I Can't Open My ZDOCK Output File Into Chimera
Hello and hi! My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem? Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review. Thank you in advanced!
And these as well, I missed to upload it earlier. Sorry for the inconvenient! :-( On Fri, Aug 18, 2017 at 3:18 PM, Nissa Nabila < nissanabilaabdulrazak@gmail.com> wrote:
Hello and hi!
My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem?
Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review.
Thank you in advanced!
Hi Nissa, Well, the “.out” file is not PDB format or any format that Chimera knows about, and the rec[…]pdb and lig[…]pdb files are not really correct PDB format either. They have some extra stuff after the X,Y,Z coordinates in each line that is different from the standard PDB format. Maybe some other programs tolerate this extra stuff, but Chimera doesn’t. See our “introduction to PDB format”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.htm...> … and here’s a list of the kinds of docking outputs Chimera reads: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...> So if you want to use Chimera to view the PDB files, you would have to edit them to delete the part of each ATOM line after the X,Y,Z coordinate values. I attach edited versions of your two files. You could use whatever text-editing method you prefer. After you did that, you would be able to see the atomic structures, but Chimera still would not know how to read the ZDOCK “.out” file. 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 18, 2017, at 12:20 AM, Nissa Nabila <nissanabilaabdulrazak@gmail.com> wrote:
And these as well, I missed to upload it earlier. Sorry for the inconvenient! :-(
On Fri, Aug 18, 2017 at 3:18 PM, Nissa Nabila <nissanabilaabdulrazak@gmail.com> wrote: Hello and hi!
My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem?
Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review.
Thank you in advanced!
<lig.job122931.bl.pdb><rec.job122931.bl.pdb>
Hi, I am trying to use Chimera-X t for solvent-accessible-surface display (in my system surface display fails almost every time in Chimera). I managed to get it to work in Chimer-X once but now when I click the appropriate icon on the top in chimera-X menu this icon and most others (except the one to open files) are inactive. Is there anything that I should do to activate these icons? I am I missing something? I tried selecting the model that was opened but that didn't help. Thanks.
Hi Hernando, Not sure I understand this question, because there is no “inactive” status of the ChimeraX toolbar icons. When I use ChimeraX, these icons always look the same and can be clicked, even when nothing is open. It doesn’t require selecting, unless you want to limit the action to some subset of what is open. I assume you are referring to the icons described here: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html> If you could send a screenshot of the ChimeraX window with this problem, maybe that would help. However, the icons are just shortcuts to commands. After opening your atomic structure, you could try entering the ChimeraX command “surface” and seeing if that works. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 19, 2017, at 10:32 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Hi, I am trying to use Chimera-X t for solvent-accessible-surface display (in my system surface display fails almost every time in Chimera). I managed to get it to work in Chimer-X once but now when I click the appropriate icon on the top in chimera-X menu this icon and most others (except the one to open files) are inactive. Is there anything that I should do to activate these icons? I am I missing something? I tried selecting the model that was opened but that didn't help. Thanks.
Hi Elaine, I figured it out what the problem may be. For some reason the mouse position it is not mapped out correctly in the ChimeraX window. I.e. the icons are active but the cursor has to be placed not on top of the icon but somewhere else close by (below). This occurs with the latest daily build or the latest alpha version. I am running it in a Windows 10 laptop. Best H. ________________________________ Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Saturday, August 19, 2017 5:04 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Chimera-X Hi Hernando, Not sure I understand this question, because there is no “inactive” status of the ChimeraX toolbar icons. When I use ChimeraX, these icons always look the same and can be clicked, even when nothing is open. It doesn’t require selecting, unless you want to limit the action to some subset of what is open. I assume you are referring to the icons described here: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html> If you could send a screenshot of the ChimeraX window with this problem, maybe that would help. However, the icons are just shortcuts to commands. After opening your atomic structure, you could try entering the ChimeraX command “surface” and seeing if that works. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 19, 2017, at 10:32 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Hi, I am trying to use Chimera-X t for solvent-accessible-surface display (in my system surface display fails almost every time in Chimera). I managed to get it to work in Chimer-X once but now when I click the appropriate icon on the top in chimera-X menu this icon and most others (except the one to open files) are inactive. Is there anything that I should do to activate these icons? I am I missing something? I tried selecting the model that was opened but that didn't help. Thanks.
Hi Hernando, This seems like a Qt window toolkit bug. We do not observe this on Windows 10 or any other operating system, although reports on the web suggest Qt can sometimes get confused about the window position if you minimize or maximize the window. Does it fix itself if you manually resize the ChimeraX window or move the window? You can send email to chimerax-bugs@cgl.ucsf.edu <mailto:chimerax-bugs@cgl.ucsf.edu> to make a bug report. It will be hard for us to do anything about it if we cannot make it happen on one of our machines. Tom
On Aug 19, 2017, at 5:27 PM, Hernando J Sosa wrote:
Hi Elaine,
I figured it out what the problem may be. For some reason the mouse position it is not mapped out correctly in the ChimeraX window. I.e. the icons are active but the cursor has to be placed not on top of the icon but somewhere else close by (below). This occurs with the latest daily build or the latest alpha version. I am running it in a Windows 10 laptop.
Best
H.
________________________________ Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu
________________________________________ From: Elaine Meng Sent: Saturday, August 19, 2017 5:04 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Chimera-X
Hi Hernando, Not sure I understand this question, because there is no “inactive” status of the ChimeraX toolbar icons. When I use ChimeraX, these icons always look the same and can be clicked, even when nothing is open. It doesn’t require selecting, unless you want to limit the action to some subset of what is open. I assume you are referring to the icons described here:
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html>
If you could send a screenshot of the ChimeraX window with this problem, maybe that would help.
However, the icons are just shortcuts to commands. After opening your atomic structure, you could try entering the ChimeraX command “surface” and seeing if that works.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 19, 2017, at 10:32 AM, Hernando J Sosa wrote:
Hi, I am trying to use Chimera-X t for solvent-accessible-surface display (in my system surface display fails almost every time in Chimera). I managed to get it to work in Chimer-X once but now when I click the appropriate icon on the top in chimera-X menu this icon and most others (except the one to open files) are inactive. Is there anything that I should do to activate these icons? I am I missing something? I tried selecting the model that was opened but that didn't help. Thanks.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Alright, thank you for your responses. Have a nice day ahead! :-) On Sat, Aug 19, 2017 at 12:21 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Nissa, Well, the “.out” file is not PDB format or any format that Chimera knows about, and the rec[…]pdb and lig[…]pdb files are not really correct PDB format either. They have some extra stuff after the X,Y,Z coordinates in each line that is different from the standard PDB format. Maybe some other programs tolerate this extra stuff, but Chimera doesn’t.
See our “introduction to PDB format”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/ tutorials/framepdbintro.html>
… and here’s a list of the kinds of docking outputs Chimera reads: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/ framevd.html>
So if you want to use Chimera to view the PDB files, you would have to edit them to delete the part of each ATOM line after the X,Y,Z coordinate values. I attach edited versions of your two files. You could use whatever text-editing method you prefer.
After you did that, you would be able to see the atomic structures, but Chimera still would not know how to read the ZDOCK “.out” file.
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 18, 2017, at 12:20 AM, Nissa Nabila <nissanabilaabdulrazak@gmail. com> wrote:
And these as well, I missed to upload it earlier. Sorry for the inconvenient! :-(
On Fri, Aug 18, 2017 at 3:18 PM, Nissa Nabila < nissanabilaabdulrazak@gmail.com> wrote: Hello and hi!
My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem?
Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review.
Thank you in advanced!
<lig.job122931.bl.pdb><rec.job122931.bl.pdb>
participants (4)
-
Elaine Meng -
Hernando J Sosa -
Nissa Nabila -
Tom Goddard