Fitting multiple atomic structures in a density map
Dear All, I need to fit atomic structures of two different proteins of different sizes in a density map. The location of both the proteins in the map is well known. While using the fitting tool, I can get the atomic structure of the bigger protein docked very well, the problem arises while fitting the smaller one. The fit option fails and docks the structure into the region of the density map where the atomic structure of the larger protein is docked , an incorrect position. How can I fit both the atomic structures in the density map correctly? The resolution of the density map is ~10Å at FSC cutoff of 0.5 Thanks Andy Dr. Anindito Sen (Ph.D)
Department of Cell Biology & Anatomy Graduate School of Medicine University of Tokyo Tel & fax: +81-3-5841-3339
Hi Andy, You might try the sequential fitting option of the "fitmap" command. After it fits one structure, it removes the density from that part of the map before fitting the next. Details here including link to an example video: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.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 Jul 12, 2013, at 12:43 AM, Anindito Sen wrote:
Dear All, I need to fit atomic structures of two different proteins of different sizes in a density map. The location of both the proteins in the map is well known. While using the fitting tool, I can get the atomic structure of the bigger protein docked very well, the problem arises while fitting the smaller one. The fit option fails and docks the structure into the region of the density map where the atomic structure of the larger protein is docked , an incorrect position.
How can I fit both the atomic structures in the density map correctly? The resolution of the density map is ~10Å at FSC cutoff of 0.5 Thanks Andy
Whoops, second link was supposed to be: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence> On Jul 12, 2013, at 9:51 AM, Elaine Meng wrote:
Hi Andy, You might try the sequential fitting option of the "fitmap" command. After it fits one structure, it removes the density from that part of the map before fitting the next. Details here including link to an example video:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.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 Jul 12, 2013, at 12:43 AM, Anindito Sen wrote:
Dear All, I need to fit atomic structures of two different proteins of different sizes in a density map. The location of both the proteins in the map is well known. While using the fitting tool, I can get the atomic structure of the bigger protein docked very well, the problem arises while fitting the smaller one. The fit option fails and docks the structure into the region of the density map where the atomic structure of the larger protein is docked , an incorrect position.
How can I fit both the atomic structures in the density map correctly? The resolution of the density map is ~10Å at FSC cutoff of 0.5 Thanks Andy
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, I followed the protocol shown in the video tutorial (the link you provided), unfortunately it did'nt help. Is there any other way I can tackle the problem? Thanks Andy Dr. Anindito Sen (Ph.D)
Department of Cell Biology & Anatomy Graduate School of Medicine University of Tokyo Tel & fax: +81-3-5841-3339
________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> To: "<chimera-users@cgl.ucsf.edu> List" <chimera-users@cgl.ucsf.edu> Cc: Anindito Sen <emailanindito@yahoo.co.in> Sent: Saturday, 13 July 2013, 1:53 Subject: Re: [Chimera-users] Fitting multiple atomic structures in a density map Whoops, second link was supposed to be: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence> On Jul 12, 2013, at 9:51 AM, Elaine Meng wrote:
Hi Andy, You might try the sequential fitting option of the "fitmap" command. After it fits one structure, it removes the density from that part of the map before fitting the next. Details here including link to an example video:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.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 Jul 12, 2013, at 12:43 AM, Anindito Sen wrote:
Dear All, I need to fit atomic structures of two different proteins of different sizes in a density map. The location of both the proteins in the map is well known. While using the fitting tool, I can get the atomic structure of the bigger protein docked very well, the problem arises while fitting the smaller one. The fit option fails and docks the structure into the region of the density map where the atomic structure of the larger protein is docked , an incorrect position.
How can I fit both the atomic structures in the density map correctly? The resolution of the density map is ~10Å at FSC cutoff of 0.5 Thanks Andy
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Andy, I'm not sure what you mean by didn't help. Sequential fitting should not allow multiple atomic structures to go in the same place. There is more than one video linked to that page, doublecheck if you looked at the one for "sequential fitting": <http://www.cgl.ucsf.edu/chimera/videodoc/FitSeq/> You would first put both structures in starting locations approximately where you think they should be, and then fit both structures using the same command. For example, if map were #0 and structures #1,2, something like: fitmap #1,2 #0 sequence 10 resolution 10 Sequential fitting is my only idea because this option was created specifically to fit multiple structures without overlaps. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence> Best, Elaine On Jul 16, 2013, at 2:56 AM, Anindito Sen <emailanindito@yahoo.co.in> wrote:
Hi Elaine, I followed the protocol shown in the video tutorial (the link you provided), unfortunately it did'nt help. Is there any other way I can tackle the problem? Thanks Andy
From: Elaine Meng <meng@cgl.ucsf.edu> To: "<chimera-users@cgl.ucsf.edu> List" <chimera-users@cgl.ucsf.edu> Cc: Anindito Sen <emailanindito@yahoo.co.in> Sent: Saturday, 13 July 2013, 1:53 Subject: Re: [Chimera-users] Fitting multiple atomic structures in a density map
Whoops, second link was supposed to be: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence>
On Jul 12, 2013, at 9:51 AM, Elaine Meng wrote:
Hi Andy, You might try the sequential fitting option of the "fitmap" command. After it fits one structure, it removes the density from that part of the map before fitting the next. Details here including link to an example video:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
I hope this helps, Elaine
On Jul 12, 2013, at 12:43 AM, Anindito Sen wrote:
Dear All, I need to fit atomic structures of two different proteins of different sizes in a density map. The location of both the proteins in the map is well known. While using the fitting tool, I can get the atomic structure of the bigger protein docked very well, the problem arises while fitting the smaller one. The fit option fails and docks the structure into the region of the density map where the atomic structure of the larger protein is docked , an incorrect position.
How can I fit both the atomic structures in the density map correctly? The resolution of the density map is ~10Å at FSC cutoff of 0.5 Thanks Andy
Hi Andy, If the sequential fitting option doesn't help you I'd suggest subtracting the density for your first fit molecule from the map, then fitting the second molecule in the remaining map. This is essentially what the sequential fitting does, but you'll have better control and insight into what is going on if you do it by hand. To subtract a fit of molecule #1 from map #0 at 8.5 Angstroms resolution use the molmap and "vop subtract" commands, for example molmap #1 8.5 model #5 vop subtract #0 #5 minRMS true The first command creates a simulated map from the molecule, and the second command subtracts it from the experimental map. The minRMS option handles the fact that the experimental map and the simulated map have different normalization. It says to subtract a multiple of the simulated map that minimizes the residual of the difference map. Using the difference map you should be able to fit your second molecule in without it migrating into the location where the first molecule was fit. Tom On Jul 16, 2013, at 9:05 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Andy, I'm not sure what you mean by didn't help. Sequential fitting should not allow multiple atomic structures to go in the same place. There is more than one video linked to that page, doublecheck if you looked at the one for "sequential fitting":
<http://www.cgl.ucsf.edu/chimera/videodoc/FitSeq/>
You would first put both structures in starting locations approximately where you think they should be, and then fit both structures using the same command. For example, if map were #0 and structures #1,2, something like:
fitmap #1,2 #0 sequence 10 resolution 10
Sequential fitting is my only idea because this option was created specifically to fit multiple structures without overlaps. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence>
Best, Elaine
On Jul 16, 2013, at 2:56 AM, Anindito Sen <emailanindito@yahoo.co.in> wrote:
Hi Elaine, I followed the protocol shown in the video tutorial (the link you provided), unfortunately it did'nt help. Is there any other way I can tackle the problem? Thanks Andy
From: Elaine Meng <meng@cgl.ucsf.edu> To: "<chimera-users@cgl.ucsf.edu> List" <chimera-users@cgl.ucsf.edu> Cc: Anindito Sen <emailanindito@yahoo.co.in> Sent: Saturday, 13 July 2013, 1:53 Subject: Re: [Chimera-users] Fitting multiple atomic structures in a density map
Whoops, second link was supposed to be: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence>
On Jul 12, 2013, at 9:51 AM, Elaine Meng wrote:
Hi Andy, You might try the sequential fitting option of the "fitmap" command. After it fits one structure, it removes the density from that part of the map before fitting the next. Details here including link to an example video:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
I hope this helps, Elaine
On Jul 12, 2013, at 12:43 AM, Anindito Sen wrote:
Dear All, I need to fit atomic structures of two different proteins of different sizes in a density map. The location of both the proteins in the map is well known. While using the fitting tool, I can get the atomic structure of the bigger protein docked very well, the problem arises while fitting the smaller one. The fit option fails and docks the structure into the region of the density map where the atomic structure of the larger protein is docked , an incorrect position.
How can I fit both the atomic structures in the density map correctly? The resolution of the density map is ~10Å at FSC cutoff of 0.5 Thanks Andy
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Anindito Sen -
Elaine Meng -
Tom Goddard