e2pdb2mrc.py returned 0 density for certain pdb file

[Doo Nam Kim]

I could convert my other pdb file (3qjx-clean.pdb) into mrc by 

e2pdb2mrc.py 3qjx-clean.pdb 3qjx-clean.mrc apix=0.5 res=1.5 box=256 het center solvate full

generated mrc is ok.

However, when I ran other pdb file as

e2pdb2mrc.py PDX1_2_mini.pdb PDX1_2_mini.mrc apix=0.5 res=1.5 box=256 het center solvate full

18 atoms used with a total charge of 114 e- and a mass of 0 kDa

Atomic center at 177.6,107.4,164.1 (center of volume at 0,0,0)

Bounding box: x:  173.10 -  182.83

              y:  105.62 -  110.67

              z:  162.61 -  166.10

Conversion complete

I see 0 density as

(base) [kimd999@deception03 by_eman2]$ header PDX1_2_mini.mrc

 RO image file on unit   1 : PDX1_2_mini.mrc     Size=         55 K

 Number of columns, rows, sections .....      24      24      24

 Map mode ..............................    2   (32-bit real)

 Start cols, rows, sects, grid x,y,z ...  -12   -12   -12      24     24     24

 Pixel spacing (Angstroms)..............   1.000      1.000      1.000

 Cell angles ...........................   90.000   90.000   90.000

 Fast, medium, slow axes ...............    X    Y    Z

 Origin on x,y,z .......................   -12.00      -12.00      -12.00

 Minimum density .......................   0.0000

 Maximum density .......................   0.0000

 Mean density ..........................   0.0000

 tilt angles (original,current) ........   0.0   0.0   0.0   0.0   0.0   0.0

 Space group,# extra bytes,idtype,lens .        0        0        0        0

     2 Titles :

EMAN 8/24/2021 8:26

EMAN 8/24/2021 8:51

Indeed, chimera loading of this mrc shows an empty cube as attached.

Can I get some advice?

Here I attach PDX1_2_mini.pdb

ATOM      1  N   PRO A   1     181.355 106.453 163.714  0.75 71.59           N

ATOM      2  CA  PRO A   1     180.600 105.617 164.653  0.75 71.59           C

ATOM      3  C   PRO A   1     179.209 106.172 164.936  0.75 71.59           C

ATOM      4  O   PRO A   1     178.828 106.311 166.096  0.75 71.59           O

ATOM      5  CB  PRO A   1     181.462 105.641 165.919  0.75 71.59           C

ATOM      6  CG  PRO A   1     182.830 105.989 165.446  0.49 71.59           C

ATOM      7  CD  PRO A   1     182.631 106.911 164.286  0.49 71.59           C

ATOM      8  N   PHE A   2     178.463 106.498 163.880  0.75 69.87           N

ATOM      9  CA  PHE A   2     177.110 107.009 164.068  0.75 69.87           C

ATOM     10  C   PHE A   2     176.136 105.895 164.426  0.75 69.87           C

ATOM     11  O   PHE A   2     175.168 106.128 165.159  0.75 69.87           O

ATOM     12  CB  PHE A   2     176.648 107.739 162.807  0.75 69.87           C

ATOM     13  CG  PHE A   2     175.454 108.621 163.021  0.49 69.87           C

ATOM     14  CD1 PHE A   2     175.591 109.858 163.624  0.49 69.87           C

ATOM     15  CD2 PHE A   2     174.196 108.219 162.610  0.49 69.87           C

ATOM     16  CE1 PHE A   2     174.495 110.673 163.819  0.49 69.87           C

ATOM     17  CE2 PHE A   2     173.096 109.031 162.801  0.49 69.87           C

ATOM     18  CZ  PHE A   2     173.246 110.258 163.408  0.49 69.87           C

best,

Doonam

[Muyuan Chen]

Can you provide the full command you run? It is quite odd that the box size is 24 in your mrc while you specify --box=256. 

Also, sometimes adding --center helps.

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[Ludtke, Steven J.]

Was that the exact command you used, or did you have the required "--" before each option?

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<Screen Shot 2021-08-24 at 8.53.36 AM.png>

[Doo Nam Kim]

Muyuan, Steven,

These are exact (verbatim) commands that I originally used.

For 3qjx-clean.pdb,

I used

e2pdb2mrc.py 3qjx-clean.pdb 3qjx-clean.mrc apix=0.5 res=1.5 box=256 het center solvate full

and its generated mrc seems ok.

For PDX1_2_mini.pdb (that I attached its full contents in a previous email),

I used

e2pdb2mrc.py PDX1_2_mini.pdb PDX1_2_mini.mrc apix=0.5 res=1.5 box=256 het center solvate full

and its generated mrc has 0 density only.

As I see

https://blake.bcm.edu/eman2/EMAN2.html/node100.html

'single dash' seems needed instead of double-dash. However, as I see

e2pdb2mrc.py code itself, double-dash seems needed and there is no

--solvate option.

Therefore, I used

e2pdb2mrc.py PDX1_2_mini.pdb PDX1_2_mini.mrc --apix=0.5 --res=1.5 --box=256

--het --center --full

then, the result is

18 atoms used with a total charge of 114 e- and a mass of 0 kDa

Atomic center at 177.6,107.4,164.1 (center of volume at 0,0,0)

Bounding box: x:  173.10 -  182.83

              y:  105.62 -  110.67

              z:  162.61 -  166.10

Traceback (most recent call last):

  File "/people/kimd999/bin/eman2p9/bin/e2pdb2mrc.py", line 476, in <module>

    main()

  File "/people/kimd999/bin/eman2p9/bin/e2pdb2mrc.py", line 297, in main

    pts = np.concatenate(points).flatten()

  File "<__array_function__ internals>", line 6, in concatenate

ValueError: need at least one array to concatenate

So, I removed --full

(e2pdb2mrc.py PDX1_2_mini.pdb PDX1_2_mini.mrc --apix=0.5 --res=1.5 --box=256

--het --center)

then, its mrc has expected density like attached.

Muyuan is right.

Without --center option, generated map lacks density.

With --center option, generated map has a higher density overall.

Even when I used other pdb file, adding 

--center option tends to increase mean map density.

Thank you,

Doo Nam

[Ludtke, Steven J.]

You need -- in front of all EMAN2 options. This page:

https://blake.bcm.edu/eman2/EMAN2.html/node100.html

is not valid. I can see who it says created it, but that person wasn't working at BCM any more at that time...  I guess you found it by googling?  It's a Wiki, so anyone with an account can create anything they like. To get accurate, up-to date usage for command-line programs run the program with -h or --help

e2pdb2mrc.py --help

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/16b03644-6a1b-4f82-ab25-1dae58081ee0n%40googlegroups.com.

[Ludtke, Steven J.]

Ok, I should ammend my statement, there are a few options in a few programs which have a single letter abbreviation which accepts a single '-', but these are being retired in the future. The pages you ran across are incorrect, regardless. Will see if we can easily clean them up.

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/BC2F8FAB-82E1-4FA0-8FA2-7BD99E79E0E1%40bcm.edu.