Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

[Zhijie Li]

Hi Kevin,

a)

If your goal is merely to display EM maps, then UCSF Chimera, COOT, 
pymol, etc. should all do. The EM maps are saved in the MRC format (.mrc 
or .mrcs). Despite a different extension and some minor differences in 
the headers, the MRC format is essentially the same format as our 
electron density maps (.ccp4 .map, etc.). Your favorite software for 
displaying crystallographic maps should work just fine. You will later 
find that owing to the fact that images are just 2D pixels, movies are 
series of 2D pixels,  maps are (saved as) 3D voxels, the single MRC/CCP4 
format can hold many different types of data, including images, stacks 
of images, movies, maps, masks, etc..  That is why there is often also a 
.star file (similar to CIF files) that holds information on what is 
inside one or more MRC files. So be aware of what type of data you are 
opening.


b)

To get an idea how cryo-EM single particle data processing works, the 
minimum you need would be RELION/EMAN2+UCSF Chimera (best for this job), 
which are all free to everyone. These will get you from the raw EM 
movies to the EM maps.


If you have a computer with enough memory (16GB minimum, the more the 
better) and an Nvidia 1080TI card (~USD 800? a $150 1050TI can also get 
you started) you can already solve some EM structures! To do this, you 
need to get RELION and/or EMAN2 (ideally both):


https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Download_%26_install

http://blake.bcm.edu/emanwiki/EMAN2/Install

The reason for the 1080TI card is that it allows the programs to use its 
300+ GPU cores to accelerate computations. This capability is provided 
by Nvidia's CUDA library. You need to download the CUDA 8.0 library from 
Nvidia. CUDA 8.0 needs to be installed before you compile RELION if you 
are going to compile it yourself (not quite necessary).


At present, EMAN2 only uses GPU at the particle picking step so it is 
not essential to have a GPU card just for running EMAN2. But 
classifications and refinements will be very slow (days and weeks) 
without a GPU.


Ideally you should install everything in Linux, such as Ubuntu 16.04 
mate. You will also need softwares such as Motioncor2, GCTF, CTFFind, 
for some jobs in the workflow. Certain settings need to be put as 
environmental variables in the Linux system. Please figure them out 
yourself. It will take days to succeed for first-timers.



You can start playing by following the tutorials of either RELION or 
EMAN2 with their own tutorial datasets. These datasets are not really 
raw data though: they are particle "stacks" that contain the particles 
picked from the raw micrographs. But starting from there would be the 
easiest way to learn the essentials. BTW, following the EMAN2 tutorial 
does not involve using a GPU at all. This might be true for the non-GPU 
version of RELION too.



If you want to start from the very beginning, you can download the 396GB 
proteasome movie dataset from EMPIAR:


https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10025/


On youtube, Grant Jensen has a great series on cryoEM basics. I strongly 
suggest you to watch at least the part1, especially those having to do 
with CTF.


https://www.youtube.com/watch?v=gDgFbAqdM_c&list=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8-

Zhijie




On 10/09/2018 1:01 PM, Kevin Jin wrote:

Dear Herman and all ccp4ers,

Many thanks for the helps and education from all of you.

I am a fresh beginner in Cryo-EM,  and have no access to those 
resource, like Chimera, Phenix, Rosetta and papers, etc. For me, any 
answer will be valuable.


Please forgive me for asking such a naive question.  I highly 
appreciate your comments and education.


Kevin

On Mon, Sep 10, 2018 at 5:28 AM > wrote:


Hi Kevin, Pavel and others,

Since it seems that so far nobody answered the primary question:
“Is there any sever available to create electron density maps for
cryo-em structures?” So I will do it. The answer is very simple:
They do not need to be created, they are available from the pdb!

To give an example: On the RCSB pdb web-site, I searched for entry
5vai. Then under the button “Download Files” I selected “Download
EM Map” and downloaded emd_8653.map.gz. As the name suggests, this
file needs to be unzipped, but this is trivial.

Then in Coot in the “File” pull-down menu, I select “Open Map” to
load the map.

Next, you may not see anything since to contour level might be too
high (when I load the map, the contour level is around 6 rmsd) so
you have to scroll down the contour level to see anything. As
Marin and Ian pointed out, the maps are very similar to regular
electron density maps, probably with the exception that the EM
“electron density” maps are influenced by the local charge
density. However in coot they behave 100% identical and you can
scroll up and down the contour level as you like.

Of course, if the authors

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

[Kevin Jin]

Dear Garib,

Thank you! I will definitely check the website immediately.

Sorry, I forgot to mention that I have been a user for CCP4 since 1998.
CCP4 is a great tool and reliable for crystallography, love it!

Cheers,

Kevin


On Mon, Sep 10, 2018 at 10:09 AM Garib Murshudov 
wrote:

> Dear Kevin,
>
> You can have access to all these resources (And ccpem, ccp4). They are
> free for non-commercial users.
>
> (You can also have access to any papers you want via https://sci-hub.tw/
> , it is also free but …)
>
> If you want to see some of the maps then you can go to emdb at
> https://www.ebi.ac.uk/pdbe/emdb/, they have many cryoEM maps and tools to
> visualise them.
>
> If you want to generate maps from coordinates then refmac  from ccp4 and
> ccpem has an option to generate 3D electrostatic potential from
> coordinates. I can send a script for that.
>
> Regards
> Garib
>
> P.S. In spite of some unusual answers you should not be afraid asking
> questions on ccp4 bb. This bulletin board is exactly for this type of
> questions.
>
>
> On 10 Sep 2018, at 18:01, Kevin Jin  wrote:
>
> Dear Herman and all ccp4ers,
>
> Many thanks for the helps and education from all of you.
>
> I am a fresh beginner in Cryo-EM,  and have no access to those resource,
> like Chimera, Phenix, Rosetta and papers, etc. For me, any answer will be
> valuable.
>
> Please forgive me for asking such a naive question.  I highly appreciate
> your comments and education.
>
> Kevin
>
> On Mon, Sep 10, 2018 at 5:28 AM  wrote:
>
>> Hi Kevin, Pavel and others,
>>
>>
>>
>> Since it seems that so far nobody answered the primary question: “Is
>> there any sever available to create electron density maps for cryo-em
>> structures?” So I will do it. The answer is very simple: They do not need
>> to be created, they are available from the pdb!
>>
>>
>>
>> To give an example: On the RCSB pdb web-site, I searched for entry 5vai.
>> Then under the button “Download Files” I selected “Download EM Map” and
>> downloaded emd_8653.map.gz. As the name suggests, this file needs to be
>> unzipped, but this is trivial.
>>
>>
>>
>> Then in Coot in the “File” pull-down menu, I select “Open Map” to load
>> the map.
>>
>> Next, you may not see anything since to contour level might be too high
>> (when I load the map, the contour level is around 6 rmsd) so you have to
>> scroll down the contour level to see anything. As Marin and Ian pointed
>> out, the maps are very similar to regular electron density maps, probably
>> with the exception that the EM “electron density” maps are influenced by
>> the local charge density. However in coot they behave 100% identical and
>> you can scroll up and down the contour level as you like.
>>
>>
>>
>> Of course, if the authors did not deposit their EM-map, you cannot
>> download it, but the same is true for X-ray structure factors.
>>
>>
>>
>> Happy viewing!
>>
>>
>>
>> Herman
>>
>>
>>
>>
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Ian Tickle
>> *Gesendet:* Montag, 10. September 2018 12:58
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM
>> structures.
>>
>>
>>
>>
>>
>> Hi Marin
>>
>>
>>
>> I was about to comment on that too but then I realised that Pavel is
>> referring to the map _contours_  (which is what most people using a map
>> visualisation program like Coot actually see).  So the contoured map does
>> represent an iso-potential surface.  I'm sure Pavel is aware that the
>> original cryo-EM maps are 3-dimensional objects.
>>
>>
>>
>> Cheers
>>
>>
>>
>> -- Ian
>>
>>
>>
>> On Mon, 10 Sep 2018 at 10:49, Marin van Heel <
>> 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>
>> Unfortunately,
>>
>> The problem here lies primarily in the answer given,  not so much in the
>> question asked by a newcomer:
>>
>> "1) In cryo-EM maps are not electron density maps but surfaces
>> representing electric potential. "
>>
>> The answer appears to reflect the widespread misunderstanding that EM
>> images (and hence cryo-EM maps)  only show the surfaces not the internal
>> density of the complexes we study.
>> In my Imperial College/Leiden University  lecture notes, I have always
>> used the below slide to illustrate this point.
>>
>> Cheers,
>>
>> Marin
>>
>>
>>
>>
>>
>> On 10/09/2018 01:38, Pavel Afonine wrote:
>>
>> Hi,
>>
>>
>>
>> Is there any sever available to create electron density maps for cryo-em
>> structures?
>>
>>
>>
>> The questions are nonsensical. Here is why:
>>
>>
>>
>> 1) In cryo-EM maps are not electron density maps but surfaces
>> representing electric potential.
>>
>>
>>
>> 2) Creating such a map is essentially carrying on from cryo-EM experiment
>> and obtaining the 3D reconstruction.
>>
>>
>>
>> Are you really sure about what you are asking for?
>>
>>
>>
>> Or, we should create the maps from mmCIF.
>>
>>
>>
>> mmCIF is a file format. It may contain representations of rabbits,
>> boysenberries or so

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

[Garib Murshudov]

Dear Kevin,

You can have access to all these resources (And ccpem, ccp4). They are free for 
non-commercial users. 

(You can also have access to any papers you want via https://sci-hub.tw/ 
, it is also free but …)

If you want to see some of the maps then you can go to emdb at 
https://www.ebi.ac.uk/pdbe/emdb/ , they have 
many cryoEM maps and tools to visualise them.

If you want to generate maps from coordinates then refmac  from ccp4 and ccpem 
has an option to generate 3D electrostatic potential from coordinates. I can 
send a script for that.

Regards
Garib

P.S. In spite of some unusual answers you should not be afraid asking questions 
on ccp4 bb. This bulletin board is exactly for this type of questions.


> On 10 Sep 2018, at 18:01, Kevin Jin  wrote:
> 
> Dear Herman and all ccp4ers,
> 
> Many thanks for the helps and education from all of you. 
> 
> I am a fresh beginner in Cryo-EM,  and have no access to those resource, like 
> Chimera, Phenix, Rosetta and papers, etc. For me, any answer will be 
> valuable. 
> 
> Please forgive me for asking such a naive question.  I highly appreciate your 
> comments and education.
> 
> Kevin
> 
> On Mon, Sep 10, 2018 at 5:28 AM  > wrote:
> Hi Kevin, Pavel and others,
> 
>  
> 
> Since it seems that so far nobody answered the primary question: “Is there 
> any sever available to create electron density maps for cryo-em structures?” 
> So I will do it. The answer is very simple: They do not need to be created, 
> they are available from the pdb!
> 
>  
> 
> To give an example: On the RCSB pdb web-site, I searched for entry 5vai. Then 
> under the button “Download Files” I selected “Download EM Map” and downloaded 
> emd_8653.map.gz. As the name suggests, this file needs to be unzipped, but 
> this is trivial.
> 
>  
> 
> Then in Coot in the “File” pull-down menu, I select “Open Map” to load the 
> map.
> 
> Next, you may not see anything since to contour level might be too high (when 
> I load the map, the contour level is around 6 rmsd) so you have to scroll 
> down the contour level to see anything. As Marin and Ian pointed out, the 
> maps are very similar to regular electron density maps, probably with the 
> exception that the EM “electron density” maps are influenced by the local 
> charge density. However in coot they behave 100% identical and you can scroll 
> up and down the contour level as you like.
> 
>  
> 
> Of course, if the authors did not deposit their EM-map, you cannot download 
> it, but the same is true for X-ray structure factors.
> 
>  
> 
> Happy viewing!
> 
>  
> 
> Herman
> 
>  
> 
>  
> 
>  
> 
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
> ] Im Auftrag von Ian Tickle
> Gesendet: Montag, 10. September 2018 12:58
> An: CCP4BB@JISCMAIL.AC.UK 
> Betreff: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.
> 
>  
> 
>  
> 
> Hi Marin
> 
>  
> 
> I was about to comment on that too but then I realised that Pavel is 
> referring to the map _contours_  (which is what most people using a map 
> visualisation program like Coot actually see).  So the contoured map does 
> represent an iso-potential surface.  I'm sure Pavel is aware that the 
> original cryo-EM maps are 3-dimensional objects.
> 
>  
> 
> Cheers
> 
>  
> 
> -- Ian
> 
>  
> 
> On Mon, 10 Sep 2018 at 10:49, Marin van Heel 
> <057a89ab08a1-dmarc-requ...@jiscmail.ac.uk 
> > wrote:
> 
> 
> Unfortunately,
> 
> The problem here lies primarily in the answer given,  not so much in the 
> question asked by a newcomer:
> 
> "1) In cryo-EM maps are not electron density maps but surfaces representing 
> electric potential. "
> 
> The answer appears to reflect the widespread misunderstanding that EM images 
> (and hence cryo-EM maps)  only show the surfaces not the internal density of 
> the complexes we study.
> In my Imperial College/Leiden University  lecture notes, I have always used 
> the below slide to illustrate this point.
> 
> Cheers,
> 
> Marin
> 
> 
> 
> 
> 
> On 10/09/2018 01:38, Pavel Afonine wrote:
> 
> Hi,
> 
>  
> 
> Is there any sever available to create electron density maps for cryo-em 
> structures?
> 
>  
> 
> The questions are nonsensical. Here is why:
> 
>  
> 
> 1) In cryo-EM maps are not electron density maps but surfaces representing 
> electric potential.
> 
>  
> 
> 2) Creating such a map is essentially carrying on from cryo-EM experiment and 
> obtaining the 3D reconstruction.
> 
>  
> 
> Are you really sure about what you are asking for?
> 
>  
> 
> Or, we should create the maps from mmCIF.
> 
>  
> 
> mmCIF is a file format. It may contain representations of rabbits, 
> boysenberries or some diffraction data. So.. how you think it may be related 
> to cryo-EM, in your particular case?
> 
>  
> 
> I am particularly interested i

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

[Kevin Jin]

Dear Herman and all ccp4ers,

Many thanks for the helps and education from all of you.

I am a fresh beginner in Cryo-EM,  and have no access to those resource,
like Chimera, Phenix, Rosetta and papers, etc. For me, any answer will be
valuable.

Please forgive me for asking such a naive question.  I highly appreciate
your comments and education.

Kevin

On Mon, Sep 10, 2018 at 5:28 AM  wrote:

> Hi Kevin, Pavel and others,
>
>
>
> Since it seems that so far nobody answered the primary question: “Is there
> any sever available to create electron density maps for cryo-em
> structures?” So I will do it. The answer is very simple: They do not need
> to be created, they are available from the pdb!
>
>
>
> To give an example: On the RCSB pdb web-site, I searched for entry 5vai.
> Then under the button “Download Files” I selected “Download EM Map” and
> downloaded emd_8653.map.gz. As the name suggests, this file needs to be
> unzipped, but this is trivial.
>
>
>
> Then in Coot in the “File” pull-down menu, I select “Open Map” to load the
> map.
>
> Next, you may not see anything since to contour level might be too high
> (when I load the map, the contour level is around 6 rmsd) so you have to
> scroll down the contour level to see anything. As Marin and Ian pointed
> out, the maps are very similar to regular electron density maps, probably
> with the exception that the EM “electron density” maps are influenced by
> the local charge density. However in coot they behave 100% identical and
> you can scroll up and down the contour level as you like.
>
>
>
> Of course, if the authors did not deposit their EM-map, you cannot
> download it, but the same is true for X-ray structure factors.
>
>
>
> Happy viewing!
>
>
>
> Herman
>
>
>
>
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Ian Tickle
> *Gesendet:* Montag, 10. September 2018 12:58
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM
> structures.
>
>
>
>
>
> Hi Marin
>
>
>
> I was about to comment on that too but then I realised that Pavel is
> referring to the map _contours_  (which is what most people using a map
> visualisation program like Coot actually see).  So the contoured map does
> represent an iso-potential surface.  I'm sure Pavel is aware that the
> original cryo-EM maps are 3-dimensional objects.
>
>
>
> Cheers
>
>
>
> -- Ian
>
>
>
> On Mon, 10 Sep 2018 at 10:49, Marin van Heel <
> 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Unfortunately,
>
> The problem here lies primarily in the answer given,  not so much in the
> question asked by a newcomer:
>
> "1) In cryo-EM maps are not electron density maps but surfaces
> representing electric potential. "
>
> The answer appears to reflect the widespread misunderstanding that EM
> images (and hence cryo-EM maps)  only show the surfaces not the internal
> density of the complexes we study.
> In my Imperial College/Leiden University  lecture notes, I have always
> used the below slide to illustrate this point.
>
> Cheers,
>
> Marin
>
>
>
>
>
> On 10/09/2018 01:38, Pavel Afonine wrote:
>
> Hi,
>
>
>
> Is there any sever available to create electron density maps for cryo-em
> structures?
>
>
>
> The questions are nonsensical. Here is why:
>
>
>
> 1) In cryo-EM maps are not electron density maps but surfaces representing
> electric potential.
>
>
>
> 2) Creating such a map is essentially carrying on from cryo-EM experiment
> and obtaining the 3D reconstruction.
>
>
>
> Are you really sure about what you are asking for?
>
>
>
> Or, we should create the maps from mmCIF.
>
>
>
> mmCIF is a file format. It may contain representations of rabbits,
> boysenberries or some diffraction data. So.. how you think it may be
> related to cryo-EM, in your particular case?
>
>
>
> I am particularly interested in those cryo-em structures with high
> resolution, like 2.6~2.8A.
>
>
>
> Sure, all are excited about high-res cryo-EM!!!
>
>
>
> Please give me an education.
>
>
>
> Sure. One of available universities can do this.
>
>
>
> Cheers,
>
> Pavel
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
>
>
>
> --
>
> ==
>
>
>
> Prof Dr Ir Marin van Heel
>
>
>
> Laboratório Nacional de Nanotecnologia - LNNano
>
> CNPEM/LNNano, Campinas, Brazil
>
>
>
> Skype:  Marin.van.Heel
>
> email:  marin.vanheel(A_T)gmail.com 
> 

[ccp4bb] Does Saturn furnish an ultra large water crystal?

[Carter, Charlie]

https://cosmosmagazine.com/space/saturn-s-hexagon-may-tower-to-the-stratosphere


Does this arise from a phenomenon related to snowflakes?

http://www.iceandclimate.nbi.ku.dk/research/flowofice/ice_crystal_structure/





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] unexpected errors in LSQKAB

[Carter, Charlie]

Eleanor,

I’ve come up with a work-around for both problems. The problem with the tRNA 
file, I countered by using that pdb file as the fixed file, and so got round 
the need to write out a rotated pdb file (it still did not write out the output 
file, even though the rmsd was 0!).

The second problem, with the Stau coordinates, I got round by rotating them 
first into a new orientation. That suggests that there is a mathematical 
singular point for the rotation problem. I don’t know whether or not that can 
be fixed by some test on the singularity of the rotation matrix or something 
like that.

Many thanks for your shoulders while I worked out of this rabbit hole!

Charlie

On Sep 10, 2018, at 8:12 AM, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:

yes - I see that but when I run lsqkab on your two coordinate sets   lsqkab 
works OK.

Here is the command file  - i made a guess on what to match..


***
/tmp/shiftField_15_1_com.tmp
***
 title [No title given]
fit res CA 11 to 100 -
chain A
match 8 to 97 -
chain A
fit res CA 101 to 130 -
chain A
match 100 to 129 -
chain A
output -
xyz
end
## This script run with the command   ##
# /y/programs/xtal/64bit/ccp4-7.0/2016-08-23-1/ccp4-7.0/bin/lsqkab XYZIN2 
"/y/people/ccp4/Downloads/Ecoli_HSS_rot.pdb" XYZIN1 
"/y/people/ccp4/Downloads/Stau__urz_rot.pdb" XYZOUT 
"/y/people/ccp4/projects/shiftField/Ecoli_HSS_rot_lsq1.pdb"


And I attach the log file.
Indeed the Ecoli one is now rotated by ~ 90 degrees and fits quite well.. There 
is a lot of unmatched stuff of course for the Ecoli one but that shouldnt 
prevent the fit..


Eleanor


On 10 September 2018 at 12:53, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
Hmm - when I try to read Therm_tRNA into the CCP4I2 GUI it says


Cordinate file failed vaildation test!
Not sure what that test is but will ask around..
e

On 10 September 2018 at 12:15, Carter, Charlie 
mailto:car...@med.unc.edu>> wrote:
Eleanor,

I’ll check into the tRNA TER cards. I have probably experienced difficulties 
with them before, so that may solve one of the problems, but not, I think, the 
other.

Here are two pdb files from the pymol session. Ecoli_HSS_rot.pdb is the target 
structure; Stau_urz_rot.pdb is the result output for the input Stau_urz.pdb 
file. As you can see, even though the residues are, as far as I can tell 
correctly indicated, the rotated file is off by about 90 degrees.

Many thanks for any help.

Charlie



On Sep 10, 2018, at 5:36 AM, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:

Charlie - I will try to check this, but cant read your pse file - can you find 
another format?

Thanks Eleanor

On 8 September 2018 at 12:28, Carter, Charlie 
mailto:car...@med.unc.edu>> wrote:
Hi folks,

I continue to use lsqkab because it offers unique flexibility and features 
appropriate to what I do.

Currently, I’ve a project that requires such superposition and for that I 
created from the original pdb files a set of monomeric pdb files that have 
already been superposed by POSA. The POSA alignment used all the residues, and 
I want to orient only a subset that is structurally invariant, in order to 
identify possible interdomain motions.

There are ten such files; eight appear to work properly and have aligned. The 
other two give one or another of two pathologies. The first appears simply to 
get confused and output a rotated coordinate file that appears to be ~90 
degrees off, despite the fact that the residue numbering is correct (see 
attached .pse file in which three _Urz coordinate sets are illustrated, which 
were superimposed on Ecoli_Urz. The Ttherm_H file is correctly rotated; the 
Stau_LF file is not.).

I decided to try to rotate the two files into an intermediate orientation that 
gave a satisfactory result, i.e. Ttherm_H. The first attempt at this involved a 
second problematic file, Ttherm_tRNA. LSQKSB gave the following error message, 
which instructs me to contact the developers. The problematic pdb file, 
Ttherm_tRNA.pdb, is also attached.


 *** RWBROOK error: point code unitfunction
 ***1 -1022MMDB_F_Atom
 *** file   : Ttherm_tRNA_rot.pdb
 *** reason : internal error #2 -- report to developer
 *** Execution stopped.

I should note that I am still using the following version of the software:

source  /usr/local/bin/ccp4-7.0/include/ccp4.setup

The commands in my script are:

#source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
lsqkab XYZINM $1 XYZINF $2 XYZOUT $1_rot.pdb << END-lsqkab
FIT RESIDUE MAIN 8 TO 82
MATCH 10 to 84
FIT RESIDUE MAIN 83 TO 111
MATCH 85 to 113
FIT RESIDUE MAIN 122 TO 129
MATCH 124 to 131
OUTPUT XYZ
END
END-lsqkab

Many thanks in advance for any help.







<15_superpose.log>


###

Re: [ccp4bb] Electron density maps for Cryo-EM structures.

[Natesh Ramanathan]

Dear Kevin,

 Are you referring to "generating a  map"  from the model (PDB
coordinates) generated from tracing the chain in the ab-initio EM map?

Best wishes,
Natesh

On Mon, 10 Sep 2018 at 09:58, Kevin Jin  wrote:

>  Dear All,
>
> Is there any sever available to create electron density maps for cryo-em
> structures? Or, we should create the maps from mmCIF. I am particularly
> interested in those cryo-em structures with high resolution, like 2.6~2.8A.
>
> Please give me an education.
>
> Thanks,
>
> Kevin
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>


-- 
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Assistant Professor,
School of Biology,
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
ORCID: http://orcid.org/-0002-1145-5962
https://publons.com/author/1520837/ramanathan-natesh#profile
http://faculty.iisertvm.ac.in/natesh

Office Ph. 0091- 471-2778087



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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

[Herman . Schreuder]

Hi Kevin, Pavel and others,

Since it seems that so far nobody answered the primary question: “Is there any 
sever available to create electron density maps for cryo-em structures?” So I 
will do it. The answer is very simple: They do not need to be created, they are 
available from the pdb!

To give an example: On the RCSB pdb web-site, I searched for entry 5vai. Then 
under the button “Download Files” I selected “Download EM Map” and downloaded 
emd_8653.map.gz. As the name suggests, this file needs to be unzipped, but this 
is trivial.

Then in Coot in the “File” pull-down menu, I select “Open Map” to load the map.
Next, you may not see anything since to contour level might be too high (when I 
load the map, the contour level is around 6 rmsd) so you have to scroll down 
the contour level to see anything. As Marin and Ian pointed out, the maps are 
very similar to regular electron density maps, probably with the exception that 
the EM “electron density” maps are influenced by the local charge density. 
However in coot they behave 100% identical and you can scroll up and down the 
contour level as you like.

Of course, if the authors did not deposit their EM-map, you cannot download it, 
but the same is true for X-ray structure factors.

Happy viewing!

Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Ian 
Tickle
Gesendet: Montag, 10. September 2018 12:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.


Hi Marin

I was about to comment on that too but then I realised that Pavel is referring 
to the map _contours_  (which is what most people using a map visualisation 
program like Coot actually see).  So the contoured map does represent an 
iso-potential surface.  I'm sure Pavel is aware that the original cryo-EM maps 
are 3-dimensional objects.

Cheers

-- Ian

On Mon, 10 Sep 2018 at 10:49, Marin van Heel 
<057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Unfortunately,

The problem here lies primarily in the answer given,  not so much in the 
question asked by a newcomer:

"1) In cryo-EM maps are not electron density maps but surfaces representing 
electric potential. "

The answer appears to reflect the widespread misunderstanding that EM images 
(and hence cryo-EM maps)  only show the surfaces not the internal density of 
the complexes we study.
In my Imperial College/Leiden University  lecture notes, I have always used the 
below slide to illustrate this point.

Cheers,

Marin

[cid:part1.5DA80E33.F02E5B7D@googlemail.com]



On 10/09/2018 01:38, Pavel Afonine wrote:
Hi,

Is there any sever available to create electron density maps for cryo-em 
structures?

The questions are nonsensical. Here is why:

1) In cryo-EM maps are not electron density maps but surfaces representing 
electric potential.

2) Creating such a map is essentially carrying on from cryo-EM experiment and 
obtaining the 3D reconstruction.

Are you really sure about what you are asking for?

Or, we should create the maps from mmCIF.

mmCIF is a file format. It may contain representations of rabbits, 
boysenberries or some diffraction data. So.. how you think it may be related to 
cryo-EM, in your particular case?

I am particularly interested in those cryo-em structures with high resolution, 
like 2.6~2.8A.

Sure, all are excited about high-res cryo-EM!!!

Please give me an education.

Sure. One of available universities can do this.

Cheers,
Pavel




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--

==



Prof Dr Ir Marin van Heel



Laboratório Nacional de Nanotecnologia - LNNano

CNPEM/LNNano, Campinas, Brazil



Skype:  Marin.van.Heel

email:  
marin.vanheel(A_T)gmail.com


marin.vanheel(A_T)lnnano.cnpem.br

and:
mvh.office(A_T)gmail.com

[ccp4bb] AW: [ccp4bb] Electron density maps for Cryo-EM structures.

[Hughes, Jon]

yes, but irrespective of how much one knows or thinks one knows, one should 
avoid being gratuitously offensive.
cheers
jon

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Ian 
Tickle
Gesendet: Montag, 10. September 2018 12:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Electron density maps for Cryo-EM structures.


Hi Marin

I was about to comment on that too but then I realised that Pavel is referring 
to the map _contours_  (which is what most people using a map visualisation 
program like Coot actually see).  So the contoured map does represent an 
iso-potential surface.  I'm sure Pavel is aware that the original cryo-EM maps 
are 3-dimensional objects.

Cheers

-- Ian

On Mon, 10 Sep 2018 at 10:49, Marin van Heel 
<057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Unfortunately,

The problem here lies primarily in the answer given,  not so much in the 
question asked by a newcomer:

"1) In cryo-EM maps are not electron density maps but surfaces representing 
electric potential. "

The answer appears to reflect the widespread misunderstanding that EM images 
(and hence cryo-EM maps)  only show the surfaces not the internal density of 
the complexes we study.
In my Imperial College/Leiden University  lecture notes, I have always used the 
below slide to illustrate this point.

Cheers,

Marin

[cid:part1.5DA80E33.F02E5B7D@googlemail.com]



On 10/09/2018 01:38, Pavel Afonine wrote:
Hi,

Is there any sever available to create electron density maps for cryo-em 
structures?

The questions are nonsensical. Here is why:

1) In cryo-EM maps are not electron density maps but surfaces representing 
electric potential.

2) Creating such a map is essentially carrying on from cryo-EM experiment and 
obtaining the 3D reconstruction.

Are you really sure about what you are asking for?

Or, we should create the maps from mmCIF.

mmCIF is a file format. It may contain representations of rabbits, 
boysenberries or some diffraction data. So.. how you think it may be related to 
cryo-EM, in your particular case?

I am particularly interested in those cryo-em structures with high resolution, 
like 2.6~2.8A.

Sure, all are excited about high-res cryo-EM!!!

Please give me an education.

Sure. One of available universities can do this.

Cheers,
Pavel




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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1



--

==



Prof Dr Ir Marin van Heel



Laboratório Nacional de Nanotecnologia - LNNano

CNPEM/LNNano, Campinas, Brazil



Skype:  Marin.van.Heel

email:  marin.vanheel(A_T)gmail.com

marin.vanheel(A_T)lnnano.cnpem.br

and:mvh.office(A_T)gmail.com



--

Emeritus Professor of Cryo-EM Data Processing

Leiden University

--

Emeritus Professor of Structural Biology

Imperial College London

Faculty of Natural Sciences

email: m.vanheel(A_T)imperial.ac.uk

--



I receive many emails per day and, although I try,

there is no guarantee that I will actually read each incoming email.



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Re: [ccp4bb] unexpected errors in LSQKAB

[Eleanor Dodson]

yes - I see that but when I run lsqkab on your two coordinate sets   lsqkab
works OK.

Here is the command file  - i made a guess on what to match..


***
/tmp/shiftField_15_1_com.tmp
***
 title [No title given]
fit res CA 11 to 100 -
chain A
match 8 to 97 -
chain A
fit res CA 101 to 130 -
chain A
match 100 to 129 -
chain A
output -
xyz
end
## This script run with the command   ##
# /y/programs/xtal/64bit/ccp4-7.0/2016-08-23-1/ccp4-7.0/bin/lsqkab XYZIN2
"/y/people/ccp4/Downloads/Ecoli_HSS_rot.pdb" XYZIN1
"/y/people/ccp4/Downloads/Stau__urz_rot.pdb" XYZOUT
"/y/people/ccp4/projects/shiftField/Ecoli_HSS_rot_lsq1.pdb"


And I attach the log file.
Indeed the Ecoli one is now rotated by ~ 90 degrees and fits quite well..
There is a lot of unmatched stuff of course for the Ecoli one but that
shouldnt prevent the fit..


Eleanor


On 10 September 2018 at 12:53, Eleanor Dodson 
wrote:

> Hmm - when I try to read Therm_tRNA into the CCP4I2 GUI it says
>
>
> Cordinate file failed vaildation test!
> Not sure what that test is but will ask around..
> e
>
> On 10 September 2018 at 12:15, Carter, Charlie  wrote:
>
>> Eleanor,
>>
>> I’ll check into the tRNA TER cards. I have probably experienced
>> difficulties with them before, so that may solve one of the problems, but
>> not, I think, the other.
>>
>> Here are two pdb files from the pymol session. Ecoli_HSS_rot.pdb is the
>> target structure; Stau_urz_rot.pdb is the result output for the input
>> Stau_urz.pdb file. As you can see, even though the residues are, as far as
>> I can tell correctly indicated, the rotated file is off by about 90 degrees.
>>
>> Many thanks for any help.
>>
>> Charlie
>>
>>
>>
>> On Sep 10, 2018, at 5:36 AM, Eleanor Dodson > > wrote:
>>
>> Charlie - I will try to check this, but cant read your pse file - can you
>> find another format?
>>
>> Thanks Eleanor
>>
>> On 8 September 2018 at 12:28, Carter, Charlie  wrote:
>>
>> Hi folks,
>>
>> I continue to use lsqkab because it offers unique flexibility and
>> features appropriate to what I do.
>>
>> Currently, I’ve a project that requires such superposition and for that I
>> created from the original pdb files a set of monomeric pdb files that have
>> already been superposed by POSA. The POSA alignment used all the residues,
>> and I want to orient only a subset that is structurally invariant, in order
>> to identify possible interdomain motions.
>>
>> There are ten such files; eight appear to work properly and have aligned.
>> The other two give one or another of two pathologies. The first appears
>> simply to get confused and output a rotated coordinate file that appears to
>> be ~90 degrees off, despite the fact that the residue numbering is correct
>> (see attached .pse file in which three _Urz coordinate sets are
>> illustrated, which were superimposed on Ecoli_Urz. The Ttherm_H file is
>> correctly rotated; the Stau_LF file is not.).
>>
>> I decided to try to rotate the two files into an intermediate orientation
>> that gave a satisfactory result, i.e. Ttherm_H. The first attempt at this
>> involved a second problematic file, Ttherm_tRNA. LSQKSB gave the following
>> error message, which instructs me to contact the developers. The
>> problematic pdb file, Ttherm_tRNA.pdb, is also attached.
>>
>>
>> * *** RWBROOK error: point code unitfunction*
>> * ***1 -1022MMDB_F_Atom*
>> * *** file   : Ttherm_tRNA_rot.pdb*
>> * *** reason : internal error #2 -- report to developer*
>> * *** Execution stopped.*
>>
>> I should note that I am still using the following version of the software:
>>
>> source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
>>
>> The commands in my script are:
>>
>> #source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
>> lsqkab XYZINM $1 XYZINF $2 XYZOUT $1_rot.pdb << END-lsqkab
>> FIT RESIDUE MAIN 8 TO 82
>> MATCH 10 to 84
>> FIT RESIDUE MAIN 83 TO 111
>> MATCH 85 to 113
>> FIT RESIDUE MAIN 122 TO 129
>> MATCH 124 to 131
>> OUTPUT XYZ
>> END
>> END-lsqkab
>>
>> Many thanks in advance for any help.
>>
>>
>>
>>
>>
>>
>



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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
#CCP4I VERSION CCP4Interface 7.0.063
#CCP4I SCRIPT LOG superpose
#CCP4I DATE 10 Sep 2018  13:06:30
#CCP4I USER ed1
#CCP4I PROJECT shiftField
#CCP4I JOB_ID 15
#CCP4I SCRATCH /tmp/ed1
#CCP4I HOSTNAME kanga.chem.york.ac.uk
#CCP4I PID 2910


 




 
 ###
 ###
 ###
 ### CCP4 7.0.063: LSQKAB   version 7.0.063 : ##
 ###

Re: [ccp4bb] unexpected errors in LSQKAB

[Eleanor Dodson]

Hmm - when I try to read Therm_tRNA into the CCP4I2 GUI it says


Cordinate file failed vaildation test!
Not sure what that test is but will ask around..
e

On 10 September 2018 at 12:15, Carter, Charlie  wrote:

> Eleanor,
>
> I’ll check into the tRNA TER cards. I have probably experienced
> difficulties with them before, so that may solve one of the problems, but
> not, I think, the other.
>
> Here are two pdb files from the pymol session. Ecoli_HSS_rot.pdb is the
> target structure; Stau_urz_rot.pdb is the result output for the input
> Stau_urz.pdb file. As you can see, even though the residues are, as far as
> I can tell correctly indicated, the rotated file is off by about 90 degrees.
>
> Many thanks for any help.
>
> Charlie
>
>
>
> On Sep 10, 2018, at 5:36 AM, Eleanor Dodson  > wrote:
>
> Charlie - I will try to check this, but cant read your pse file - can you
> find another format?
>
> Thanks Eleanor
>
> On 8 September 2018 at 12:28, Carter, Charlie  wrote:
>
> Hi folks,
>
> I continue to use lsqkab because it offers unique flexibility and features
> appropriate to what I do.
>
> Currently, I’ve a project that requires such superposition and for that I
> created from the original pdb files a set of monomeric pdb files that have
> already been superposed by POSA. The POSA alignment used all the residues,
> and I want to orient only a subset that is structurally invariant, in order
> to identify possible interdomain motions.
>
> There are ten such files; eight appear to work properly and have aligned.
> The other two give one or another of two pathologies. The first appears
> simply to get confused and output a rotated coordinate file that appears to
> be ~90 degrees off, despite the fact that the residue numbering is correct
> (see attached .pse file in which three _Urz coordinate sets are
> illustrated, which were superimposed on Ecoli_Urz. The Ttherm_H file is
> correctly rotated; the Stau_LF file is not.).
>
> I decided to try to rotate the two files into an intermediate orientation
> that gave a satisfactory result, i.e. Ttherm_H. The first attempt at this
> involved a second problematic file, Ttherm_tRNA. LSQKSB gave the following
> error message, which instructs me to contact the developers. The
> problematic pdb file, Ttherm_tRNA.pdb, is also attached.
>
>
> * *** RWBROOK error: point code unitfunction*
> * ***1 -1022MMDB_F_Atom*
> * *** file   : Ttherm_tRNA_rot.pdb*
> * *** reason : internal error #2 -- report to developer*
> * *** Execution stopped.*
>
> I should note that I am still using the following version of the software:
>
> source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
>
> The commands in my script are:
>
> #source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
> lsqkab XYZINM $1 XYZINF $2 XYZOUT $1_rot.pdb << END-lsqkab
> FIT RESIDUE MAIN 8 TO 82
> MATCH 10 to 84
> FIT RESIDUE MAIN 83 TO 111
> MATCH 85 to 113
> FIT RESIDUE MAIN 122 TO 129
> MATCH 124 to 131
> OUTPUT XYZ
> END
> END-lsqkab
>
> Many thanks in advance for any help.
>
>
>
>
>
>



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Re: [ccp4bb] unexpected errors in LSQKAB

[Eleanor Dodson]

Thank you Robbie! A bit clearer now to me..


On 10 September 2018 at 11:19, Robbie Joosten 
wrote:

> Hi Eleanor,
>
> You point out two major problems with PDB files. The TER record nightmare
> is pretty bad. Although it seems that at least now they are written by
> programs, they end op at the weirdest places due to aggressive addition of
> the TERs. At the same time, they are sometimes missing when there are for
> instance (mono/di)peptide ligands. The problem is that most programs that
> write PDB files are not aware of the sequence of entire protein. That, or
> they just blatantly ignore it. This should work better in mmCIF as long as
> programs enforce the presence of a sequence for the macromolecular
> entities.
>
> The charges thing has been getting on my nerves lately because most of the
> time it is a load of dingo's kidneys. There is no localized integral charge
> on the NH atoms of ARG! Neither is there for ASP and GLU sidechains,
> especially not a 1+. The PDB is aware of the problem now, but the source of
> these charges is not obvious. They do not seem to come from refinement
> programs, but these programs do use the charges to modify the scattering
> factors and write them out again. One hopes that this problem is solved
> soon.
>
> Sorry for straying off topic.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Eleanor
> > Dodson
> > Sent: Monday, September 10, 2018 12:03
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] unexpected errors in LSQKAB
> >
> > Eugenere - are you responsible for mmdb?  Could these features cause
> > problems?
> > Eleanor
> >
> >
> > The PDB file Thern_tRNA has some anomalies -
> >
> > 1) several unneeded TER cards
> >
> > TER 399  LYS A  52   - there is a chain break here but not a
> chain
> > termination
> > TER3219  GLY A 421
> >
> >
> > TER3343  GTP C  -1  - Never sure about these but GTP is not part
> of chain
> >
> > TER4163G C  37
> > TER4967A C  76
> >
> >
> > 2) Some of the atom types are unusual
> >
> > eg  N1+ here instead of N
> >
> > I am not sure whether that is important of not.
> >
> > ATOM 22  NH1 ARG A   4  24.496 181.121 132.218  1.00103.17
>  N1+
> > ANISOU   22  NH1 ARG A   415732  10019  13448   1911785   -419
>  N1+
> >
> >
> >
> >
> > On 10 September 2018 at 10:36, Eleanor Dodson
> > mailto:eleanor.dod...@york.ac.uk> > wrote:
> >
> >
> >   Charlie - I will try to check this, but cant read your pse file -
> can you
> > find another format?
> >
> >   Thanks Eleanor
> >
> >
> >   On 8 September 2018 at 12:28, Carter, Charlie  >  > wrote:
> >
> >
> >   Hi folks,
> >
> >
> >   I continue to use lsqkab because it offers unique
> flexibility
> > and features appropriate to what I do.
> >
> >
> >   Currently, I’ve a project that requires such superposition
> and
> > for that I created from the original pdb files a set of monomeric pdb
> files that
> > have already been superposed by POSA. The POSA alignment used all the
> > residues, and I want to orient only a subset that is structurally
> invariant, in
> > order to identify possible interdomain motions.
> >
> >
> >   There are ten such files; eight appear to work properly and
> > have aligned. The other two give one or another of two pathologies. The
> first
> > appears simply to get confused and output a rotated coordinate file that
> > appears to be ~90 degrees off, despite the fact that the residue
> numbering is
> > correct (see attached .pse file in which three _Urz coordinate sets are
> > illustrated, which were superimposed on Ecoli_Urz. The Ttherm_H file is
> > correctly rotated; the Stau_LF file is not.).
> >
> >
> >   I decided to try to rotate the two files into an
> intermediate
> > orientation that gave a satisfactory result, i.e. Ttherm_H. The first
> attempt at
> > this involved a second problematic file, Ttherm_tRNA. LSQKSB gave the
> > following error message, which instructs me to contact the developers.
> The
> > problematic pdb file, Ttherm_tRNA.pdb, is also attached.
> >
> >
> >
> >
> >*** RWBROOK error: point code unitfunction
> >***1 -1022MMDB_F_Atom
> >*** file   : Ttherm_tRNA_rot.pdb
> >*** reason : internal error #2 -- report to developer
> >*** Execution stopped.
> >
> >
> >   I should note that I am still using the following version
> of the
> > software:
> >
> >
> >   source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
> >
> >
> >   The commands in my script are:
> >
> >
> >
> >   #source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
> >   lsqkab XYZINM $1 XYZINF $2 XYZOUT $1_rot.pdb << END-
> > lsqkab
> >   FIT RESIDUE MAIN 8 TO 82
> >   MATCH 10 to 84
> >

Re: [ccp4bb] unexpected errors in LSQKAB

[Robbie Joosten]

Hi Eleanor,

You point out two major problems with PDB files. The TER record nightmare is 
pretty bad. Although it seems that at least now they are written by programs, 
they end op at the weirdest places due to aggressive addition of the TERs. At 
the same time, they are sometimes missing when there are for instance 
(mono/di)peptide ligands. The problem is that most programs that write PDB 
files are not aware of the sequence of entire protein. That, or they just 
blatantly ignore it. This should work better in mmCIF as long as programs 
enforce the presence of a sequence for the macromolecular entities.  

The charges thing has been getting on my nerves lately because most of the time 
it is a load of dingo's kidneys. There is no localized integral charge on the 
NH atoms of ARG! Neither is there for ASP and GLU sidechains, especially not a 
1+. The PDB is aware of the problem now, but the source of these charges is not 
obvious. They do not seem to come from refinement programs, but these programs 
do use the charges to modify the scattering factors and write them out again. 
One hopes that this problem is solved soon.

Sorry for straying off topic.

Cheers,
Robbie 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Eleanor
> Dodson
> Sent: Monday, September 10, 2018 12:03
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] unexpected errors in LSQKAB
> 
> Eugenere - are you responsible for mmdb?  Could these features cause
> problems?
> Eleanor
> 
> 
> The PDB file Thern_tRNA has some anomalies -
> 
> 1) several unneeded TER cards
> 
> TER 399  LYS A  52   - there is a chain break here but not a chain
> termination
> TER3219  GLY A 421
> 
> 
> TER3343  GTP C  -1  - Never sure about these but GTP is not part of 
> chain
> 
> TER4163G C  37
> TER4967A C  76
> 
> 
> 2) Some of the atom types are unusual
> 
> eg  N1+ here instead of N
> 
> I am not sure whether that is important of not.
> 
> ATOM 22  NH1 ARG A   4  24.496 181.121 132.218  1.00103.17   
> N1+
> ANISOU   22  NH1 ARG A   415732  10019  13448   1911785   -419   
> N1+
> 
> 
> 
> 
> On 10 September 2018 at 10:36, Eleanor Dodson
> mailto:eleanor.dod...@york.ac.uk> > wrote:
> 
> 
>   Charlie - I will try to check this, but cant read your pse file - can 
> you
> find another format?
> 
>   Thanks Eleanor
> 
> 
>   On 8 September 2018 at 12:28, Carter, Charlie   > wrote:
> 
> 
>   Hi folks,
> 
> 
>   I continue to use lsqkab because it offers unique flexibility
> and features appropriate to what I do.
> 
> 
>   Currently, I’ve a project that requires such superposition and
> for that I created from the original pdb files a set of monomeric pdb files 
> that
> have already been superposed by POSA. The POSA alignment used all the
> residues, and I want to orient only a subset that is structurally invariant, 
> in
> order to identify possible interdomain motions.
> 
> 
>   There are ten such files; eight appear to work properly and
> have aligned. The other two give one or another of two pathologies. The first
> appears simply to get confused and output a rotated coordinate file that
> appears to be ~90 degrees off, despite the fact that the residue numbering is
> correct (see attached .pse file in which three _Urz coordinate sets are
> illustrated, which were superimposed on Ecoli_Urz. The Ttherm_H file is
> correctly rotated; the Stau_LF file is not.).
> 
> 
>   I decided to try to rotate the two files into an intermediate
> orientation that gave a satisfactory result, i.e. Ttherm_H. The first attempt 
> at
> this involved a second problematic file, Ttherm_tRNA. LSQKSB gave the
> following error message, which instructs me to contact the developers. The
> problematic pdb file, Ttherm_tRNA.pdb, is also attached.
> 
> 
> 
> 
>*** RWBROOK error: point code unitfunction
>***1 -1022MMDB_F_Atom
>*** file   : Ttherm_tRNA_rot.pdb
>*** reason : internal error #2 -- report to developer
>*** Execution stopped.
> 
> 
>   I should note that I am still using the following version of the
> software:
> 
> 
>   source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
> 
> 
>   The commands in my script are:
> 
> 
> 
>   #source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
>   lsqkab XYZINM $1 XYZINF $2 XYZOUT $1_rot.pdb << END-
> lsqkab
>   FIT RESIDUE MAIN 8 TO 82
>   MATCH 10 to 84
>   FIT RESIDUE MAIN 83 TO 111
>   MATCH 85 to 113
>   FIT RESIDUE MAIN 122 TO 129
>   MATCH 124 to 131
>   OUTPUT XYZ
>   END
>   END-lsqkab
> 
> 
>   Many thanks in advance for any help.
> 
> 
> 
> 
> 
> 
> 
> 

Re: [ccp4bb] unexpected errors in LSQKAB

[Eleanor Dodson]

Eugenere - are you responsible for mmdb?  Could these features cause
problems?
Eleanor

The PDB file Thern_tRNA has some anomalies -

1) several unneeded TER cards

TER 399  LYS A  52   - there is a chain break here but not a chain
termination
TER3219  GLY A 421

TER3343  GTP C  -1  - Never sure about these but GTP is not part of
chain

TER4163G C  37
TER4967A C  76

2) Some of the atom types are unusual
eg  N1+ here instead of N
I am not sure whether that is important of not.

ATOM 22  NH1 ARG A   4  24.496 181.121 132.218
1.00103.17   N1+
ANISOU   22  NH1 ARG A   415732  10019  13448   1911785
-419   N1+



On 10 September 2018 at 10:36, Eleanor Dodson 
wrote:

> Charlie - I will try to check this, but cant read your pse file - can you
> find another format?
>
> Thanks Eleanor
>
> On 8 September 2018 at 12:28, Carter, Charlie  wrote:
>
>> Hi folks,
>>
>> I continue to use lsqkab because it offers unique flexibility and
>> features appropriate to what I do.
>>
>> Currently, I’ve a project that requires such superposition and for that I
>> created from the original pdb files a set of monomeric pdb files that have
>> already been superposed by POSA. The POSA alignment used all the residues,
>> and I want to orient only a subset that is structurally invariant, in order
>> to identify possible interdomain motions.
>>
>> There are ten such files; eight appear to work properly and have aligned.
>> The other two give one or another of two pathologies. The first appears
>> simply to get confused and output a rotated coordinate file that appears to
>> be ~90 degrees off, despite the fact that the residue numbering is correct
>> (see attached .pse file in which three _Urz coordinate sets are
>> illustrated, which were superimposed on Ecoli_Urz. The Ttherm_H file is
>> correctly rotated; the Stau_LF file is not.).
>>
>> I decided to try to rotate the two files into an intermediate orientation
>> that gave a satisfactory result, i.e. Ttherm_H. The first attempt at this
>> involved a second problematic file, Ttherm_tRNA. LSQKSB gave the following
>> error message, which instructs me to contact the developers. The
>> problematic pdb file, Ttherm_tRNA.pdb, is also attached.
>>
>>
>> * *** RWBROOK error: point code unitfunction*
>> * ***1 -1022MMDB_F_Atom*
>> * *** file   : Ttherm_tRNA_rot.pdb*
>> * *** reason : internal error #2 -- report to developer*
>> * *** Execution stopped.*
>>
>> I should note that I am still using the following version of the software:
>>
>> source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
>>
>> The commands in my script are:
>>
>> #source  /usr/local/bin/ccp4-7.0/include/ccp4.setup
>> lsqkab XYZINM $1 XYZINF $2 XYZOUT $1_rot.pdb << END-lsqkab
>> FIT RESIDUE MAIN 8 TO 82
>> MATCH 10 to 84
>> FIT RESIDUE MAIN 83 TO 111
>> MATCH 85 to 113
>> FIT RESIDUE MAIN 122 TO 129
>> MATCH 124 to 131
>> OUTPUT XYZ
>> END
>> END-lsqkab
>>
>> Many thanks in advance for any help.
>>
>>
>>
>>
>



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