[ccp4bb] edit chi angles of DNA in coot

[LISA]

Hi all,
I am refining a protein-DNA complex. But when I adjust the position of DNA
by "edit chi angels", the phosphate does not move. Only the sugar and base
move
Here is partial DNA pdb. Is there any format problem of my pdb or I miss
some library?
ATOM  10825  PAd D  11  17.140  11.607  42.723  1.00
29.20   P
ATOM  10826  O1P  Ad D  11  16.898  12.582  41.641  1.00
29.72   O
ATOM  10827  O2P  Ad D  11  18.154  11.916  43.743  1.00
33.07   O
ATOM  10828  O5*  Ad D  11  17.537  10.169  42.137  1.00
31.19   O
ATOM  10829  C5*  Ad D  11  17.790   9.108  43.047  1.00
25.02   C
ATOM  10830  C4*  Ad D  11  17.956   7.803  42.314  1.00
30.93   C
ATOM  10831  O4*  Ad D  11  16.670   7.304  41.858  1.00
29.79   O
ATOM  10832  C1*  Ad D  11  16.870   6.713  40.601  1.00
36.62   C
ATOM  10833  N9   Ad D  11  15.636   6.710  39.824  1.00
33.20   N
ATOM  10834  C8   Ad D  11  14.968   7.801  39.371  1.00
22.90   C
ATOM  10835  N7   Ad D  11  13.896   7.505  38.680  1.00
26.56   N
ATOM  10836  C5   Ad D  11  13.870   6.121  38.654  1.00
31.80   C
ATOM  10837  C4   Ad D  11  14.942   5.617  39.358  1.00
32.61   C
ATOM  10838  N3   Ad D  11  15.238   4.325  39.551  1.00
27.80   N
ATOM  10839  C2   Ad D  11  14.334   3.546  38.961  1.00
27.51   C
ATOM  10840  N1   Ad D  11  13.252   3.882  38.250  1.00
21.29   N
ATOM  10841  C6   Ad D  11  12.980   5.187  38.073  1.00
31.66   C
ATOM  10842  N6   Ad D  11  11.890   5.516  37.368  1.00
29.64   N
ATOM  10843  C2*  Ad D  11  17.929   7.576  39.923  1.00
36.75   C
ATOM  10844  C3*  Ad D  11  18.836   7.949  41.084  1.00
36.29   C
ATOM  10845  O3*  Ad D  11  19.919   7.056  41.170  1.00
37.96   O
ATOM  10846  PCd D  12  21.191   7.246  40.214  1.00
55.12   P
ATOM  10847  O1P  Cd D  12  22.397   7.328  41.071  1.00
49.33   O
ATOM  10848  O2P  Cd D  12  20.886   8.343  39.272  1.00
47.47   O
ATOM  10849  O5*  Cd D  12  21.226   5.885  39.374  1.00
51.47   O
ATOM  10850  C5*  Cd D  12  21.346   4.667  40.093  1.00
49.75   C
ATOM  10851  C4*  Cd D  12  20.769   3.488  39.334  1.00
39.32   C
ATOM  10852  O4*  Cd D  12  19.343   3.656  39.226  1.00
32.96   O
ATOM  10853  C1*  Cd D  12  18.882   2.909  38.120  1.00
30.55   C
ATOM  10854  N1   Cd D  12  17.966   3.801  37.377  1.00
31.81   N
ATOM  10855  C2   Cd D  12  16.867   3.239  36.734  1.00
24.72   C
ATOM  10856  O2   Cd D  12  16.717   2.019  36.807  1.00
32.01   O
ATOM  10857  N3   Cd D  12  16.011   4.047  36.070  1.00
23.04   N
ATOM  10858  C4   Cd D  12  16.243   5.365  36.022  1.00
28.69   C
ATOM  10859  N4   Cd D  12  15.377   6.135  35.351  1.00
18.23   N
ATOM  10860  C5   Cd D  12  17.370   5.958  36.668  1.00
27.01   C
ATOM  10861  C6   Cd D  12  18.198   5.145  37.329  1.00
28.78   C
ATOM  10862  C2*  Cd D  12  20.104   2.429  37.341  1.00
34.57   C
ATOM  10863  C3*  Cd D  12  21.222   3.310  37.890  1.00
31.03   C
ATOM  10864  O3*  Cd D  12  22.469   2.619  37.840  1.00
34.98   O

Re: [ccp4bb] edit chi angles of DNA in coot

[Paul Emsley]

On 27/01/13 12:18, LISA wrote:

Hi all,
I am refining a protein-DNA complex. But when I adjust the position of 
DNA by "edit chi angels", the phosphate does not move. Only the sugar 
and base move
Here is partial DNA pdb. Is there any format problem of my pdb or I 
miss some library?


Hello Lisa,

Recent Coots use PDB v3 names for nucleotide - which means, for the most 
part, using primes rather than star.


HTH,

Paul.

Re: [ccp4bb] edit chi angles of DNA in coot

[Robbie Joosten]

Hi Lisa,

I'm not sure it's the source of your problem, but your atom names are still in 
PDBv2 format. That's 'so last decade'. Start by fixing that. There must be a 
CCP4 tool that will do that. You can also use the MolProbity server to fix the 
format.
For the developers: the problem with atom and residues in the old naming scheme 
is really annoying. Are there still programs that write this? Perhaps support 
for the PDBv2 should be dropped by now except in a few format converters.

Cheers,
Robbie

Sent from my Windows Phone

From: LISA
Sent: 2013-01-27 13:19
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] edit chi angles of DNA in coot

Hi all,
I am refining a protein-DNA complex. But when I adjust the position of DNA
by "edit chi angels", the phosphate does not move. Only the sugar and base
move
Here is partial DNA pdb. Is there any format problem of my pdb or I miss
some library?
ATOM  10825  PAd D  11  17.140  11.607  42.723  1.00
29.20   P
ATOM  10826  O1P  Ad D  11  16.898  12.582  41.641  1.00
29.72   O
ATOM  10827  O2P  Ad D  11  18.154  11.916  43.743  1.00
33.07   O
ATOM  10828  O5*  Ad D  11  17.537  10.169  42.137  1.00
31.19   O
ATOM  10829  C5*  Ad D  11  17.790   9.108  43.047  1.00
25.02   C
ATOM  10830  C4*  Ad D  11  17.956   7.803  42.314  1.00
30.93   C
ATOM  10831  O4*  Ad D  11  16.670   7.304  41.858  1.00
29.79   O
ATOM  10832  C1*  Ad D  11  16.870   6.713  40.601  1.00
36.62   C
ATOM  10833  N9   Ad D  11  15.636   6.710  39.824  1.00
33.20   N
ATOM  10834  C8   Ad D  11  14.968   7.801  39.371  1.00
22.90   C
ATOM  10835  N7   Ad D  11  13.896   7.505  38.680  1.00
26.56   N
ATOM  10836  C5   Ad D  11  13.870   6.121  38.654  1.00
31.80   C
ATOM  10837  C4   Ad D  11  14.942   5.617  39.358  1.00
32.61   C
ATOM  10838  N3   Ad D  11  15.238   4.325  39.551  1.00
27.80   N
ATOM  10839  C2   Ad D  11  14.334   3.546  38.961  1.00
27.51   C
ATOM  10840  N1   Ad D  11  13.252   3.882  38.250  1.00
21.29   N
ATOM  10841  C6   Ad D  11  12.980   5.187  38.073  1.00
31.66   C
ATOM  10842  N6   Ad D  11  11.890   5.516  37.368  1.00
29.64   N
ATOM  10843  C2*  Ad D  11  17.929   7.576  39.923  1.00
36.75   C
ATOM  10844  C3*  Ad D  11  18.836   7.949  41.084  1.00
36.29   C
ATOM  10845  O3*  Ad D  11  19.919   7.056  41.170  1.00
37.96   O
ATOM  10846  PCd D  12  21.191   7.246  40.214  1.00
55.12   P
ATOM  10847  O1P  Cd D  12  22.397   7.328  41.071  1.00
49.33   O
ATOM  10848  O2P  Cd D  12  20.886   8.343  39.272  1.00
47.47   O
ATOM  10849  O5*  Cd D  12  21.226   5.885  39.374  1.00
51.47   O
ATOM  10850  C5*  Cd D  12  21.346   4.667  40.093  1.00
49.75   C
ATOM  10851  C4*  Cd D  12  20.769   3.488  39.334  1.00
39.32   C
ATOM  10852  O4*  Cd D  12  19.343   3.656  39.226  1.00
32.96   O
ATOM  10853  C1*  Cd D  12  18.882   2.909  38.120  1.00
30.55   C
ATOM  10854  N1   Cd D  12  17.966   3.801  37.377  1.00
31.81   N
ATOM  10855  C2   Cd D  12  16.867   3.239  36.734  1.00
24.72   C
ATOM  10856  O2   Cd D  12  16.717   2.019  36.807  1.00
32.01   O
ATOM  10857  N3   Cd D  12  16.011   4.047  36.070  1.00
23.04   N
ATOM  10858  C4   Cd D  12  16.243   5.365  36.022  1.00
28.69   C
ATOM  10859  N4   Cd D  12  15.377   6.135  35.351  1.00
18.23   N
ATOM  10860  C5   Cd D  12  17.370   5.958  36.668  1.00
27.01   C
ATOM  10861  C6   Cd D  12  18.198   5.145  37.329  1.00
28.78   C
ATOM  10862  C2*  Cd D  12  20.104   2.429  37.341  1.00
34.57   C
ATOM  10863  C3*  Cd D  12  21.222   3.310  37.890  1.00
31.03   C
ATOM  10864  O3*  Cd D  12  22.469   2.619  37.840  1.00
34.98   O

Re: [ccp4bb] edit chi angles of DNA in coot

[Read, Jon]

Yes, a good pdb converter jiffy that picks up and corrects/highlights 
differences and errors  in the atom name from the residue name would be great 
to have. I’m using pdbvconv from Global Phasing which is pretty good. It gets a 
little confused when the atoms names are a mixture of pdbv2 and v3. This has 
happened with NAD which a couple of times,



Jon Read

Associate Principal Scientist

_

Astrazeneca

R&D, Decs,

Astrazeneca, Mereside, Alderley Park, Cheshire, SK10 4TG UK

Tel +44 (0)1625 510661  Mobile +44 (0)7775 040376



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie 
Joosten
Sent: 27 January 2013 13:27
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] edit chi angles of DNA in coot



Hi Lisa,

I'm not sure it's the source of your problem, but your atom names are still in 
PDBv2 format. That's 'so last decade'. Start by fixing that. There must be a 
CCP4 tool that will do that. You can also use the MolProbity server to fix the 
format.
For the developers: the problem with atom and residues in the old naming scheme 
is really annoying. Are there still programs that write this? Perhaps support 
for the PDBv2 should be dropped by now except in a few format converters.

Cheers,
Robbie

Sent from my Windows Phone



From: LISA
Sent: 2013-01-27 13:19
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] edit chi angles of DNA in coot

Hi all,

I am refining a protein-DNA complex. But when I adjust the position of DNA by 
"edit chi angels", the phosphate does not move. Only the sugar and base move

Here is partial DNA pdb. Is there any format problem of my pdb or I miss some 
library?
ATOM  10825  PAd D  11  17.140  11.607  42.723  1.00 29.20   P
ATOM  10826  O1P  Ad D  11  16.898  12.582  41.641  1.00 29.72   O
ATOM  10827  O2P  Ad D  11  18.154  11.916  43.743  1.00 33.07   O
ATOM  10828  O5*  Ad D  11  17.537  10.169  42.137  1.00 31.19   O
ATOM  10829  C5*  Ad D  11  17.790   9.108  43.047  1.00 25.02   C
ATOM  10830  C4*  Ad D  11  17.956   7.803  42.314  1.00 30.93   C
ATOM  10831  O4*  Ad D  11  16.670   7.304  41.858  1.00 29.79   O
ATOM  10832  C1*  Ad D  11  16.870   6.713  40.601  1.00 36.62   C
ATOM  10833  N9   Ad D  11  15.636   6.710  39.824  1.00 33.20   N
ATOM  10834  C8   Ad D  11  14.968   7.801  39.371  1.00 22.90   C
ATOM  10835  N7   Ad D  11  13.896   7.505  38.680  1.00 26.56   N
ATOM  10836  C5   Ad D  11  13.870   6.121  38.654  1.00 31.80   C
ATOM  10837  C4   Ad D  11  14.942   5.617  39.358  1.00 32.61   C
ATOM  10838  N3   Ad D  11  15.238   4.325  39.551  1.00 27.80   N
ATOM  10839  C2   Ad D  11  14.334   3.546  38.961  1.00 27.51   C
ATOM  10840  N1   Ad D  11  13.252   3.882  38.250  1.00 21.29   N
ATOM  10841  C6   Ad D  11  12.980   5.187  38.073  1.00 31.66   C
ATOM  10842  N6   Ad D  11  11.890   5.516  37.368  1.00 29.64   N
ATOM  10843  C2*  Ad D  11  17.929   7.576  39.923  1.00 36.75   C
ATOM  10844  C3*  Ad D  11  18.836   7.949  41.084  1.00 36.29   C
ATOM  10845  O3*  Ad D  11  19.919   7.056  41.170  1.00 37.96   O
ATOM  10846  PCd D  12  21.191   7.246  40.214  1.00 55.12   P
ATOM  10847  O1P  Cd D  12  22.397   7.328  41.071  1.00 49.33   O
ATOM  10848  O2P  Cd D  12  20.886   8.343  39.272  1.00 47.47   O
ATOM  10849  O5*  Cd D  12  21.226   5.885  39.374  1.00 51.47   O
ATOM  10850  C5*  Cd D  12  21.346   4.667  40.093  1.00 49.75   C
ATOM  10851  C4*  Cd D  12  20.769   3.488  39.334  1.00 39.32   C
ATOM  10852  O4*  Cd D  12  19.343   3.656  39.226  1.00 32.96   O
ATOM  10853  C1*  Cd D  12  18.882   2.909  38.120  1.00 30.55   C
ATOM  10854  N1   Cd D  12  17.966   3.801  37.377  1.00 31.81   N
ATOM  10855  C2   Cd D  12  16.867   3.239  36.734  1.00 24.72   C
ATOM  10856  O2   Cd D  12  16.717   2.019  36.807  1.00 32.01   O
ATOM  10857  N3   Cd D  12  16.011   4.047  36.070  1.00 23.04   N
ATOM  10858  C4   Cd D  12  16.243   5.365  36.022  1.00 28.69   C
ATOM  10859  N4   Cd D  12  15.377   6.135  35.351  1.00 18.23   N
ATOM  10860  C5   Cd D  12  17.370   5.958  36.668  1.00 27.01   C
ATOM  10861  C6   Cd D  12  18.198   5.145  37.329  1.00 28.78   C
ATOM  10862  C2*  Cd D  12  20.104   2.429  37.341  1.00 34.57   C
ATOM  10863  C3*  Cd D  12  21.222   3.310  37.890  1.00 31.03   C
ATOM  10864  O3*  Cd D  12  22.469   2.619  37.840  1.00 34.98   O


--
AstraZeneca UK Limited is a

Re: [ccp4bb] edit chi angles of DNA in coot

[eugene . krissinel]

There is a new tool for that in CCP4, pdb2to3. It will try to convert 
everything what is convertible, even when it is not "PDB2" or residue names do 
not match, by applying graph matching and some heuristics.

Eugene

On 27 Jan 2013, at 13:27, Robbie Joosten wrote:

Hi Lisa,

I'm not sure it's the source of your problem, but your atom names are still in 
PDBv2 format. That's 'so last decade'. Start by fixing that. There must be a 
CCP4 tool that will do that. You can also use the MolProbity server to fix the 
format.
For the developers: the problem with atom and residues in the old naming scheme 
is really annoying. Are there still programs that write this? Perhaps support 
for the PDBv2 should be dropped by now except in a few format converters.

Cheers,
Robbie

Sent from my Windows Phone

From: LISA
Sent: 2013-01-27 13:19
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] edit chi angles of DNA in coot

Hi all,
I am refining a protein-DNA complex. But when I adjust the position of DNA by 
"edit chi angels", the phosphate does not move. Only the sugar and base move
Here is partial DNA pdb. Is there any format problem of my pdb or I miss some 
library?
ATOM  10825  PAd D  11  17.140  11.607  42.723  1.00 29.20   P
ATOM  10826  O1P  Ad D  11  16.898  12.582  41.641  1.00 29.72   O
ATOM  10827  O2P  Ad D  11  18.154  11.916  43.743  1.00 33.07   O
ATOM  10828  O5*  Ad D  11  17.537  10.169  42.137  1.00 31.19   O
ATOM  10829  C5*  Ad D  11  17.790   9.108  43.047  1.00 25.02   C
ATOM  10830  C4*  Ad D  11  17.956   7.803  42.314  1.00 30.93   C
ATOM  10831  O4*  Ad D  11  16.670   7.304  41.858  1.00 29.79   O
ATOM  10832  C1*  Ad D  11  16.870   6.713  40.601  1.00 36.62   C
ATOM  10833  N9   Ad D  11  15.636   6.710  39.824  1.00 33.20   N
ATOM  10834  C8   Ad D  11  14.968   7.801  39.371  1.00 22.90   C
ATOM  10835  N7   Ad D  11  13.896   7.505  38.680  1.00 26.56   N
ATOM  10836  C5   Ad D  11  13.870   6.121  38.654  1.00 31.80   C
ATOM  10837  C4   Ad D  11  14.942   5.617  39.358  1.00 32.61   C
ATOM  10838  N3   Ad D  11  15.238   4.325  39.551  1.00 27.80   N
ATOM  10839  C2   Ad D  11  14.334   3.546  38.961  1.00 27.51   C
ATOM  10840  N1   Ad D  11  13.252   3.882  38.250  1.00 21.29   N
ATOM  10841  C6   Ad D  11  12.980   5.187  38.073  1.00 31.66   C
ATOM  10842  N6   Ad D  11  11.890   5.516  37.368  1.00 29.64   N
ATOM  10843  C2*  Ad D  11  17.929   7.576  39.923  1.00 36.75   C
ATOM  10844  C3*  Ad D  11  18.836   7.949  41.084  1.00 36.29   C
ATOM  10845  O3*  Ad D  11  19.919   7.056  41.170  1.00 37.96   O
ATOM  10846  PCd D  12  21.191   7.246  40.214  1.00 55.12   P
ATOM  10847  O1P  Cd D  12  22.397   7.328  41.071  1.00 49.33   O
ATOM  10848  O2P  Cd D  12  20.886   8.343  39.272  1.00 47.47   O
ATOM  10849  O5*  Cd D  12  21.226   5.885  39.374  1.00 51.47   O
ATOM  10850  C5*  Cd D  12  21.346   4.667  40.093  1.00 49.75   C
ATOM  10851  C4*  Cd D  12  20.769   3.488  39.334  1.00 39.32   C
ATOM  10852  O4*  Cd D  12  19.343   3.656  39.226  1.00 32.96   O
ATOM  10853  C1*  Cd D  12  18.882   2.909  38.120  1.00 30.55   C
ATOM  10854  N1   Cd D  12  17.966   3.801  37.377  1.00 31.81   N
ATOM  10855  C2   Cd D  12  16.867   3.239  36.734  1.00 24.72   C
ATOM  10856  O2   Cd D  12  16.717   2.019  36.807  1.00 32.01   O
ATOM  10857  N3   Cd D  12  16.011   4.047  36.070  1.00 23.04   N
ATOM  10858  C4   Cd D  12  16.243   5.365  36.022  1.00 28.69   C
ATOM  10859  N4   Cd D  12  15.377   6.135  35.351  1.00 18.23   N
ATOM  10860  C5   Cd D  12  17.370   5.958  36.668  1.00 27.01   C
ATOM  10861  C6   Cd D  12  18.198   5.145  37.329  1.00 28.78   C
ATOM  10862  C2*  Cd D  12  20.104   2.429  37.341  1.00 34.57   C
ATOM  10863  C3*  Cd D  12  21.222   3.310  37.890  1.00 31.03   C
ATOM  10864  O3*  Cd D  12  22.469   2.619  37.840  1.00 34.98   O


-- 
Scanned by iCritical.

Re: [ccp4bb] 3D Monitors

[Peng GONG]

Sabine,

I am using LG D2342P and it works fine with coot and pymol.

Peng
---
Peng Gong
Wuhan Institute of Virology, CAS
---



 From: Sabine Schneider 
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Friday, January 25, 2013 12:13 AM
Subject: [ccp4bb] 3D Monitors
 
Hello everyone,

I know there already has been discussion about 3D monitors on the Coot/CCP4bb.
However since there are a few more out there now and I am currently thinking 
about buying one, I thought to get a few opinions from crystallographers would 
be nice! Especially if there are people happily model building with the cheaper 
LG 3D monitors? :-)

So I am looking at the moment at:
- Zalman ZM-M215W 21,5in
- Zalman ZM-M240W 24in
- Samsung SyncMaster S27A750D 27in
- LG D2342P 23in / LG D2542P 25in

Thanks a lot!

Sabine

Re: [ccp4bb] 3D Monitors

[David Roberts]

I use the Zalman 21" monitor and it works great.  Glasses from 3D movies work, 
so when students go to the movies I ask them to save a pair of glasses for me.  
It's easy and cheap - software controlled so works on all crystallographic 
packages that I've tried thus far.

Frankly, since going to an LCD monitor from the old CRT displays, I find stereo 
is not really needed.  It's cool, and occasionally nice to look at, but the 
display is so good that I find 2D is just fine for all modeling needs.  So we 
really don't use the Zalman's much

Dave

Sent from my iPad

On Jan 27, 2013, at 11:00 AM, Peng GONG  wrote:

> Sabine,
> 
> I am using LG D2342P and it works fine with coot and pymol.
> 
> Peng
> ---
> Peng Gong
> Wuhan Institute of Virology, CAS
> ---
> 
> From: Sabine Schneider 
> To: CCP4BB@JISCMAIL.AC.UK 
> Sent: Friday, January 25, 2013 12:13 AM
> Subject: [ccp4bb] 3D Monitors
> 
> Hello everyone,
> 
> I know there already has been discussion about 3D monitors on the Coot/CCP4bb.
> However since there are a few more out there now and I am currently thinking 
> about buying one, I thought to get a few opinions from crystallographers 
> would be nice! Especially if there are people happily model building with the 
> cheaper LG 3D monitors? :-)
> 
> So I am looking at the moment at:
> - Zalman ZM-M215W 21,5in
> - Zalman ZM-M240W 24in
> - Samsung SyncMaster S27A750D 27in
> - LG D2342P 23in / LG D2542P 25in
> 
> Thanks a lot!
> 
> Sabine
> 
> 

Re: [ccp4bb] 3D Monitors

[mesters]

Hello Sabine,

the Asus VG287H (not the HE model)! Why?

- nvidia certified, so all nvidia drivers will recognize the screen 
correctly (we have it working under SuSe linux and windows 7)
- build-in IR emitter (so works with the cheaper quadro cards), we run 
it with quadro 600, k1000m and 2000 models, all without 3-pin connector

- one pair of nvidia glasses already included (Value 100 EUR)
- lightboost technology, so the picture is more bright than other screens
- the bigger the screen, the better the stereo feels (this screen is 27 
inch diameter)


Just under 500 EUR it may seem expensive but once you substract the 
price of a pair of glasses (± 100EUR) and consider it is large, nvidia 
certified, has a build-in IR emitter and is best of class, it is 
actually a very good deal.


p.s. here is a thread at computerbase.de (german language) ranking many 
monitors: http://www.computerbase.de/forum/showthread.php?t=949874


- J. -

--

Dr. Jeroen R. Mesters

Gruppenleiter Strukturelle Neurobiologie und Kristallogenese
Institut für Biochemie
Universität zu Lübeck
Zentrum für Medizinische Struktur- und Zellbiologie
Ratzeburger Allee 160, D-23538 Lübeck
Tel: +49-451-5004065
Fax: +49-451-5004068
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.selfish-brain.org
Http://www.opticryst.org
--