Dears, I need to depict a map generated from CCP4/Sfall and a .pdb file corrected by Coot. I would like to create images by Chimera. Unfortunately, I cannot figure out how to make a correct view (in Coot, the map fits the molecule well), please, see the image/session in the attachment. I could not have found a guidance in the User's guide. Can you help me please? Thank you in advance for your help. Best regards, Michaela Nekardova Institute of Biotechnology CAS, v. v. i. Laboratory of Biomolecular Recognition Address: Průmyslová 595, 252 50 Vestec.
Dear Michaela, Sessions do not include the map file, so you would have to attach that in addition to the session file. However, I can see what is happening from the image. Please see this previous post, “visualizing maps from Coot in Chimera”: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-July/012514.html> The following might also be useful, but I haven’t tried the script to see what it does: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-May/012313.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 Mar 14, 2018, at 7:58 AM, <ela.nekardova@gmail.com> <ela.nekardova@gmail.com> wrote:
Dears, I need to depict a map generated from CCP4/Sfall and a .pdb file corrected by Coot. I would like to create images by Chimera. Unfortunately, I cannot figure out how to make a correct view (in Coot, the map fits the molecule well), please, see the image/session in the attachment. I could not have found a guidance in the User's guide. Can you help me please? Thank you in advance for your help. Best regards, Michaela Nekardova
Dear Elaine, Thank you for your answer. Please accept my apologies for the delayed reply. Probably I did a mistake when I saved the session because the map was included. I work with Chimera briefly. The first link describes the same or similar problem but in my case, the suggested solution depicts the map not quite correctly. I understand that Chimera was created for a different purpose than crystallography. Unfortunately, the COOT graphics is unacceptable for papers and websites. I have used Pymol but a map fitting and other options have certain imperfections as well. I work on a bioinformatics study based on analysis of tens of map files with the described problem. In case that you find the problem interesting, I am sending you the files: the map of water density and the dinucleotide with its hydration sites. Best regards, Michaela -- Institute of Biotechnology of the CAS, v. v. i. Laboratory of Biomolecular Recognition Address: Průmyslová 595 252 50 Vestec The Czech Republic Email: nekardovam@ibt.cas.cz ---------- Původní e-mail ---------- Od: Elaine Meng <meng@cgl.ucsf.edu> Komu: ela.nekardova@gmail.com Datum: 14. 3. 2018 17:28:23 Předmět: Re: [Chimera-users] problem with ccp4 map fitting "Dear Michaela, Sessions do not include the map file, so you would have to attach that in addition to the session file. However, I can see what is happening from the image. Please see this previous post, “visualizing maps from Coot in Chimera”: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-July/012514.html> The following might also be useful, but I haven’t tried the script to see what it does: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-May/012313.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 Mar 14, 2018, at 7:58 AM, <ela.nekardova@gmail.com> <ela.nekardova@ gmail.com> wrote:
Dears, I need to depict a map generated from CCP4/Sfall and a .pdb file corrected by Coot. I would like to create images by Chimera. Unfortunately, I cannot figure out how to make a correct view (in Coot, the map fits the molecule well), please, see the image/session in the attachment. I could not have found a guidance in the User's guide. Can you help me please? Thank you in advance for your help. Best regards, Michaela Nekardova
"
Hi Michaela, I opened you atomic model and map and used Chimera command vop cover #1 atom #0 and it extended the map to cover the water that was outside the original unit cell map. Tom
On Mar 27, 2018, at 6:47 AM, Michaela wrote:
Dear Elaine,
Thank you for your answer. Please accept my apologies for the delayed reply. Probably I did a mistake when I saved the session because the map was included. I work with Chimera briefly. The first link describes the same or similar problem but in my case, the suggested solution depicts the map not quite correctly. I understand that Chimera was created for a different purpose than crystallography. Unfortunately, the COOT graphics is unacceptable for papers and websites. I have used Pymol but a map fitting and other options have certain imperfections as well. I work on a bioinformatics study based on analysis of tens of map files with the described problem.
In case that you find the problem interesting, I am sending you the files: the map of water density and the dinucleotide with its hydration sites.
Best regards,
Michaela
-- Institute of Biotechnology of the CAS, v. v. i. Laboratory of Biomolecular Recognition Address: Průmyslová 595 252 50 Vestec The Czech Republic Email: nekardovam@ibt.cas.cz
---------- Původní e-mail ---------- Od: Elaine Meng <meng@cgl.ucsf.edu> Komu: ela.nekardova@gmail.com Datum: 14. 3. 2018 17:28:23 Předmět: Re: [Chimera-users] problem with ccp4 map fitting
Dear Michaela, Sessions do not include the map file, so you would have to attach that in addition to the session file.
However, I can see what is happening from the image. Please see this previous post, “visualizing maps from Coot in Chimera”: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-July/012514.html>
The following might also be useful, but I haven’t tried the script to see what it does: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-May/012313.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 Mar 14, 2018, at 7:58 AM, <ela.nekardova@gmail.com> <ela.nekardova@gmail.com> wrote:
Dears, I need to depict a map generated from CCP4/Sfall and a .pdb file corrected by Coot. I would like to create images by Chimera. Unfortunately, I cannot figure out how to make a correct view (in Coot, the map fits the molecule well), please, see the image/session in the attachment. I could not have found a guidance in the User's guide. Can you help me please? Thank you in advance for your help. Best regards, Michaela Nekardova
<coot_map.ccp4><coot_geom.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
ela.nekardova＠gmail.com -
Elaine Meng -
Tom Goddard