[Chimera-users] problem with ccp4 map fitting
ela.nekardova at gmail.com
ela.nekardova at gmail.com
Tue Mar 27 06:47:18 PDT 2018
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 at ibt.cas.cz
---------- Původní e-mail ----------
Od: Elaine Meng <meng at cgl.ucsf.edu>
Komu: ela.nekardova at 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 at 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
"
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ATOM 1 C5' DA A 1 17.338 12.740 13.347 1.00 73.96 @ C
ATOM 2 C4' DA A 1 16.606 11.456 13.007 1.00 70.49 @ C
ATOM 3 O4' DA A 1 17.463 10.532 12.269 1.00 66.68 @ O
ATOM 4 C3' DA A 1 16.078 10.698 14.225 1.00 72.19 @ C
ATOM 5 O3' DA A 1 14.769 10.241 13.923 1.00 69.87 @ O
ATOM 6 C2' DA A 1 17.107 9.584 14.419 1.00 69.75 @ C
ATOM 7 C1' DA A 1 17.486 9.294 12.971 1.00 65.99 @ C
ATOM 8 N9 DA A 1 18.812 8.706 12.821 1.00 63.54 @ N
ATOM 9 C8 DA A 1 19.986 9.118 13.399 1.00 65.32 @ C
ATOM 10 N7 DA A 1 21.023 8.384 13.054 1.00 62.52 @ N
ATOM 11 C5 DA A 1 20.496 7.428 12.205 1.00 57.41 @ C
ATOM 12 C6 DA A 1 21.068 6.346 11.497 1.00 53.85 @ C
ATOM 13 N6 DA A 1 22.365 6.025 11.534 1.00 53.85 @ N
ATOM 14 N1 DA A 1 20.250 5.573 10.752 1.00 49.93 @ N
ATOM 15 C2 DA A 1 18.947 5.874 10.700 1.00 51.08 @ C
ATOM 16 N3 DA A 1 18.288 6.867 11.315 1.00 55.68 @ N
ATOM 17 C4 DA A 1 19.130 7.615 12.054 1.00 58.05 @ C
ATOM 18 P DA A 2 13.979 9.337 14.968 1.00 73.72 @ P
ATOM 19 OP1 DA A 2 12.539 9.642 14.865 1.00 73.96 @ O
ATOM 20 OP2 DA A 2 14.712 9.269 16.248 1.00 73.32 @ O
ATOM 21 O5' DA A 2 14.185 7.936 14.271 1.00 69.41 @ O
ATOM 22 C5' DA A 2 13.883 7.828 12.891 1.00 64.18 @ C
ATOM 23 C4' DA A 2 13.951 6.376 12.551 1.00 59.36 @ C
ATOM 24 O4' DA A 2 15.336 5.992 12.548 1.00 56.84 @ O
ATOM 25 C3' DA A 2 13.288 5.491 13.604 1.00 62.85 @ C
ATOM 26 O3' DA A 2 12.677 4.465 12.880 1.00 61.14 @ O
ATOM 27 C2' DA A 2 14.423 4.982 14.514 1.00 61.98 @ C
ATOM 28 C1' DA A 2 15.520 4.894 13.442 1.00 57.90 @ C
ATOM 29 N9 DA A 2 16.912 4.998 13.881 1.00 57.01 @ N
ATOM 30 C8 DA A 2 17.475 5.866 14.794 1.00 59.62 @ C
ATOM 31 N7 DA A 2 18.773 5.702 14.938 1.00 57.72 @ N
ATOM 32 C5 DA A 2 19.081 4.664 14.054 1.00 53.02 @ C
ATOM 33 C6 DA A 2 20.279 3.979 13.696 1.00 50.11 @ C
ATOM 34 N6 DA A 2 21.489 4.223 14.193 1.00 49.94 @ N
ATOM 35 N1 DA A 2 20.209 2.989 12.780 1.00 47.13 @ N
ATOM 36 C2 DA A 2 19.027 2.684 12.227 1.00 46.72 @ C
ATOM 37 N3 DA A 2 17.842 3.228 12.470 1.00 48.58 @ N
ATOM 38 C4 DA A 2 17.939 4.219 13.398 1.00 52.90 @ C
ATOM 39 O HOH B 1 15.884 7.198 17.198 29.35 29.35 O
ATOM 40 O HOH B 2 16.235 2.503 10.176 22.58 22.58 O
ATOM 41 O HOH B 3 15.948 7.087 9.729 21.77 21.77 O
ATOM 42 O HOH B 4 20.254 7.111 16.642 14.04 14.04 O
ATOM 43 O HOH B 6 10.426 8.174 14.485 11.38 11.38 O
ATOM 44 O HOH B 7 22.433 6.350 16.301 11.25 11.25 O
ATOM 45 O HOH B 9 14.807 4.452 9.387 9.85 9.85 O
ATOM 46 O HOH B 10 17.490 11.455 9.361 9.76 9.76 O
ATOM 47 O HOH B 11 12.070 10.875 12.322 8.35 8.35 O
ATOM 48 O HOH B 12 23.788 7.939 13.779 11.13 11.13 O
END
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