ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> Subject: Re: chimera download I am associated with a school and need for my project (that small work that I am left with. Any chance? On Wed, May 10, 2017 at 8:23 PM, Williams, Joanne <Joanne.Williams@ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> wrote: Hello, Thank you for your inquiry. I am sorry, we do not offer a free trial period. Are you affiliated with a school or company? Thank you, JoAnne From: bushra TAJ <bushraistaj@gmail.com<mailto:bushraistaj@gmail.com>> Date: Monday, May 8, 2017 at 1:22 AM To: "chimera@cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera@cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: chimera download Hello Sir Can I download chimera as free trial on my laptop. windows 7, 500GB, 32bits???
Hello Maria Taj Muhammad, The address for questions about using Chimera is chimera-users@cgl.ucsf.edu (CC’d here). Chimera does not read chemdraw.cdx files, sorry. Here is a list of the atomic-structure formats that Chimera can read: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#molstruct> You would probably want to use PDB, Mol2, or (MOL) SDF for your ligands, to read them in to Chimera. Then you can use the Dock Prep tool (in menu under Tools… Structure Editing) to add hydrogens and charges and save as Mol2. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2017, at 7:55 AM, Williams, Joanne <Joanne.Williams@ucsf.edu> wrote:
From: bushra TAJ <bushraistaj@gmail.com> Date: Thursday, May 18, 2017 at 10:53 PM Subject: Re: chimera download
Hello Sir will you please guide me for one more thing, I got pdb of my protein and have Autodock installed in my PC. I have 6 derivatives that I synthesized myself, can I load chemdraw.cdx file in chimera to prepare it for docking and finally safe it in Mol2 format??? What format I can take of my ligand to load in Chimera??
On Fri, May 19, 2017 at 9:50 AM, bushra TAJ <bushraistaj@gmail.com> wrote:
My full name is Maria Taj Muhammad and I am doing PhD at Karachi University Chemistry department in Karachi city of PAKISTAN. is that OK Regards
Thank you Sir Actually I intend to work on AutoDock and since it need a pdb file format I wanted Chimera (but since you are saying I need pdb to load ligand file in Chimera I will probably need some other tool. Can I still get the chance to analyse my Docked results on Chimera software. Thanks for your guidance Regards On Tue, May 23, 2017 at 2:11 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Maria Taj Muhammad, The address for questions about using Chimera is chimera-users@cgl.ucsf.edu (CC’d here).
Chimera does not read chemdraw.cdx files, sorry.
Here is a list of the atomic-structure formats that Chimera can read: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#molstruct
You would probably want to use PDB, Mol2, or (MOL) SDF for your ligands, to read them in to Chimera. Then you can use the Dock Prep tool (in menu under Tools… Structure Editing) to add hydrogens and charges and save as Mol2. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2017, at 7:55 AM, Williams, Joanne <Joanne.Williams@ucsf.edu> wrote:
From: bushra TAJ <bushraistaj@gmail.com> Date: Thursday, May 18, 2017 at 10:53 PM Subject: Re: chimera download
Hello Sir will you please guide me for one more thing, I got pdb of my protein and have Autodock installed in my PC. I have 6 derivatives that I synthesized myself, can I load chemdraw.cdx file in chimera to prepare it for docking and finally safe it in Mol2 format??? What format I can take of my ligand to load in Chimera??
On Fri, May 19, 2017 at 9:50 AM, bushra TAJ <bushraistaj@gmail.com> wrote:
My full name is Maria Taj Muhammad and I am doing PhD at Karachi University Chemistry department in Karachi city of PAKISTAN. is that OK Regards
Yes, many people use Chimera to analyse results from AutoDock. You would use the “ViewDock” tool (in menu under Tools… Surface/Binding Analysis). AutoDock pdbqt file is one of the input formats. ViewDock tool: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html> See also the ViewDock tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2017, at 10:30 PM, bushra TAJ <bushraistaj@gmail.com> wrote:
Thank you Sir Actually I intend to work on AutoDock and since it need a pdb file format I wanted Chimera (but since you are saying I need pdb to load ligand file in Chimera I will probably need some other tool. Can I still get the chance to analyse my Docked results on Chimera software. Thanks for your guidance Regards
Thank You You have been very helpful Rgards On Tue, May 23, 2017 at 9:31 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Yes, many people use Chimera to analyse results from AutoDock. You would use the “ViewDock” tool (in menu under Tools… Surface/Binding Analysis). AutoDock pdbqt file is one of the input formats.
ViewDock tool: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/ framevd.html>
See also the ViewDock tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2017, at 10:30 PM, bushra TAJ <bushraistaj@gmail.com> wrote:
Thank you Sir Actually I intend to work on AutoDock and since it need a pdb file format I wanted Chimera (but since you are saying I need pdb to load ligand file in Chimera I will probably need some other tool. Can I still get the chance to analyse my Docked results on Chimera software. Thanks for your guidance Regards
participants (3)
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bushra TAJ -
Elaine Meng -
Williams, Joanne