[ccp4bb] Fortran runtime error in Procheck on Mac OS X 10.6.8

[Alexander Batyuk]

Dear colleagues,

I have a problem running procheck on Mac OS X 10.6.8. It stops with the 
following error:

..
 
Stereochemical quality plots and residue-by-residue listing
 
At line 2639 of file 
/sw64/src/fink.build/ccp4-6.2.0-101/ccp4-6.2.0/src/procheck/pplot.f (unit = 14, 
file = 'rama.sum')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, 
possibly use REWIND or BACKSPACE


I would appreciate any help.

Thank you and best wishes,

Alex


--
Alex Batyuk
The Plueckthun Lab
www.bioc.uzh.ch/plueckthun

Re: [ccp4bb] Structure problem

[Yuri Pompeu]

Just echoing what has been said.
I would make sure you have the right space group.
It may be worthwhile tyring to find a MR solution in different space groups 
with different compositions.
Another imporatant thing is how complete is your model?
Do you have all the protein and DNA modeled in? How many waters (you should see 
plenty at 1.5 A)
How good is the difference map?
These are all things that should be checked before panic sets in

Cheers

Re: [ccp4bb] refmac and DNA bond angles

[Gregory Bowman]

OK, I updated ccp4 to 6.2.0 (and refmac to 5.6.0117) and now the angles coming 
out close to the ideal values. Also, I see now the the "MODRES" in the pdb 
header from before was tell future refmac runs to rename those residues - which 
confused the newer refmac version as it thought the DT (renamed Td) were 
somehow "DY". By just deleting these MODRES lines it was fine.


On Sep 14, 2011, at 7:10 PM, Gregory Bowman wrote:

> I'm running into some geometry problems with my DNA model after refinement 
> with refmac (version 5.5.0109), and would appreciate any feedback. 
> 
> The problem is that the angles for many of the glycosidic bonds are 2 to 4 
> degrees off of the ideal values, and so are several standard deviations 
> outside what's expected. Our data (from MR) is ~2 Å, and the density is well 
> defined for the DNA. I was thinking that perhaps refmac was not recognizing 
> my DNA and so just taking the poor geometry from one model and enforcing it 
> for the next, but in the log file it does not indicate that a new molecule 
> has been found, and I do not feed in a cif file from previous runs. Another 
> indication that refmac recognizes the DNA bases is that it says it is 
> renaming them. The DNA bases are named DA, DC, DT, DG, and the header of the 
> output pdb file says:
> 
> MODRES   DC B1  Cd  RENAME
> MODRES   DC B2  Cd  RENAME
> MODRES   DA B3  Ad  RENAME
> MODRES   DT B4  Td  RENAME
> (etc...)
> 
> In the output, strangely (to me), it is actually not renaming them. That is, 
> it is keeping the "DC" etc names.
> 
> In coot, I'm measuring the glycosidic bond (O4'-C1'-N9) to be 104.6, whereas 
> in AD.cif, it is listed as 108.4.
> 
> The bond lengths are fine, and there are no distortions of the protein model.
> 
> Thanks,
> Greg
> 

--
Department of Biophysics
Johns Hopkins University
302 Jenkins Hall
3400 N. Charles St.
Baltimore, MD 21218
Phone: (410) 516-7850 (office)
Phone: (410) 516-3476 (lab)
Fax: (410) 516-4118
gdbow...@jhu.edu

[ccp4bb] JOB POSITION AVAILABLE

[RONG hui Rong]

*JOB POSITION AVAILABLE***

* *

*Postdoctoral Fellow/Researcher *– *Protein Crystallography position *is
available for participating in the chemical genomics drug discovery projects
targeting GPCRs and stem cells (http://www.cbligand.org/xielab/).

Qualifications: PhD (or equivalent working experience) in Biochemistry or
Biophysics, good knowledge and experience with protein expression and
purification in E. coli and insect cells as well as protein crystallization
for X-ray crystallography or NMR studies.  Must demonstrated ability to
design, execute and analyze experiments independently.  Good written,
verbal, and interpersonal skills are needed. Salary will be commensurate
with experience. Please email your CV and three references to: Prof. XQ
(Sean) Xie, Dept. of Pharmaceutical Sciences/Drug Discovery Institute,
University
of Pittsburgh*, *Pittsburgh, PA 15261.  xi...@pitt.edu,
http://www.pharmacy.pitt.edu/directory/profile.lasso?Page=425&Type=Faculty

[ccp4bb] refmac and DNA bond angles

[Gregory Bowman]

I'm running into some geometry problems with my DNA model after refinement with 
refmac (version 5.5.0109), and would appreciate any feedback. 

The problem is that the angles for many of the glycosidic bonds are 2 to 4 
degrees off of the ideal values, and so are several standard deviations outside 
what's expected. Our data (from MR) is ~2 Å, and the density is well defined 
for the DNA. I was thinking that perhaps refmac was not recognizing my DNA and 
so just taking the poor geometry from one model and enforcing it for the next, 
but in the log file it does not indicate that a new molecule has been found, 
and I do not feed in a cif file from previous runs. Another indication that 
refmac recognizes the DNA bases is that it says it is renaming them. The DNA 
bases are named DA, DC, DT, DG, and the header of the output pdb file says:

MODRES   DC B1  Cd  RENAME
MODRES   DC B2  Cd  RENAME
MODRES   DA B3  Ad  RENAME
MODRES   DT B4  Td  RENAME
(etc...)

In the output, strangely (to me), it is actually not renaming them. That is, it 
is keeping the "DC" etc names.

In coot, I'm measuring the glycosidic bond (O4'-C1'-N9) to be 104.6, whereas in 
AD.cif, it is listed as 108.4.

The bond lengths are fine, and there are no distortions of the protein model.

Thanks,
Greg

Re: [ccp4bb] stereo

[Sabuj Pattanayek]

On Wed, Sep 14, 2011 at 3:23 PM, Hena Dutta  wrote:
> Hi,
>
> Isn't that an LCD monitor (Acer HS244HQ)?

It's edge LED backlit. I don't know if there are any direct LED
backlit 120Hz monitors. Couldn't find much information on those types.

Re: [ccp4bb] stereo

[David Schuller]

On 09/14/11 13:53, Sabuj Pattanayek wrote:

Hi,

On Wed, Sep 14, 2011 at 10:52 AM, Hena Dutta  wrote:

Hi Sabuj,

Can I use LED monitor instead LCD? I heard the color contrast is better. If


What is being marketed as "LED" monitors recently are actually LCD 
monitors which use LEDs rather than fluorescent lamps for backlighting. 
So long as your monitor is compatible with the stereo technology you are 
using, LED backlighting is fine (and more efficient).


--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] glycerol on three-fold axis

[Jacqueline Vitali]

Dear colleagues,

Has anyone seen glycerol on a three-fold axis?

THis is possible as the glycerol can be disordered but I want to know if
there is an actual case.

Any information would be greatly appreciated.

Jackie Vitali

Re: [ccp4bb] Space Group Table

[Ethan Merritt]

On Wednesday, September 14, 2011 10:16:53 am James Stroud wrote:
> Hello All,
> 
> Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative 
> mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count 
> on major software packages to honor this mapping if present in a PDB file)? 

I'm not sure that's the right question.  I think you need to start with
the question "Is this the list used by PDB files?".
And I'm pretty sure the answer is no, if only because the table you
link to does not list rhombohedral/hexagonal settings as starting with "H"
or "R".

See the note on the definition of the PDB field contents:
  http://www.wwpdb.org/documentation/format33/sect8.html

See also many threads over the past several years about inconsistent
handling of H3/R3.

Ethan




> I notice that this web page was authored by a couple of prominent developers.
> 
> Thank you,
> 
> James
> 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] stereo

[Sabuj Pattanayek]

Hi,

On Wed, Sep 14, 2011 at 10:52 AM, Hena Dutta  wrote:
> Hi Sabuj,
>
> Can I use LED monitor instead LCD? I heard the color contrast is better. If

We haven't tried any, but here's an interesting 120 HZ LED monitor
(Acer HS244HQ):

http://www.newegg.com/Product/Product.aspx?Item=N82E16824009301&nm_mc=OTC-Froogle&cm_mmc=OTC-Froogle-_-Monitors+-+LCD+Flat+Panel-_-Acer+America-_-24009301

It comes with active 3D goggles, but it's noted that these only work
with the 3D sync signal built into Bluray movies which I think is
transmitted off the monitor. Now if this works like 3D DLP link stereo
then you don't necessarily need the 3D vision stereo kit/emitter at
all. In fact, we have an Infocus IN3116 projector that does 120Hz at
720p and a bunch of $50 DLP link goggles, a quadro 3700 video card in
the box, and can do stereo in Windows 7 and Linux using Option
"Stereo" "3" (standard quad buffered stereo). We use a cheap $2 DVI to
HDMI converter to connect a long HDMI cable into the projector from
the Quadro 3700 and that's it, no super long 3 pin mini din cable is
needed. The only downside is that sometimes the left and right eye
images are on the wrong sides when stereo is enabled, but most apps
(e.g. pymol, chimera, and coot too probably) have an option to swap
the eyes when in stereo so that's easily fixed.

> I buy higher level quadro graphics card (say FX 5600), will it improve the
> stereo quality? How big difference the prices are? Thanks for your

A better card won't improve the stereo quality itself, but will
improve surface, vdw, etc renderings with high polygon counts. For
building models, most people are looking at wireframes/lines which you
can still do for huge macromolecules on an SGI Octane. So yes, the
5600 will work with nvidia 3d vision, it has at least a G8x core
(http://en.wikipedia.org/wiki/Nvidia_Quadro) and the stereo connector
in the back. If you decide to go with something like that Acer HS244HQ
it would be interesting to see if it can be made to work without the
nvidia 3d vision kit at all.

HTH,
Sabuj

> information.
>
> Hena
>
> On Wed, Sep 14, 2011 at 11:26 AM, Sabuj Pattanayek  wrote:
>>
>> Hi,
>>
>> On Wed, Sep 14, 2011 at 9:48 AM, Hena Dutta  wrote:
>> > Dear Members,
>> >
>> > Is any one using NVidia NVision 3D Setup with active stereo in linux
>>
>> Yes
>>
>> > distribution for crystallographic work? Which one would be the best
>> > choice
>> > to set up, an active stereo or a passive stereo for crystallographic
>> > work?
>>
>> Active has better quality, greater 3D viewing area for people not
>> sitting right in front of the monitor, but is more expensive if you
>> have to purchase additional goggles ($70 non-nvidia online retailers -
>> $120 currently from nvidia)
>>
>> > Can anyone shade some details on this? I am planning to buy or build a
>> > new
>> > workstation with stereo set up. It would be great if someone can give
>> > some
>> > estimate on this.
>>
>> Going with the lowest prices:
>>
>> $300 Quadro 3700 :
>>
>> http://www.google.com/products/catalog?q=quadro+3700&cid=5758926893192813358&ei=i8FwTpqJGpGkwgXtw9H4CQ&ved=0CAkQgggwAA#scoring=tp
>> $320 Acer GD235HZ :
>>
>> http://www.google.com/products/catalog?q=acer+gd235hz&hl=en&um=1&ie=UTF-8&tbm=shop&cid=114906938122589343&sa=X&ei=d8JwTr7TM8WgtwfFuZWJCg&ved=0CHsQgggwAA#scoring=tp
>> $150 3D Vision kit with the 3 pin mini din "VESA" to 2.5mm stereo
>> cable : http://www.nvidia.com/object/product_geforce_3D_VisionKit_us.html
>>
>> Total = $770
>>
>> Passive stereo :
>>
>> $490 (open box) - $550 : Zalman ZM-M240W :
>>
>> http://www.compuvest.com/Search.jsp?Search=ZM-M240W&advsite=froogle&sku=756009288-08&dp=3:CVS:51392:0:21
>>
>> You can use the black RealD 3D movie theater goggles with the Zalman
>> if you need extras. People also sell these online for a $1 + shipping.
>>
>> HTH,
>> Sabuj
>>
>> > Many thanks,
>> >
>> > Hena
>> >
>
>

Re: [ccp4bb] Pointless problems

[Ed Pozharski]

On Wed, 2011-09-14 at 14:06 -0400, Emmanuel Saridakis wrote:
> If
> not, is there another way to check my point group/spacegroup starting
> from
> Denzo/Scalepack?
> 

If you are trying to choose the screw axes, you can always look at the
systematic absences. This script may be useful in extracting the (h00),
(0k0),(00l) and such (assuming you used P222 and thus scalepack kept
everything):
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Get_systematic_absences_from_.sca_file


Cheers,

Ed.

-- 
"Hurry up before we all come back to our senses!"
   Julian, King of Lemurs

[ccp4bb] Space Group Table

[James Stroud]

Hello All,

Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative 
mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count 
on major software packages to honor this mapping if present in a PDB file)? I 
notice that this web page was authored by a couple of prominent developers.

Thank you,

James

[ccp4bb] Pointless problems

[Emmanuel Saridakis]

Dear All,

I am having problems when trying to run Pointless with input from
Denzo/Scalepack.

(1) Pointless refuses to work from the .sca file. The error message is:

CCP4 library signal mtz:File not identified as MTZ (Error)
CCP4MTZfile: open_read - File missing or corrupted: rn7e222test.sca

or

The program run with command: /programs/CCP4/ccp4-6.1.1/bin/pointless
has failed with error message
child process exited abnormally

(when run from ccp4i)

(2) Scalepack2mtz refuses to convert a Scalepack file produced using the
command: "NO MERGE original index" (i.e. as instructed by the Pointless
instructions). It fails with the rather tactless message:

*  Resolution Range :
0.002020.00485 ( 22.256 - 14.357 A )
 * Sort Order :
  0 0 0 0 0
 * Space group = 'P 2 2 2' (number 16)

 SCALEPACK2MTZ:  Check your data!

And, no my resolution range is not 22.2-14.3 A!!

(3) Pointless refuses to work with an .mtz file produced by Scalepack2mtz
from a .sca file obtained with the simple "NO MERGE" instruction (remember
the "NO MERGE original index" instruction is a no-go for Scalepack2mtz).
The error message in this case is quite simply:

HKLIN is merged and no HKLREF file is defined, SPACEGROUP or REINDEX.

I know the orthodox ccp4 reply would be "stop whining and use Mosflm!",
but is there an alternative if I really want to use Denzo/Scalepack? If
not, is there another way to check my point group/spacegroup starting from
Denzo/Scalepack?

Thanks a lot!

Emmanuel

[ccp4bb] Quips about greasy pockets

[Gerard DVD Kleywegt]

Hi all,

As you may recall, the Protein Data Bank in Europe (PDBe; pdbe.org) regularly 
produces Quips, short stories about QUite Interesting Pdb Structures 
(pdbe.org/quips). Quips address biologically interesting aspects of one or 
more PDB entries, coupled with interactive graphics views and often a 
mini-tutorial or suggestions for further exploration using PDBe services and 
resources.


Today another Quips episode was released. It is about autotaxins, 
physiologically important proteins that are pursued as anti-cancer drug 
targets. This Quips was developed together with scientists from the 
Netherlands Cancer Institute (Tassos Perrakis and Wouter Moolenaar) to 
accompany their review paper in Nature Reviews Molecular Cell Biology on 
autotaxin structure and function that was also published today.


- For the Quips story ("Autotaxins: inhibiting a greasy pocket"), go to: 
http://pdbe.org/quips?story=Autotaxin


- For the review paper ("Insights into autotaxin: how to produce and present a 
lipid mediator"), go to: 
http://www.nature.com/nrm/journal/vaop/ncurrent/full/nrm3188.html


---

If you have an interesting structure whose story you would like to tell (with 
our help) in the form of a Quips episode, please contact us at p...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] Refinement with Low resolution data

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Md. Munan Shaik,
a couple of aspects you might check:
- - first build the model AS MUCH AS POSSIBLE before running the first
  refinement cycle
- - switch off automatic weight determination in refmac and use a low
  weight (e.g. 0.005) and many cycles of refinement
- - check that the geometry does not distort (rmsd angles and bond
  lengths reported in the refmac log-file must not go too high). if it
  does, lower the weight even further.

if your model stems from higher resolution data and is actually in good
agreement with the model you are going at, refinement might ruin the
good model if you use inappropriate settings, causing Rfree to go up.

Cheers, Tim

On 09/14/2011 04:34 PM, Md Shaik wrote:
> Dear ccp4,
> 
> I am refining one structure at low resolution (3.5 A). I solved the 
> structure in space group P622 by molecular replacement. The Rw/Rf 
> after some cycle of rigid body refinement in Refmac5 is 34/37. But 
> when I am trying to refine with Restrain refinement in Refmac the Rw 
> is going down but the Rf is going up. This same happens with the 
> phenix refinement. The protein is quite big 520 residues and one 
> molecule is present in the crystal asymmetric unit. The maps are
> also not so bad except some region.
> 
> Please give me suggestion, what should I have to care during low 
> resolution refinement? or is there any other tricks for this types
> of data?
> 
> Thanks in advance.
> 
> 
> Md. Munan Shaik PhD Student Department of Biotehnology School of 
> Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy 
> Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com 
> munan.sh...@unipd.it
> 
> 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
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Re: [ccp4bb] stereo

[Sabuj Pattanayek]

Hi,

On Wed, Sep 14, 2011 at 9:48 AM, Hena Dutta  wrote:
> Dear Members,
>
> Is any one using NVidia NVision 3D Setup with active stereo in linux

Yes

> distribution for crystallographic work? Which one would be the best choice
> to set up, an active stereo or a passive stereo for crystallographic work?

Active has better quality, greater 3D viewing area for people not
sitting right in front of the monitor, but is more expensive if you
have to purchase additional goggles ($70 non-nvidia online retailers -
$120 currently from nvidia)

> Can anyone shade some details on this? I am planning to buy or build a new
> workstation with stereo set up. It would be great if someone can give some
> estimate on this.

Going with the lowest prices:

$300 Quadro 3700 :
http://www.google.com/products/catalog?q=quadro+3700&cid=5758926893192813358&ei=i8FwTpqJGpGkwgXtw9H4CQ&ved=0CAkQgggwAA#scoring=tp
$320 Acer GD235HZ :
http://www.google.com/products/catalog?q=acer+gd235hz&hl=en&um=1&ie=UTF-8&tbm=shop&cid=114906938122589343&sa=X&ei=d8JwTr7TM8WgtwfFuZWJCg&ved=0CHsQgggwAA#scoring=tp
$150 3D Vision kit with the 3 pin mini din "VESA" to 2.5mm stereo
cable : http://www.nvidia.com/object/product_geforce_3D_VisionKit_us.html

Total = $770

Passive stereo :

$490 (open box) - $550 : Zalman ZM-M240W :
http://www.compuvest.com/Search.jsp?Search=ZM-M240W&advsite=froogle&sku=756009288-08&dp=3:CVS:51392:0:21

You can use the black RealD 3D movie theater goggles with the Zalman
if you need extras. People also sell these online for a $1 + shipping.

HTH,
Sabuj

> Many thanks,
>
> Hena
>

Re: [ccp4bb] Refinement with Low resolution data

[Phil Evans]

Are you sure of the space group? P622 is much rarer than P6(x)22 where x > 0
Phil

On 14 Sep 2011, at 15:34, Md Shaik wrote:

> Dear ccp4,
> 
> I am refining one structure at low resolution (3.5 A). I solved the structure 
> in space group P622 by molecular replacement. The Rw/Rf after some cycle of 
> rigid body refinement in Refmac5 is 34/37. But when I am trying to refine 
> with Restrain refinement in Refmac the Rw is going down but the Rf is going 
> up. This same happens with the phenix refinement. The protein is quite big 
> 520 residues and one molecule is present in the crystal asymmetric unit. The 
> maps are also not so bad except some region.
> 
> Please give me suggestion, what should I have to care during low resolution 
> refinement? or is there any other tricks for this types of data?
> 
> Thanks in advance.
> 
> 
> Md. Munan Shaik
> PhD Student
> Department of Biotehnology
> School of Bioscience and Biotechnology
> via G. Colombo 03
> Padova 35131, Italy
> Mobile: 00393275671896
> E-mail: munanbt2...@yahoo.com
> munan.sh...@unipd.it
> 

Re: [ccp4bb] stereo

[Jim Fairman]

I run the Alienware OptX AW2310 on two of our 3D Linux workstations and it
looks spectacular. Make sure that you have a Quadro FX Nvidia video card
that is on the approved list (
http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html) with
3-pin stereo (3-pin stereo connector required for Linux, it will work
without one in Windows through USB) output and not just a normal GeForce
Nvidia card or you won't be able to run stereoscopic 3D in Linux.



One option that supports both Mac and Linux are the "Zalman" brand 3D
monitors.  Some people like them, some people don't.  Unless Zalman
significantly improved the technology on their monitors (ie: the right eye
can see odd numbered rows of pixels and the left eye can see even numbered
rows of pixels) you lose a significant amount of resolution from displaying
3D on these.  Due to half the pixels being drawn to each eye, the display on
the 3D Vision system using a 120 Hz monitor will look crisper and higher
quality than the equivalent Zalman monitor when displaying stereoscopic 3D.
 That being said, this solution is significantly cheaper than the Nvidia
system.



I've used and seen both and prefer the quality of the Nvidia 3D Vision, but
some people are happy with the Zalman setup.  It's really up to personal
preference as to which you will choose.

Cheers, Jim

On Wed, Sep 14, 2011 at 10:48 AM, Hena Dutta  wrote:

> Dear Members,
>
> Is any one using NVidia NVision 3D Setup with active stereo in linux
> distribution for crystallographic work? Which one would be the best choice
> to set up, an active stereo or a passive stereo for crystallographic work?
> Can anyone shade some details on this? I am planning to buy or build a new
> workstation with stereo set up. It would be great if someone can give some
> estimate on this.
> Many thanks,
>
> Hena
>



-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab 
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Refinement with Low resolution data

[Pavel Afonine]

Hi,

did you use refinement strategy suitable for low (3.5A) resolution
(secondary structure restraints, Ramachandran plot restraints, proper ADP
parameterization, SA, etc etc...)?

If you send me the data and model files off-list I will have a look.

Pavel

On Wed, Sep 14, 2011 at 7:34 AM, Md Shaik  wrote:

> Dear ccp4,
>
> I am refining one structure at low resolution (3.5 A). I solved the
> structure in space group P622 by molecular replacement. The Rw/Rf after some
> cycle of rigid body refinement in Refmac5 is 34/37. But when I am trying to
> refine with Restrain refinement in Refmac the Rw is going down but the Rf is
> going up. This same happens with the phenix refinement. The protein is quite
> big 520 residues and one molecule is present in the crystal asymmetric unit.
> The maps are also not so bad except some region.
>
> Please give me suggestion, what should I have to care during low resolution
> refinement? or is there any other tricks for this types of data?
>
> Thanks in advance.
>
>
> Md. Munan Shaik
> PhD Student
> Department of Biotehnology
> School of Bioscience and Biotechnology
> via G. Colombo 03
> Padova 35131, Italy
> Mobile: 00393275671896
> E-mail: munanbt2...@yahoo.com
> munan.sh...@unipd.it
>
>

[ccp4bb] stereo

[Hena Dutta]

Dear Members,

Is any one using NVidia NVision 3D Setup with active stereo in linux
distribution for crystallographic work? Which one would be the best choice
to set up, an active stereo or a passive stereo for crystallographic work?
Can anyone shade some details on this? I am planning to buy or build a new
workstation with stereo set up. It would be great if someone can give some
estimate on this.
Many thanks,

Hena

[ccp4bb] Refinement with Low resolution data

[Md Shaik]

Dear ccp4,

I am refining one structure at low resolution (3.5 A). I solved the structure 
in space group P622 by molecular replacement. The Rw/Rf after some cycle of 
rigid body refinement in Refmac5 is 34/37. But when I am trying to refine with 
Restrain refinement in Refmac the Rw is going down but the Rf is going up. This 
same happens with the phenix refinement. The protein is quite big 520 residues 
and one molecule is present in the crystal asymmetric unit. The maps are also 
not so bad except some region.

Please give me suggestion, what should I have to care during low resolution 
refinement? or is there any other tricks for this types of data?

Thanks in advance.


Md. Munan Shaik
PhD Student
Department of Biotehnology
School of Bioscience and Biotechnology
via G. Colombo 03
Padova 35131, Italy
Mobile: 00393275671896
E-mail: munanbt2...@yahoo.com
munan.sh...@unipd.it

Re: [ccp4bb] neutron diffraction 'difference' map?

[Tim Gruene]

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Dear Francis,

ad [1]: if you are going for neutron diffraction, you probably want the
ligand to have its hydrogens replaced with deuteria, rather than a
'heavy atom derivative' of your ligand. The scattering power for
neutrons does not correlate with the weight of the nucleus und deuterium
scatters as strongly as O,C, ... (see ITCr, Vol. C, Chapter 4.4) In that
case you also do not need a difference map against the X-ray data
because the scattering of X-rays by hydrogens can be neglected.
ad [1b]: see [1]; remark: since we are doing science as opposed to math
or philosophy, there is no 'unambiguity'. There is only a model for the
experimental data which - depending on your means of validation - fits
the data more or less well.
ad [2]: That probably depends on whether your ligand site is fully
occupied and whether the ligand is disordered or not.

Cheers,
Tim

On 09/13/2011 09:01 PM, Francis E Reyes wrote:
> Hi all
> 
> Suppose you have a high resolution xtal structure (from usual x-ray 
> diffraction) and you wanted to verify the location of a ligand. You can 
> purchase a heavy atom isotope version of the ligand. 
> 
> [1] Is it possible to do a neutron diffraction difference map (where you 
> simply calculated Fobs(heavy) - Fobs(light) to verify the location of the 
> ligand? 
> 
> [1b] Suppose you couldn't measure the diffraction of the light version of the 
> ligand. Can the x-ray data be combined with the neutron diffraction of the 
> heavy atom isotope to unambiguously assign the ligand site? 
> 
> [2] What would be the minimum resolution required from the neutron 
> diffraction? (This is particularly important as you may be unable to grow 
> high diffracting crystals or large crystals)
> 
> 
> Note that you don't necessarily want to solve the structure of the structure 
> from neutron diffraction from scratch, but rather you want to use it as a 
> tool to verify the location of a ligand binding site. 
> 
> 
> Thanks!
> 
> F
> 
> 
> 
> -
> Francis E. Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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Re: [ccp4bb] Structure problem

[Kay Diederichs]

 Original Message 
Subject: Structure problem
Date: Tue, 13 Sep 2011 08:55:47 +
From: #HEW KAI LI KELLY# 



Hi,

I am facing some problems in solving my structure now, so I am wondering
if anyone is able to give me any tips and tricks on this matter.

My protein-DNA complex structure diffracted to 1.5A. There are 4 missing
residues, 2 on each terminal. There is no twinning in the data. The
angles, the bonds, the rotamers and the Ramachandran plot are okay too.
I am using molecular replacement for the phasing and the sequence
homology between my protein and my homologous model is 33%. The electron
density map for the protein looks very nice and there is also nice
density for the DNA. Rfree converged from the initial 39%. However,
Rfree refused to go down any further and it's still around 30-31%. Does
anyone have any suggestions for me? Thank you in advance!

Warmest Regards,
Kelly Hew


Hi,

pls check out 



To get more specific help, you'll have to tell us much more - number of 
residues and bases, spacegroup, ... (at least) everything that would end 
up in "Table 1" of your paper describing the structure, and in the 
header of the PDB file.


HTH,

Kay
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

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