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Messages - xiangjun

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1
I'm glad to hear that things are sorted out.

Quote
Once I re-did what you did earlier (find_pair, cp_std, and then rebuild), I did not get any error, although the two .pdb models have a coordinate shift. My error seems to be with emDNA_parser and, therefore, not through you.

The "coordinate shift" is what the diagnostic message "xyz coordinate under f8.3 limit. reset origin to minimum xyz coordinates" is about. The "rebuild" program is simply resetting the center of the structure so that the atomic coordinates can be better fitted into the f8.3 limit of PDB format.
 
Quote
However, is there a way to generate a reference frame file from a starting .par file using x3dna?

Did you notice that after running "rebuild", a file named "ref_frames.dat" is also generated? Presumably, that's what you are looking for.

Enjoy using 3DNA.

Xiang-Jun

2
Please follow the instructions to help me identify where the problem is.

I got confused by your two posts dated Nov. 8. For one thing, the attached file is named tbru_mc004.par, whilst in your posts, the parameter file is called "x.par" and "new.par". What is emDNA_parser, and how is it relevant the issue at hand? The sequence in the parameter should not affect how "rebuild" runs.

Xiang-Jun




3
Thanks for your follow-up. Could you please install the 3DNA v2.3.4-2018nov06 so we are playing with the same version? Here are my results using the 64-bit Linux version, with the structure004.pdb file you emailed me. In my hand, 3DNA works as expected.

x3dna@tstx [2035] find_pair structure004.pdb | analyze

handling file <structure004.pdb>

Time used: 00:00:00:01
This structure has broken O3' to P[i+1] linkages

Time used: 00:00:00:03
x3dna@tstx [2036] x3dna_utils cp_std BDNA
x3dna@tstx [2037] rebuild -atomic bp_step.par 3dna-str04.pdb
xyz coordinate under f8.3 limit. reset origin to minimum xyz coordinates

Time used: 00:00:00:01

The bp_step.par and an image of 3dna-str04.pdb are attached.

Please repeat the commands above and post back your results.

Xiang-Jun

4
General discussions (Q&As) / Re: 3DNA 2.4.3 Rebuild
« on: November 06, 2018, 07:29:56 pm »
After copying in the files in ConEmu, please re-run the rebuild program with the -atomic option as in your screenshot. You'll see your rebuilt structure with B-form backbone atoms.

Installing MSYS2 is a separate issue. I strongly suggest you, or any 3DNA user on Windows, do so since it makes using 3DNA (a command-line tool) so much easier.

Best regards,

Xiang-Jun

5
FAQs / Re: How to set up 3DNA on Windows
« on: November 06, 2018, 07:06:12 pm »
Thanks --- the output result is as expected. Then 3DNA should work with the original config folder, without creating a new x3dna-v2.3config folder. Yours is the first reported 'weird' case. Let's see if other 3DNA users have a similar problem in the future.

Best regards,

Xiang-Jun



6
On what platform (Windows, macOS, or Linux) did you run 3DNA? Could you post the bp_step.par file for the problematic structure?

Thanks,

Xiang-Jun

7
FAQs / Re: How to set up 3DNA on Windows
« on: November 06, 2018, 03:09:48 pm »
Great! Please do the following, and report back with a screenshot:

Code: [Select]
dir %X3DNA%config\version
Thanks,

Xiang-Jun

8
Given only the description in your post, it is impossible to decipher where the problem is. The title mentions the f8.3 limit of PDB format, would a 3DNA-rebuilt structure in mmCIF file help?

Please clarify.

Xiang-Jun

9
General discussions (Q&As) / Re: 3DNA 2.4.3 Rebuild
« on: November 06, 2018, 02:47:54 pm »
Got it -- thanks.

The error message is due to a limitation with Windows command environment. The x3dna_utils Ruby script is not recognized in native Windows. You may consider installing MSYS2 which is more flexible and much Linux-like.

Or, you could simply run the following commands in your working directory:

Code: [Select]
copy %X3DNA%\config\atomic\BDNA_A.pdb Atomic_A.pdb
copy %X3DNA%\config\atomic\BDNA_C.pdb Atomic_C.pdb
copy %X3DNA%\config\atomic\BDNA_G.pdb Atomic_G.pdb
copy %X3DNA%\config\atomic\BDNA_T.pdb Atomic_T.pdb
copy %X3DNA%\config\atomic\BDNA_U.pdb Atomic_U.pdb

You may need to adjust with the 'config' part due to your settings. Then you'll be able to build a DNA structure with B-form backbone. Have a try and report back how it goes.

Xiang-Jun



10
General discussions (Q&As) / Re: 3DNA 2.4.3 Rebuild
« on: November 06, 2018, 02:16:01 pm »
Thanks for the screenshots.

Could you please translate the error message of x3dna_utils into English?

Xiang-Jun

11
General discussions (Q&As) / Re: 3DNA 2.4.3 Rebuild
« on: November 06, 2018, 01:25:21 pm »
Please provide more details, preferably with screenshots.

Thanks,

Xiang-Jun

12
FAQs / Re: How to set up 3DNA on Windows
« on: November 06, 2018, 01:18:36 pm »
Thanks for reporting back. I'm surprised to see that with ending slash you could (still) have the originally reported problem. With ConEmu, could you please post back the output of the following commands, preferably with a screenshot?

Code: [Select]
echo %X3DNA%
echo %PATH%

I'm glad to see your smart workaround by creating a x3dna-v2.3config folder.

Thanks,

Xiang-Jun

13
FAQs / Re: How to set up 3DNA on Windows
« on: November 06, 2018, 12:06:18 pm »
As a follow-up, I've just re-installed 3DNA Windows (x3dna-v2.3.zip) in native Windows environment. I'm convinced that if you added the end slash in your setting of the X3DNA environment variable, as noted in step 4.4 (with the screenshot linked below), 3DNA would work as expected. Please have a try and report back your findings.



Thanks,

Xiang-Jun

14
FAQs / Re: How to set up 3DNA on Windows
« on: November 06, 2018, 11:49:15 am »
Hi,

Thanks for reporting. What's the output (or the setting) of your $X3DNA? Did you set it up explicitly? Adding the end slash should do the trick.

I've just tested the new release on Msys2 with Windows 7, and the programs work as expected. There could be some edge cases that need to be taken care of.

Best regards,

Xiang-Jun

15
General discussions (Q&As) / Re: mutations to 3-methyladenine
« on: November 06, 2018, 11:23:17 am »
As a follow-up, I've updated 3DNA to v2.3.4-2018nov06 which includes a 3-methyladenine (3MA) derived from PDB id 3MAG. The building block file is named Atomic_3MA.pdb, stored under the X3DNA/config folder, with the following content:

Code: [Select]
REMARK 3DNA v3 (2018), created and maintained by xiangjun@x3dna.org
HETATM    1  N9  3MA A 600      -1.287   4.521   0.006  1.00 49.87           N
HETATM    2  C4  3MA A 600      -1.262   3.133   0.004  1.00 50.46           C
HETATM    3  N3  3MA A 600      -2.337   2.286  -0.009  1.00 50.37           N
HETATM    4  CN3 3MA A 600      -3.743   2.648  -0.047  1.00 50.41           C
HETATM    5  C2  3MA A 600      -1.905   1.013   0.001  1.00 50.11           C
HETATM    6  N1  3MA A 600      -0.662   0.520   0.004  1.00 49.27           N
HETATM    7  C6  3MA A 600       0.366   1.372  -0.003  1.00 48.99           C
HETATM    8  N6  3MA A 600       1.588   0.867  -0.034  1.00 46.12           N
HETATM    9  C5  3MA A 600       0.068   2.768   0.003  1.00 49.89           C
HETATM   10  N7  3MA A 600       0.875   3.914  -0.003  1.00 49.84           N
HETATM   11  C8  3MA A 600       0.026   4.909  -0.003  1.00 49.58           C
END

Using the requested case as an example, the following command will mutate A7 to 3MA:

Code: [Select]
mutate_bases "chain=_ s=7 m=3MA" bform.pdb bform-A7to3mA.pdb
Note that since the original attached bform.pdb does not include chain id (just a space ' ' character), it is specified as "chain=_" (i.e., using an underscore).

With 3DNA, one can easily generate a B-form (or A-form, or any other of a comprehensive list of 56 fiber-based models) as shown below:

Code: [Select]
# generate a B-form DNA with base sequence GACATGATTGCC
fiber -seq=GACATGATTGCC fiber-BDNA.pdb
# mutate A7 to 3MA
mutate_bases "chain=A s=7 m=3MA" fiber-BDNA.pdb fiber-BDNA-A7to3MA.pdb

Note that 3DNA-generated fiber model has chain id A for the leading strand. For comparison, below is a list of the ATOM records for A7 as directly from the 3DNA fiber program, and those after running mutate_bases to 3MA.
REMARK 3DNA fiber-derived atomic coordinates for A7 
ATOM    126  P    DA A   7      -5.130  -7.667 -18.402  1.00  1.00           P
ATOM    127  OP1  DA A   7      -5.914  -8.669 -17.645  1.00  1.00           O
ATOM    128  OP2  DA A   7      -4.303  -8.192 -19.510  1.00  1.00           O
ATOM    129  O5'  DA A   7      -6.107  -6.526 -18.955  1.00  1.00           O
ATOM    130  C5'  DA A   7      -6.430  -5.410 -18.104  1.00  1.00           C
ATOM    131  C4'  DA A   7      -6.362  -4.119 -18.895  1.00  1.00           C
ATOM    132  O4'  DA A   7      -5.026  -3.539 -18.898  1.00  1.00           O
ATOM    133  C3'  DA A   7      -6.720  -4.227 -20.377  1.00  1.00           C
ATOM    134  O3'  DA A   7      -7.422  -3.053 -20.768  1.00  1.00           O
ATOM    135  C2'  DA A   7      -5.374  -4.251 -21.100  1.00  1.00           C
ATOM    136  C1'  DA A   7      -4.689  -3.199 -20.234  1.00  1.00           C
ATOM    137  N9   DA A   7      -3.204  -3.200 -20.351  1.00  1.00           N
ATOM    138  C8   DA A   7      -2.369  -4.263 -20.542  1.00  1.00           C
ATOM    139  N7   DA A   7      -1.114  -3.940 -20.604  1.00  1.00           N
ATOM    140  C5   DA A   7      -1.115  -2.562 -20.442  1.00  1.00           C
ATOM    141  C6   DA A   7      -0.082  -1.611 -20.412  1.00  1.00           C
ATOM    142  N6   DA A   7       1.215  -1.922 -20.551  1.00  1.00           N
ATOM    143  N1   DA A   7      -0.430  -0.323 -20.234  1.00  1.00           N
ATOM    144  C2   DA A   7      -1.720  -0.020 -20.096  1.00  1.00           C
ATOM    145  N3   DA A   7      -2.766  -0.816 -20.107  1.00  1.00           N
ATOM    146  C4   DA A   7      -2.390  -2.099 -20.287  1.00  1.00           C
----------------------------------------------------------------------------------------
REMARK    Mutation#1 A:...7@:[@@@] to [3MA]
ATOM    126  P   3MA A   7      -5.130  -7.667 -18.402  1.00  1.00           P
ATOM    127  OP1 3MA A   7      -5.914  -8.669 -17.645  1.00  1.00           O
ATOM    128  OP2 3MA A   7      -4.303  -8.192 -19.510  1.00  1.00           O
ATOM    129  O5' 3MA A   7      -6.107  -6.526 -18.955  1.00  1.00           O
ATOM    130  C5' 3MA A   7      -6.430  -5.410 -18.104  1.00  1.00           C
ATOM    131  C4' 3MA A   7      -6.362  -4.119 -18.895  1.00  1.00           C
ATOM    132  O4' 3MA A   7      -5.026  -3.539 -18.898  1.00  1.00           O
ATOM    133  C3' 3MA A   7      -6.720  -4.227 -20.377  1.00  1.00           C
ATOM    134  O3' 3MA A   7      -7.422  -3.053 -20.768  1.00  1.00           O
ATOM    135  C2' 3MA A   7      -5.374  -4.251 -21.100  1.00  1.00           C
ATOM    136  C1' 3MA A   7      -4.689  -3.199 -20.234  1.00  1.00           C
ATOM    137  N9  3MA A   7      -3.223  -3.222 -20.359  1.00  1.00           N
ATOM    138  C4  3MA A   7      -2.403  -2.103 -20.290  1.00  1.00           C
ATOM    139  N3  3MA A   7      -2.789  -0.805 -20.095  1.00  1.00           N
ATOM    140  CN3 3MA A   7      -4.138  -0.309 -19.891  1.00  1.00           C
ATOM    141  C2  3MA A   7      -1.705  -0.010 -20.097  1.00  1.00           C
ATOM    142  N1  3MA A   7      -0.410  -0.311 -20.238  1.00  1.00           N
ATOM    143  C6  3MA A   7      -0.063  -1.589 -20.408  1.00  1.00           C
ATOM    144  N6  3MA A   7       1.224  -1.873 -20.512  1.00  1.00           N
ATOM    145  C5  3MA A   7      -1.110  -2.559 -20.445  1.00  1.00           C
ATOM    146  N7  3MA A   7      -1.113  -3.952 -20.602  1.00  1.00           N
ATOM    147  C8  3MA A   7      -2.377  -4.283 -20.541  1.00  1.00           C

The new 3-methyl carbon in 3MA is named CN3. Note also the order of atom names in 3MA is as in PDB id 3MAG, and it does not follow the convention for adenine.

For completeness, attached are four PDB files mentioned in this post.

Xiang-Jun

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.