Re: [ccp4bb] new ContaMiner features

[Mike Lawrence]

Dear Radu,

here's an example from 11 years ago.

https://www.ncbi.nlm.nih.gov/pubmed/16929094

ContaMiner would have been useful here in that it would terminated the 
crystallographic endeavour earlier

(In this case, however, serendipitous crystallization and structure solution of 
the trace contaminant in fact led to some interesting results).

I guess the issue is the following: if you are trying to crystallise an 
expensive-to-produce protein (e.g., one that requires large-scale mammalian 
cell culture and multiple, high-loss chromatographic steps), would you invest 
effort in developing further rounds of purification to make absolutely sure 
that your protein is contaminant-free before at least having a crack at 
crystallization trials with the almost-pure protein while you wait for more 
cells to grow?

best wishes

Mike


On 24 Nov 2017, at 6:35 am, 
r...@mrc-lmb.cam.ac.uk wrote:

Dear Stefan,

Just a couple of thoughts:

- first of all I think that Gerard is absolutely right, it would have been
nice to raise such issues first with the developers. In my experience,
Staraniso does a fantastic job if used correctly.

- but if you're OK with public trials, may I ask: why on Earth would anybody
need ContaMiner? Are you trying to offer some sort of computational cure for
sloppy biochemistry? There is zero point in crystallizing crap samples, sorry
to say this. In my 17 or so years in Strubi I've never heard of anybody
crystallizing a "contaminant", being it a purification tag or whatever.

I suppose this might have happened to somebody you know, hence the motivation
to spend time on the bizarre ContaMiner. Which is a pity, a silly outcome
would only teach people to do their job (or train their robots) properly.

Best wishes,

Radu

--
Radu Aricescu
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44-(0)1223-267049
fax: +44-(0)1223-268305
www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu

Dear Stefan,

Regarding your final paragraph: your server carries a warning
with the exact wording:

"Submitting StarAniso files can give you suspicious results. Use
with care!"

It seems rather regrettable that you are posting such a public
warning without ever having contacted the STARANISO developers about
your observations, nor giving any information about what you call
"suspicious" or what the "care" you recommend would consist of.

We have taken a great deal of care ourselves in developing the
program and offering it to the community through a server, and the
least we would have expected is that any pattern of "suspicious"
results would be referred to us so that we could investigate them.
There may be some assumptions made in MoRDa that we are not aware of,
that might be incompatible with assumptions made in STARANISO - who
knows? Or it could be that some particularly badly collected datasets
are made to look worse after their anisotropy analysis.

Could we discuss your observations, and what it is exactly that
you call "suspicious", before they end up being referred to in such an
uninformative manner as some sort of "Government Health Warning"?

I think that would be nice :-) and we would be only too keen to
take whatever extra "care" is needed ourselves. We would all learn
something.


With best wishes,

 Gerard.

(on behalf of the STARANISO developers)

--
On Thu, Nov 23, 2017 at 05:02:39PM +0100, Stefan Arold wrote:
Dear Community,

A quick message to announce the following two new features on our
ContaMiner web server for the automated detection of unwantedly
crystallised contaminants (
https://strube.cbrc.kaust.edu.sa/contaminer/submit)

1) online visualisation of 2FoFc and FoFc maps. In cases of positive
results, the ‘UglyMol’ tab allows to inspect 2FoFc and FoFc maps
directly
in the web browser. Thi

2) life-update. Previously, results were sent to you once all ~2000 MR jobs
were finished. Now, the individual results for each potential contaminant
will appear as soon as they are finished. This feature should substantially
shorten the time for identifying positive results (i.e. contaminant
detected), which are terminated faster than negative ones.

3) custom contaminants. In the ‘Advanced’ tab, users can upload own PDB
files (more than one is possible) to be included as search models. This
feature can be used to include PDB files from your lab bench neighbour’s
project to test for potential lab internal contaminations (through
bacterial contamination or through mix-up of plasmids or glycerol stocks).
This feature could also be ‘abused’ as a means to use the MoRDa pipeline
to
run molecular replacements with template structures that are not yet
deposited in the PDB; for example to run molecular replacement and initial
refinement for liganded or complexed versions of an unpublished structure.
This might be particularly interesting for crystallographers away 

[ccp4bb] Fwd: [ccp4bb] B-factor blurring

[Mike Lawrence]

My sincere thanks to all who are responding to my request below. 

To be explicit, my question relates to B-factor blurring (+B correction), not 
to B-factor sharpening (-B correction).

thanks

Mike


Begin forwarded message:

 From: Mike Lawrence lawre...@wehi.edu.au
 Subject: [ccp4bb] B-factor blurring
 Date: 18 November 2014 12:01:07 pm AEDT
 To: CCP4BB@JISCMAIL.AC.UK
 Reply-To: Mike Lawrence lawre...@wehi.edu.au
 
 Dear all
 
 can anyone help me with literatures references to B-factor blurring as a 
 technique to reveal low resolution features in an electron density map? I 
 have seen the poster from Andrea Thorn at
 
 http://shelx.uni-ac.gwdg.de/~athorn/pdf/thorn_iucr2014_poster.pdf
 
 but was wondering if there were any alternative references?
 
 with many thanks!
 
 Mike
 
 



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[ccp4bb] B-factor blurring

[Mike Lawrence]

Dear all

can anyone help me with literatures references to B-factor blurring as a 
technique to reveal low resolution features in an electron density map? I have 
seen the poster from Andrea Thorn at

http://shelx.uni-ac.gwdg.de/~athorn/pdf/thorn_iucr2014_poster.pdf

but was wondering if there were any alternative references?

with many thanks!

Mike




Mike Lawrence, PhD

Associate Professor and WEHI Fellow
Structural Biology Division
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA

Tel. 61-3-9345-2693   
Fax 61-3-9345-2686
Email: lawre...@wehi.edu.au




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Re: [ccp4bb] how to cut back resolution of a well-refined model

[Mike Lawrence]

Having run foul of the R-factor police on a number of occasions, but having 
ultimately prevailed, I would like to offer the following opinion:

Intensity measurements in the weak outer shells are as valid as any other and, 
if they are correctly processed and properly assessed for their statistical 
robustness, their merged values are as valid as any other. These data will 
contribute little to the refinement, but they will still contribute, so why 
ignore that contribution given the sophistication of modern refinement 
software. 

Nevertheless, in light of the above, I would suggest that we now avoid using 
statements such as The structure of protein X determined at 2.0 Angstoms 
resolution, instead replacing them with now more accurate statements such as 
The structure of Protein X determined using data to 2.0A resolution and then 
let the maps speak for themselves!

with best wishes

Mike Lawrence

Associate Professor and WEHI Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA




On 11/10/2013, at 9:44 AM, Jim Pflugrath wrote:

 Please tell me why Rpim should be looked at.  Cannot one have meaningless 
 data and have lots of multiplicity to drive Rpim lower without any real 
 benefit?  Under what conditions is Rpim useful?
 
 And suppose one looks at I/sigI (and not I/sigI) and CC1/2.  What of it?
 
 And let me write what Phil wrote in a slightly different way:
 Please explain how you think that adding the resolution from 2.6 A to 2.45 A 
 will improve your model.
 
 Sorry, but maybe it is too soon after the last CC1/2 discussion to raise 
 these points, but I am truly interested in various opinions about all this.
 
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Gerard 
 Bricogne [g...@globalphasing.com]
 Sent: Thursday, October 10, 2013 5:28 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] how to cut back resolution of a well-refined model
 
 Dear Yafang,
 
 Is it the case that you collected these data on a Pilatus detector,
 using relatively low exposure and high multiplicity? These types of datasets
 always give what looks like alarmingly high values of R-merge, and many
 people who are set in their ways (like so many reviewers still are) tend to
 conclude that the alarm is about the data being bad, whereas it is about
 Rmerge being a terrible statistic in these situations. The Rpim statistic,
 on the other hand, is the one to look at if you want an R-like quantity, and
 it is well behaved in this regime. Of course, look at CC1/2 as well, and
 I/sigI as you did.
 
 
 With best wishes,
 
  Gerard.
 
 --
 On Thu, Oct 10, 2013 at 04:57:20PM -0400, Yafang Chen wrote:
 Hi All,
 
 I have a structure at 2.45A which has been well refined. However, since the
 R-merge at the last shell is above 1 (although I/sigmaI at the last shell
 is more than 2), we now decide to cut back the resolution to about 2.6A. Is
 there a way to do this based on the well-refined model instead of doing the
 MR and refinement all over again? Thank you so much for your help!
 
 Best,
 Yafang
 
 --
 Yafang Chen
 
 Graduate Research Assistant
 Mesecar Lab
 Department of Biological Sciences
 Purdue University
 Hockmeyer Hall of Structural Biology
 240 S. Martin Jischke Drive
 West Lafayette, IN 47907
 
 --
 
 ===
 * *
 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===






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Re: [ccp4bb] shape complimentarity for small molecule

[Mike Lawrence]

Hi Brett, SC was not developed for this purpose and hence may not be very 
useful with its default parametrization. Nevertheless, it could be useful for 
cross-comparing the complementarity of different inhibitors to the same site, 
but I have not experimented this. The TRIM parameter may need to be reduced in 
order to allow interrogation of a large percentage of the solvent inaccesible 
surface. If you try this, please let me know how well it works.

sincerely

Mike Lawrence, PhD

Associate Professor and WEHI Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA

Tel. 61-3-9345-2693   
Fax 61-3-9345-2686
Email: lawre...@wehi.edu.au

On 11/09/2013, at 6:56 AM, Brett, Thomas wrote:

 Hi all:
 If have used SC previously to calculate shape complimentarity for 
 macromolecular complexes. Can this also be used to calculate shape 
 complimentarity for a (say) protein/small molecule inhibitor complex? Or is 
 there some other metric/software that can/should be used to quantitate how 
 well a small molecule fits a pocket?
 thanks
 -tom
 
 
 Tom J. Brett, PhD
 Assistant Professor of Medicine
 Division of Pulmonary and Critical Care
 Washington University School of Medicine
 Campus Box 8052, 660 S. Euclid
 Saint Louis, MO 63110
 http://brettlab.dom.wustl.edu/





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[ccp4bb] Off topic: 3D printing of protein models

[Mike Lawrence]

Hi, 

Apologies for the off-topic question, but does anyone have any experience in 
using the Cubify 3D printer (http://www.cubify.com/) for printing protein 
models? Are the models robust? Is the resolution sufficient? The unit price 
suggests that the printer is very low-end (though the consumables are not that 
cheap).

sincerely

Mike Lawrence

Associate Professor and WEHI Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA

Tel. 61-3-9345-2693   
Fax 61-3-9345-2686
Email: lawre...@wehi.edu.au




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Re: [ccp4bb] shape complementarity

[Mike Lawrence]

Hi Francois

Here's a one-liner. The major concept behind the Sc coefficient is that it 
measures the extent to which, on average, the normal vectors between 
closest-neighbour opposing points within the molecular interface are 
antiparallel. 

Sc=1 implies that the surfaces fit exactly, all such vectors are perfectly 
antiparallel. Heuristically, Sc values of 0.86 are about as good as 
protein-protein interfaces get (see Nature. 2005 435, pp773-8). Values below 
0.65 indicate relatively poor shape complementarity.

Use of a normal vector -based metric is considered superior to a distance-based 
metric, though Sc does have a distance-based weight applied to the normal dot 
products. Critical to this calculation is that the boundary of the buried 
molecular interface has to be discarded from the measure, as this region is 
intrinsically geometrically divergent. Sc is thus computed across only that 
part of the buried surface that might be expected to be shape complementarity, 
which makes it somewhat ill-suited to smaller interfaces.

All these details are in the JMB paper, which, unfortunately, there is no 
substitute for reading :-)

sincerely

Mike

Mike Lawrence, PhD

Associate Professor and WEHI Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA

Tel. 61-3-9345-2693   
Fax 61-3-9345-2686
Email: lawre...@wehi.edu.au




On 08/02/2012, at 12:08 PM, Francois Berenger wrote:

 Hello,
 
 After following the discussion on
 [ccp4bb] shape complementarity between protein and DNA surface,
 is there someone here able to explain simply what the SC software
 of CCP4 is calculating?
 
 I mean, is there some intuitive/easy to understand explanation of what SC is 
 calculating?
 
 I know I should read the corresponding paper, but I'd like
 someone to enlighten me before so I have better chances of understanding the 
 article.
 
 Thanks,
 Francois.



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Re: [ccp4bb] Help me install O on ubuntu11.10

[Mike Lawrence]

Try 

sudo apt-get install ia32-libs lib32gfortran3

to install the required 32 bit libraries

On 26/12/2011, at 9:53 PM, 王瑞 wrote:

 Excuse me, could anyone can tell me how to install O on ubuntu11.10 ?Thanks a 
 lot !







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Re: [ccp4bb] Sc calculation

[Mike Lawrence]

Hi Fahimeh,

what has happened here is that the interface area in the new file is very
small, particularly after the periphery is trimmed (see the original
paper for how this is defined). For the old file, the area is about 1100
Angs**2, for the new it is about 110 Angs**2. As the log file states, Sc
is then not a very good measure of complementarity.

sincerely

Mike Lawrence

 Hello :)

 I am trying to find the shape complementarity of two structures. both of
 them are two layer of betasheet, that I have excluded hydrogens. in one of
 them (old.pdb, attached to the email) I have two complete layer in which
 chain A are all the strands in one layer and chain B are all the strands
 in
 the other layer. and in the other structure (new.pdb) I removed two
 strands
 from the middle of betasheet.
 I run Sc and the results are attached in sc_old.log and sc_new.log

 As you can see, sc factor is higher in the second structure , which is
 missing two strands in the middle?!
 How it is possible? I am confused ;)
 Am I missing something?

 Thank you in advance
 Fahimeh




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Re: [ccp4bb] Surface complementary output

[Mike Lawrence]

Hi Rojan

The tables you refer to are histograms (see the documentation and the original 
paper), with the
first two columns defining the left and right hand side bounds of each
histogram bin.  The first table is a histogram of the
distances between the surfaces, with the area being that associated with
the surface patches associated with the inter-molecular distances within that 
bin. The
remaining columns are cumulatives of this and percentages of the same. The
second table is similar, but instead the histogram bins define the spread
of the -ve dot products of the normals. The first pair of tables is for
the second surface with respect to the first, these tables are then
repeated for the first surface with respect to the second.

These tables are given mainly for diagnostic purposes. The final table at
the end summarises the mean and median values of the histograms and their
averages, and finally gives Sc.

best wishes

Mike Lawrence
On 20/06/2011, at 11:28 AM, Rojan Shrestha wrote:

 Hello,
 
  
 
 Does somebody know the meaning of output of SC?
 
  
 
 What is the meaning of From and To in “Distance between surfaces”?
 
 From To   Area  Cumulative_Area %
 Cumu. %
 
  
 
 Similarly, what is the meaning of surface complementarity?
 
 From To   Number   %
 
  
 
 Does this Number indicates the residue number?
 
  
 
 Regards,
 
  
 
 Rojan
 
  
 

Mike Lawrence, PhD

Associate Professor and WEHI Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA

Tel. 61-3-9345-2693   
Fax 61-3-9345-2686
Email: lawre...@wehi.edu.au





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Re: [ccp4bb] measuring shape complementarity

[Mike Lawrence]

Dear Mohd, CCP4 contains a program SC which does the job.

sincerely

Mike Lawrence, PhD

Associate Professor and WEHI Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA

Tel. 61-3-9345-2693   
Fax 61-3-9345-2686
Email: lawre...@wehi.edu.au

On 07/12/2010, at 1:54 AM, Salameh, Mohd A., Ph.D. wrote:

 Dear All,
 
 I’m looking for a free program that I can use to measure the geometric 
 surface complementarity of protein-protein interfaces. I have created 
 inhibitor mutants that possess different binding affinities to their cognate 
 enzyme and it would be very helpful if I can quantify the shape 
 complementarity of the protein/protein interfaces. The complexes of 
 inhibitors and enzyme crystal structures have been solved at high resolution 
 (~1.4A). Sincere thanks in advance and hope to hear from you soon.
 
 Kind regards,
 
 Mohd Salameh
 
 




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Re: [ccp4bb] SC

[Mike Lawrence]

Dear Francois, Intekhab

the correct reference for the Sc statistic is

Lawrence, M. C.  Colman, P. M. (1993). Shape complementarity at
protein/protein interfaces. J. Mol. Biol. 234, 946-950.

You can also find a description in the March 2001 CCP4 newsletter (#39).

I am not certain why you cannot find it within the Windows version - it
should simply be called SC.

sincerely

Mike

Mike Lawrence, PhD

Associate Professor and WEHI Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA

Tel. 61-3-9345-2693
Fax 61-3-9345-2686
Email: lawre...@wehi.edu.au







 Hi,

 This is the first time I read about shape complementarity statistics.

 According to:
 A structural basis for the activity of retro-Diels–Alder catalytic
 antibodies: Evidence for a catalytic aromatic residue

 As seen here:
 http://www.pnas.org/content/99/15/9674.full

 ---
 [...] compute the SHAPE COMPLEMENTARITY STATISTICS index (Sc). This
 statistics index measures the geometric surface complementarity via the
 use of normal products, and the extent to which the interacting surface
 elements are brought into proximity via an exponential distance
 separation term. Sc values usually range from 0.70 to 0.76 for
 proteinase–protein inhibitor surfaces, from 0.64 to 0.68 for
 antigen–antibody complexes, and from 0.45 to 0.70 for MHC–peptide
 complexes (30).
 ---

 I am frightened. :(
 I don't think this is in my book The cartoon guide
 to statistics. Despite the book is really nice.

 Regards,
 F.

 intekhab alam wrote:
 I want to calculate the shape comlementarity statitics (SC) of a dimeric
 protein using CCp4. I am using CCP4 6.1.3 on windows but the SC program
 is not available in that suite.
 Which version of CCP4 has that program. Are there any other programs
 that can calculate that.

 Thanks

 --
 INTEKHAB ALAM
 LABORATORY OF STRUCTURAL BIOINFORMATICS
 KOREA UNIVERSITY, SEOUL




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Re: [ccp4bb] shape complementarity

[Mike Lawrence]

Hi Reiner

I haven't seen this problem before; if you send me all the relevant files
I will try to check it out. It may relate to the fact that the GRASP files
were made with Chimera.

sincerely

Mike Lawrence

 Hello everybody,

 I recently tried to feed the shape complementarity program (sc) with GRASP
 surface files for visualisation. Sc is supposed to output modified surface
 files, again, in GRASP format. However, the program terminated without
 producing a file, or, sometimes, writing truncated ones. The GRASP files
 passed the compatibility check of sc. I tested two different pdb files
 with the according GRASP surface files (made with Chimera).

 The first run ended with: At line 2825 of file
 /usr/local/xtal/ccp4-6.1.13/src/sc_/sc.f
 Fortran runtime error: End of file

 In the second run, I removed all hydrogen atoms before I calculated the
 surface files. Sc showed the following error:  Header information from
 grasp file 1
  
  format=2
  Keywords=vertices,normals,triangles
  Properties=

  Decoding property list

  Updated property list is:,gproperty
  Number of vertices=76375
  Number of triangles=   54697
  Size of grid= 65
  Midpoint   91.033806   91.542160   89.700684
  vertices read
  accessibles read
 BFONT COLOR=#FF!--SUMMARY_BEGIN--
  SC:  read error in s/r read_real_line
  SC:  read error in s/r read_real_line
 Times: User:   8.3s System:0.4s Elapsed: 0:09
 /pre
 /html
 !--SUMMARY_END--/FONT/B

 I can't make head or tail of it, maybe someone else can.
 Thanks in advance for any information and advice


 Reiner






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Re: [ccp4bb] shape complementarity calculations

[Mike Lawrence]

Hi Vaheh

I have not had anyone report problems with sc of late. If you send me  
the relevant files or output I can check it out for you.


sincerely

Mike Lawrence, PhD

WEHI Principal Research Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA

Tel. 61-3-9345-2693
Fax 61-3-9345-2686
Email: lawre...@wehi.edu.au

On 04/03/2009, at 9:17 AM, Oganesyan, Vaheh wrote:


Colleagues,

Would some one kindly suggest software that calculates shape
complementarity of two interacting proteins based on co-crystal
structure?
I've seen number of reports with sc parameter included but none of
those mention how it was done.
Among non-runnable programs in CCP4 there is the sc program that  
indeed

does not run.

Thanks in advance.

___
Vaheh




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Mike Lawrence, PhD

WEHI Principal Research Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA

Tel. 61-3-9345-2693
Fax 61-3-9345-2686
Email: lawre...@wehi.edu.au

[ccp4bb] Post-doctoral Position at WEHI, Melbourne, AUSTRALIA

[Mike Lawrence]

An attractive post-doctoral position is available within the  
laboratory of Dr Mike Lawrence and Dr Colin Ward in the Structural  
Biology Division of the Walter and Eliza Hall Institute of Medical  
Research (WEHI) in Melbourne, Australia. The position is available  
immediately and is for two years in the first instance. Experience in  
protein purification and protein crystallization is essential.


The project involves studying the structural biology of the  
interaction between the insulin-like growth factors and the  
ectodomain of the Type 1 insulin-like growth factor receptor. The  
project builds on the PIs’ earlier success in determining the  
structure of the insulin receptor ectodomain (for a review see  
Lawrence MC, McKern NM, Ward CW, Curr Opin Struct Biol. 2007,  
17:699-705). For more information regarding the project please  
contact Dr Mike Lawrence (email lawre...@wehi.edu.au).


The Walter and Eliza Hall Institute of Medical Research is located in  
Parkville, just north of Melbourne's CBD and is one of the world's  
leading medical research centres. The work of the Institute covers  
cancer, genetics, malaria, autoimmune diseases, medicinal chemistry,  
drug discovery and translational research taking scientific  
discoveries from the laboratory to the clinic.


The Structural Biology Division is well equipped, housing in  
particular a Rigaku Micromax-007 X-ray generator, with two Raxis IV++  
detectors, AXCO micro-capillary focussing optics and X-stream cryo- 
units. In addition, WEHI is a Partner in the Bio21 Collaborative  
Crystallization Centre, which houses state-of-the-art protein  
crystallization robotics. The newly-operational Australian  
Synchrotron is approximately 20 km from WEHI and has two PX  
beamlines. Access is guaranteed by means of WEHI's Foundation  
Investor status.


Please forward applications by email to jobapplicati...@wehi.edu.au.  
Cite the ccp4bb as the advertisement source and include a covering  
letter, curriculum vitae and contact details for three referees. The  
closing date is 26 February 2009.

Re: [ccp4bb] 3D model in glass

[Mike Lawrence]

Dear Rene

I have used a company called Imaage in Australia for engraving  
proteins in glass blocks. Their web address is


http://www.imaage.com.au/

I send them VRML output from MOLSCRIPT and that usually works fine.  
You need to generate the image in a single color (black), though you  
can use a second color if you want them to map that to a different   
dot density of laser etching.


cheers

Mike Lawrence, PhD

WEHI Principal Research Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3050, AUSTRALIA

Tel. 61-3-9345-2693
Fax 61-3-9345-2686
Email: [EMAIL PROTECTED]



On 03/04/2008, at 6:29 AM, [EMAIL PROTECTED] wrote:


Dear all,

Anyone know about how to transfer a 3D image (ligand + protein  
surface)  into a format that would be compatible for 3D laser  
engraving in plexiglass.


I am aware of a few cies that can provide the final product (see  
below) but we are looking for file format information


Luminorum (UK)
Crystal Protein (California)
Molecular dimension (UK and USA)

Any others?

Thanks,

René

Rene Coulombe
Research Scientist, Chemistry
Structural Research Group
Boehringer Ingelheim (Canada) Ltd; RD
2100, rue Cunard, Laval (Quebec) Canada  H7S 2G5
[EMAIL PROTECTED]
tel 450 682-4640 fax 450 682-4642