[ccp4bb] Data reprocessing

[Lucas Souza]

Dear all,

After auditing and reprocessing a deposited structure with clear processing 
mistakes (missing/wrong residues and ligands with evident density) prior to 
some analysis that are going to be published, what should be done? Re-deposit 
the structure with a "reprocess" flag? Reopen the PDB deposition and update the 
files? Or simply state in the publication that the data was reprocessed?

I'm curious if there's a consensus on handling situations of this nature.

Cheers,
Lucas


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[ccp4bb] Volunteer for Science chats with children during lockdown (and beyond)

[Lucas Rudden]

Calling all Scientists, we need you!

In March COVID-19 lockdowns were present in 160+ countries, affecting 90%+ of 
the world's student population. The homeschooling and lockdowns have inevitably 
removed the opportunity for children to learn about STEM through activities and 
engagement with peers, thereby affecting their education.  

While difficult, this has presented us with an opportunity to create a new 
community! The Scientist Next Door project is there to provide a platform to 
you, as scientists, to share your passion and help bring up the next generation 
of scientists. 

We organize and host group video calls between scientists and children aged 4 - 
18. The idea is we have 2~4 scientists with one family, discussing scientific 
topics the children are interested in, your research, and some live experiments 
to give them a unique perspective they won't find elsewhere. We talk about what 
inspires us and think about the science that impacts our daily lives. It can be 
a learning experience for parents too!

So far we've had over 45 calls supporting children of all age, covering topics 
from extracting DNA from strawberries and COVID-19 to why balloons fly and how 
solar panels work.

This is an open call to all scientists, from undergraduate to professor, to 
join in on the project and participate in calls. Time commitment is 30 mins ~ 1 
hour a week max, where you'll need to be either involved with your calls or 
prepping some material. It is preferable (though not mandatory) if you have a 
valid DBS check or equivalent. This is also open to scientists outside the UK 
too, we currently have scientists based in Greece, Italy and more!

Please do pass this on to your colleagues too if you think they'll be 
interested, and if you know any parents (or indeed are one), please pass along 
our information!

If you're a parent and want to sign up or you just want to read more about the 
project, our website is here: https://www.scientist-next-door.org/   

Here are some recent posts and news articles about what we've been up to:

https://www.thenorthernecho.co.uk/news/18509360.scientists-help-children-learn-lockdown/
https://viralstories.co.uk/2020/05/20/scientists-bring-virtual-experiments-into-kids-homes-university-of-edinburgh-durham-university/
https://twitter.com/EdinburghUni/status/1263037203371917312?s=20

If you are interested in doing some volunteer work during the pandemic and 
beyond, this is a fantastic opportunity to do so while also talking about 
science! You can sign up by emailing outre...@scientist-next-door.org using the 
subject header: "new scientist to sign up with SND". Please include a small 
photo of yourself, where you're based and a short paragraph about your research 
in layman's terms. You can see what other people have written on the website 
for inspiration.

Thank you!

Lucas Rudden
SND Project Coordinator

Email: outre...@scientist-next-door.org
Facebook: www.facebook.com/scientistND
Twitter: twitter.com/Scientist_ND

Scientist Next Door connecting communities
Through the COVID-19 lockdown and beyond, please continue to look after 
yourself and loved ones, and stay in contact with colleagues and friends.



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[ccp4bb] Parseable residue-ligand and/or residue-nucleic acid interaction database?

[Lucas]

Just so that we don't reinvent the wheel: is there any database or
webservice on which one can parse the list of residue-ligand
interactions for the entire PDB? I'd like to programmatically obtain
information such as "in PDB 3hdl the Calcium 306 is in contact with
Asp223 or in PDB 5gjb Arg388 is in contact with the phosphate in the
nucleic acid chain B". I know this information is available through
pdbsum via ligplot/nucplot, but I'm unaware if it is possible to
download the entire interaction database and if it is parseable.



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Re: [ccp4bb] Yet another "what's my blob" thread, part II

[Lucas]

Oops, should have mentioned that - Cryoprotectant was PEG200, 20%.

Re: [ccp4bb] Verify 3D score

[Lucas]

I had the same question long ago and I was directed to the Verify3D
code, which is also not that easy to read these days. If you receive
any feedback, let me know. Perhaps there are also more recent
profile-based scores with available code somewhere?

2016-11-14 16:20 GMT-02:00, Hammond, Robert Glenn :
> Hi,
>
>
> Does anyone know how to calculate a theoretical or expected Verify 3D score
> based on the amino acid sequence length? In the reference papers ( Bowi, et
> al., 1991 and Leuthy, et al., 1992) they describe several proteins and their
> expected score but do not supply a function for how to calculate an expected
> score. I look at example proteins and come up with a ballpark value. Also, I
> consult their first table and to get an idea, but I do not have an exact
> value for what my Verify 3D would be.
>
>
> Any help is appreciated. Thank you.
>
>
> Regards,
>
> Robert Hammond
>

Re: [ccp4bb] just out of totally idle curiosity ...

[Lucas]

2016-11-09 3:56 GMT-02:00, kaiser :
> Yeah, given Europe and Canada are obvious, I think Brazil and Japan are
> actually viable alternatives if the first choices are getting too crowded.
> They do have synchrotrons and "internets".

We just had a president impeached, and the new one is forcing a law
that will freeze public spending (which is already quite low, not only
for science) for twenty years. Yes, twenty years. So I wouldn't count
Brazil as an "alternative" for refugee scientists - actually, most of
us are also among those looking for alternatives elsewhere...

[ccp4bb] Ligand relevance for bioinformaticians using PDB files

[Lucas]

This week a bioinformatics PhD candidate was talking about his PDB analysis
tool which was aimed at studying protein-ligand statistics and asked for
some advice on what should he consider as biologically relevant or not. I
told him many of the most common molecules he found were buffers,
cryoprotectants, metals used for phasing, etc., and also said that some
cases could be more complicated (e.g., PO4 is very common because of its
use as a buffer, but in the same time it could be biologically relevant in
many cases such as kinases or phosphatases).

Well, I tried my best to list most usually biologically irrelevant I
could remember, but now I wonder if that is something someone has probably
thought about doing before and there's some article/database dealing with
it somewhere. Any suggestions?

Lucas

Re: [ccp4bb] FW: [ccp4bb] PDB passes 100,000 structure milestone

[Lucas]

2014-05-15 9:53 GMT-03:00 Colin Nave colin.n...@diamond.ac.uk:

 Of course exponential growth can’t go on forever – the hidden point behind
 my question.


A nice example from another biological database is Swissprot. It had an
exponential-like growth until 2009, and now it's somewhat linear:

http://web.expasy.org/docs/relnotes/relstat.html

I didn't looked much into that, but I guess it's because the annotators
(Swissprot is human curated) simply can't keep up with everything coming
from all genome projects. The other Uniprot database, automatically
annotated Trembl, is still growing in a exponential-like fashion:

http://www.ebi.ac.uk/uniprot/TrEMBLstats

[ccp4bb] Problematic PDBs

[Lucas]

Dear all,

I've been lecturing in a structural bioinformatics course where graduate
students (always consisting of people without crystallography background to
that point) are expected to understand the basics on how x-ray structures
are obtained, so that they know what they are using in their bioinformatics
projects. Practices include letting them manually build a segment from an
excellent map and also using Coot to check problems in not so good
structures.

I wonder if there's a list of problematic structures somewhere that I could
use for that practice? Apart from a few ones I'm aware of because of (bad)
publicity, what I usually do is an advanced search on PDB for entries with
poor resolution and bound ligands, then checking then manually, hopefully
finding some examples of creative map interpretation. But it would be nice
to have specific examples for each thing that can go wrong in a PDB
construction.

Best regards,
Lucas

Re: [ccp4bb] OT: Who's Afraid of Peer Review?

[Lucas]

2013/10/9 Folmer Fredslund folm...@gmail.com

 Hi Navdeep,

 I feel disappointed. (not your fault)

 I was hoping to see what kind of science was behind the computer program
 that generated the unique papers. That doesn't seem to be contained in the
 linked article.

 The article does, however, seem to be lacking in peer review itself? Or
 can anything be done in the name of journalism? Why were only open-access
 journals selected? I guess I'm just repeating the questions that many
 others have asked since the publication.



An interesting response addressing this issue is given here:
http://www.michaeleisen.org/blog/?p=1439

Lucas

Re: [ccp4bb] The number of protein-protein complex in recent years

[Lucas]

That probably won't be very precise. A better option would be doing an
advanced search, then select Structure Features - Number of Entities
as a protein query, select protein as entity type, and then a very
wide interval starting with 2 (say, between 2 and 100). That returns
14453 hits if I click result count. Then you can add search criteria
to refine your search - in your case, Deposition-Deposit Date and
then select the desired timespan will return what you're looking for.

Lucas

2013/3/13 Wei Feng ccp4...@hotmail.com:
  Dear all,
 I want to do a statistics about the number of protein-protein complexes
 deposited in PDB in recent years.(1972~1992,1993...2012)
 I tried keywords protein-protein complex, protein complex etc. in the
 search of PDB but all of them are fail.
 Can everyone tell me how to do?
 Thank you very much!
 Wei

[ccp4bb] [MX2] EPICS driver for Amptek MCA8000A

[Lucas Sanfelici]

Dear all,

We are currently studying the migration of the control software of our PX-MAD 
beamline from Blu-Ice to EPICS.

As part of this effort we are looking for an EPICS driver/IOC for our Amptek 
MCA8000A multi-channel analyzer, which is not available at the EPICS device 
repo (http://www.aps.anl.gov/epics/modules/bus.php#RS%2d232). Since it is a 
pretty common device in the community, I believe there may be someone around 
with this guy running under EPICS.

Thanks in advance for any help,

Lucas Sanfelici
Brazilian Synchrotron Light Laboratory (LNLS/Sirius)
Brazilian Center for Research in Energy and Materials (CNPEM)
Office: + 55 (19) 3512-1153
Mobile: + 55 (19) 9638-1498
lucas.sanfel...@lnls.brmailto:lsanfel...@lnls.br
www.lnls.brhttp://www.lnls.br/

Re: [ccp4bb] do you think it is interesting?

[Lucas]

2012/6/18 Tim Gruene t...@shelx.uni-ac.gwdg.de:
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 [...]
 of monomers is called a multimer, not a polymer.
 [...]
 shiver - what a terrible mixture of languages. 'multi-' has got latin
 origin, whereas both poly and mer have got greek origin, and I don't
 think one should mix these. Please!!! think of a different _GREEK_
 syllable to express what you describe as 'multimer'.

In fact this is quite common. Automobile, for example comes from
greek autos plus latin mobilis.

[ccp4bb]

[Lucas]

Since it was powder diffraction that made me fall in love with
crystallography as an undergrad (before switching to protein
crystallography as a grad student), I was obviously very excited when
I first heard about protein powder diffraction in a meeting some years
ago, in a lecture by Andy Fitch from the ESRF. I've exchanged some
mails with him and also Irene Margiolaki, who were very kind and sent
me lots of unpublished stuff and experimental hints (sample
preparation is probably the most difficult part in protein powder
diffraction). A good idea would be to contact them (it may be easy to
find their info in the ESRF website).

The GSAS groups was also working on this, and the major difference,
from what I remember, is that they were doing all the process (until
refinement) in the same way that was done with regular powder samples
(with a modified version of the GSAS program), while the group in ESRF
converted the powder data to MTZs and then used PX software.

By that time it seemed that they were the only groups doing it, but a
quick search in pubmed using protein powder diffraction shows some
recent articles from other groups, so it seems it's pretty much alive.
The following articles are from 2011:

X-ray diffraction from membrane protein nanocrystals.
http://www.ncbi.nlm.nih.gov/pubmed/21190672

Exploiting powder X-ray diffraction for direct structure determination
in structural biology: the P2X4 receptor trafficking motif YEQGL.
http://www.ncbi.nlm.nih.gov/pubmed/21382498

Lucas Bleicher

2011/11/26 REX PALMER rex.pal...@btinternet.com:
 Does anyone have an up-to-date account of protein structure anlysis from
 powders?


 Rex Palmer
 http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
 http://rexpalmer2010.homestead.com

Re: [ccp4bb] Linux vs MacOS for crystallographic software

[Lucas]

2011/9/29 Simon Kolstoe s.kols...@ucl.ac.uk:

 Generally I think that the extra money spent on a Mac pays for less time 
 spent messing around
 installing software, sorting out dependencies, swearing at the less than 
 effective office software etc.
 that plagues Linux which is more of a computer experts platform.

For some years I had dual-boot systems, but since the only thing in
Windows that I can't live without is their Office suite, what I've
been doing for a year or two is having an easy to maintain linux
distribution in my desktop (I use Kubuntu since Dapper Drake, and by
that time it seemed to be the only distro which was anything near
easy to use, but there are probably other good options today) while
running Microsoft Office via Crossover Office, a very cheap little
program for running windows software on linux (they also have a
version for Mac). It works just perfectly, and it means I only need an
Office license (no need to install Windows, as some do in virtual
machines).

Also, back in 2003 setting up the video card was a nightmare even in
more user-friendly linux distributions. It seems not to be the case
nowadays, it's been a long time since I had that feeling for
destroying the computer with a sledgehammer after trying the nth
version of xorg.conf and still being unable to run coot.

Lucas

[ccp4bb] OT - Software articles / databases

[Lucas Bleicher]

I've been compiling a reference database and I've just noticed that it's quite 
difficult to automatically retrieve references for most articles on 
crystallographic software. Has anyone noticed that? It seems that, for some 
reasons, articles on the Computer programs section on Journal of Applied 
Crystallography (where the official reference for most of the software we use 
gets published) is not indexed on databases such as ISI Web Of Science, Pubmed, 
etc, but all other sections from that magazine are.

Lucas


  Veja quais são os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com

[ccp4bb] Monochromator Stabilization

[Lucas Sanfelici]

Hello All!
 
Does anyone know if is there available in the market some sort of
all-in-one device capable of keeping the crystals of a double crystal
monochromator tunned?
 
I've contacted colleagues around the globe who have similar systems
running, but none of them were able to indicate me some company which
still assemblies such system. It seems today's solution would be to
integrate complementary peaces of hardware or even program them in
software.
 
Hope this message finds each of you well,
 
Lucas Sanfelici
Physicist
 
Brazilian Synchrotron Light Source- LNLS (www.lnls.br
http://www.lnls.br/ )
Beam Diagnostics Group
PO Box 6192 Postal Code 13083-970
Campinas-SP Brazil
Phone: +55-19-3512-1153/1152  Fax: +55-19-3512-1006

[ccp4bb] Air Conditioning System for Optical Hutch

[Lucas Sanfelici]

Hello Everyone!...
 
I'm starting to thing about an air conditioning system for the optical
hutch of one of our beamlines, which suffers from positional and energy
drifts associated with several sources. 
 
It's clear that the specifications for such system can cover a wide
range of requirements. However at the present time I would like to just
have a feeling of how much I would probably spend with a system like
that. Someone who already had to commissioning one could give some idea?
 
I hope you are all fine,
 
Lucas Sanfelici
Physicist
 
Brazilian Synchrotron Ligth Source- LNLS ( http://www.lnls.br
www.lnls.br)
Diagnostics Group
PO Box 6192 Postal Code 13083-970
Campinas-SP Brazil
Phone: +55-19-3512-1153/1152  Fax: +55-19-3512-1006
E-mail: [EMAIL PROTECTED] 
 

[ccp4bb] RES: [ccp4bb] Beamline Stability Issues

[Lucas Sanfelici]

 
Hi Michele!
-did you go in steps from 10 to 40 C? did you monitor drifts while doing
that? has the energy range, where you do not observe problems, changed?
In fact I was not planning to do that cause 40ºC
seems to be the mono’s basal temperature. In addition, I operated near
15ºC in the past and didn’t notice any appreciable change after that…
But I agree a more careful choice will be necessary in the near future! 
-I am a bit worried about keeping the crystal at 40 C... did you speak
to the engineer who designed the mono about the optimal cooling
temperature?
Yes, but no kind of recommendation was informed in this way…

-which is actually your energy range now?
MX2 was projected to operate from 5 to 15 keV.
(http://rcsb-biosync-beta.rutgers.edu/lnls/W01B-MX2.html)
-do you have a compton scattering guard on the second crystal? We had
one, and it was surprising so see the marks that I had after a year of
being installed.
Ooh, unfortunately I don’t have one. I fear for
that.
-Check the water flow rate. Too high flow would cause turbulence, and a
too low, would not cool your crystal.
We are operating with about 0.8 liters/min. The
mono was projected to work with 1L/min.
do you have access to the machine data? electron beam position and so
on? this can help to find time correlation.
Yes I have. I’m starting to think what kind of
correlation would be elucidative…
Michele, thank you one more for your help. I’ll be pleased
to inform you about our progress.
Regards,
Lucas.

[ccp4bb] Beamline Stability Issues

[Lucas Sanfelici]

Hello Michele! Thanks for your answer!...
 
Answering your questions we have a collimating mirror upstream the mono
and the water temperature used to keep this guy cooled is within
+/-0.3°C. Regarding fluctuation in the water flow, I don’t know, maybe
not ‘cause we have a dedicated thermal bath with fixed pumping speed…
 
Let me ask you a few things:
 
-  Do you remember why you decided to keep the 1st crystal at
8ºC instead of some point nearer of room temperature? Recently we
changed from around 10ºC to 40ºC in order equalize temperature inside
the mono (motors average temperature was 40°C).
-  What kind of system do you have to tune the crystals?
-  How do you usually do long energy measurements? Scanning
theta, absorption edge…? 
-  What kind of BPM do you have installed? Are they reliable?
 
Be sure MX2 is already very popular with the neighborhood!   : )
 
Thanks for the help one more time and regards,
 
Lucas.
-Mensagem original-
De: Michele Cianci [mailto:[EMAIL PROTECTED] 
Enviada em: segunda-feira, 28 de julho de 2008 04:26
Para: [EMAIL PROTECTED]
Assunto: Re: [ccp4bb] Beamline Stability Issues
 
Hi,

I commissioned and made operational MAD 10 at Daresbury.
The machine was operating at 2 GeV with 200 mA routinely and our
beamline was on a 2.4T wiggler.
in front of the mono we had a cooled collimating mirror that would take
most of the heat out.
then the mono  had the first crystal cooled to 8 degrees. 
The second crystal was not cooled and it was saggital for horiz.
focussing. 
With that set up we could see drifts only below 5500 eV.
they would appear as an intensity drift of 50% over 30 minutes when
changing from higher to low energies.
It would disappear when returning to higher energies and half an hour of
rest.

We had other drifts related to the machine this time, but they had not
correlation with the energy set at the mono.
they would appear at any energy and usually after a shut-down or
certainly first thing in the morning. 
These could be solved by asking for a re-steering of the machine (that
makes you very popular with your
neighborhood!!).
To isolate the problem find an high energy at which you are sure about
performances and then do what you can to identify the contribution
from the machine. When you are sure about the machine then change energy
and see what happens. Take one step at time.

Do you have some optics in front of your mono? Are they cooled? are
there fluctuations in the water flow?

hope this helps,
have fun,

mkl


Michele Cianci, Ph.D.
EMBL Hamburg Outstation
Building 25a c/o DESY
Notkestrasse 85, 22603 Hamburg - Germany
Tel.  +49 (0) 40 899 02 118  Fax. +49 (0) 40 899 02 147  
e-mail: [EMAIL PROTECTED]
---
My page: http://www-db.embl.de/jss/EmblGroupsHH/per_4431.html
---
Petra-III page: http://www.embl-hamburg.de/services/petra/
- Messaggio originale -
Da: Lucas Sanfelici [EMAIL PROTECTED]
A: CCP4BB@JISCMAIL.AC.UK
Inviato: Venerdì 25 luglio 2008, 16:19:29
Oggetto: [ccp4bb] Beamline Stability Issues

Hello all!

Does someone have experience in minimize energy instabilities in
beamlines? 

MX2, our new beamline devoted to MX experiments, are facing problems
with energy drifts. As far as we could notice, theses drifts are results
of the contribution from several sources - possibly electron beam
movements, heating of optical elements, etc...

LNLS is a 2nd generation machine with 4 straight sections available for
insertion devices. MX2 is a 2T wiggler-based beamline and produces a
peak flux of 10^11 photons/s.

What I'd like to know, before start performing calculations, how far
should I expect the heating of a non-cooled 2nd crystal affects energy?
Does someone know cases of a few eVs drifts?

Thanks in advance and regards,

Lucas Sanfelici
Physicist

Brazilian Synchrotron Ligth Source- LNLS (www.lnls.br)
Diagnostics Group
PO Box 6192 Postal Code 13083-970
Campinas-SP Brazil
Phone: +55-19-3512-1153/1152  Fax: +55-19-3512-1006
E-mail: [EMAIL PROTECTED]
 
  _  

Posta, news, sport, oroscopo: tutto in una sola pagina
Crea l'home page che piace a te!
http://us.rd.yahoo.com/mailuk/taglines/isp/control/*http:/us.rd..yahoo.
com/evt=52437/*http:/www.yahoo.it/latuapagina .

[ccp4bb] Beamline Stability Issues

[Lucas Sanfelici]

Hello all!

Does someone have experience in minimize energy instabilities in
beamlines? 

MX2, our new beamline devoted to MX experiments, are facing problems
with energy drifts. As far as we could notice, theses drifts are results
of the contribution from several sources - possibly electron beam
movements, heating of optical elements, etc...

LNLS is a 2nd generation machine with 4 straight sections available for
insertion devices. MX2 is a 2T wiggler-based beamline and produces a
peak flux of 10^11 photons/s.

What I'd like to know, before start performing calculations, how far
should I expect the heating of a non-cooled 2nd crystal affects energy?
Does someone know cases of a few eVs drifts?

Thanks in advance and regards,

Lucas Sanfelici
Physicist
 
Brazilian Synchrotron Ligth Source- LNLS (www.lnls.br)
Diagnostics Group
PO Box 6192 Postal Code 13083-970
Campinas-SP Brazil
Phone: +55-19-3512-1153/1152  Fax: +55-19-3512-1006
E-mail: [EMAIL PROTECTED]

[ccp4bb] RES: [ccp4bb] Beamline Stability Issues

[Lucas Sanfelici]

Hey Andrew! Thanks for answering!
 
Does someone have experience in minimize energy instabilities in
beamlines? 
Are you sure it's an energy instability and not an intensity one?
It's quite rare to see energy instabilities from a well calibrated
monochromator. All monochromators should be in a closed
loop, if there really are energy instabilities, then it's either 
mechanical (the encoder or crystal is loose) or the closed loop 
parameters are wrong for the rotational motor and the mono
is slipping out of the closed loop window.
 
Yes, I'm sure. I'm certain most of this problem arises from thermal
issues in the monochromator. For example, we control the temperature of
our 1st crystal, but for the 2nd one there is kind of control, the
tunning between them is not closed-looped through a MOSTAB or something,
there is no kind of shielding for the Huber. Thus, I have several
reasons to be concerned! 

MX2, our new beamline devoted to MX experiments, are facing problems
with energy drifts. As far as we could notice, theses drifts are results
of the contribution from several sources - possibly electron beam
movements, heating of optical elements, etc...
Could well be, but these will result in intensity instabilities as
opposed to
energy ones
 
Yes, this is evident in my data.

LNLS is a 2nd generation machine with 4 straight sections available for
insertion devices. MX2 is a 2T wiggler-based beamline and produces a
peak flux of 10^11 photons/s.

What I'd like to know, before start performing calculations, how far
should I expect the heating of a non-cooled 2nd crystal affects energy?
Does someone know cases of a few eVs drifts?
The second crystal will have no effect on energy, it will have a major
impact on intensity. We had extreme difficulties in stabilising and
sheilding
our Khozu second crystal from thermal drifts. We eventually gave up and
installed a channel cut mono. The much simplier design is far more easy
to work with
 
Luck you! I'm in the start of the journey! I guess I'll have to try fix
that first!  :(  
Andrew, what kind of approach did you try to stabilize 2nd crystal?
 
If you know someone else who could contribute in someway to this
problem, please tell me.
 
Thank you one more time,
 
LS

[ccp4bb] Beamline Stability Issues

[Lucas Sanfelici]

Dear Mark, thanks for your answer!

Yes, there is an actual change in energy and I guess my problem does not
have a single source!

In the case you know someone who faced/have faced a similar problem
around please tell me.

Brazilian regards,

LS.


1. Is the energy drift a change in flux or actual change in wavelength?
In the case of a change in flux it could be that you require more
cooling, what temperature is the cooling water at and how constant is
the water temperature? You may need to lower the cooling water
temperature. On beamline 10 at the SRS, the 1st mirror is cooled by the
synchrotron deionised water supply at a temperature of ~20oC, however we
cool the monochromator crystals on an independent water supply,
typically at a temperature of 4oC. We do see a drastic shift in beam
intensity when we go to wavelengths 2.2A (beam fluctuates wildly),
consequently we limit operations to wavelengths between 0.875 and 2.1A.

If it is a real change in energy/wavelength then there is a more serious
problem. It would suggest a change in the beam entering the optical
elements.

[ccp4bb] Model ensemble for x-ray crystallography

[Lucas Bleicher]

Some time ago I've heard about the idea of proposing
an ensemble of models (as in NMR), instead of a single
model for x-ray crystallography structures. If I
remember correctly, this idea has been published
somewhere. Can anyone tell me what article is that?

Lucas


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Re: [ccp4bb] Molecular replacement of a multidomain protein

[Lucas Bleicher]

I've had a very good experience with MrBump:

http://www.ccp4.ac.uk/MrBUMP/

Not only because of the program itself, which was able
to find an unexpected template for the problematic
chain (the first one was straightforward in Phaser),
but also because of great support from Martyn  Ron.
It's definitely worth a try.

Lucas

--- Anjali Mehta [EMAIL PROTECTED] escreveu:

 Dear All,
 I am working with a Bifunctional protein of
 molecular weight ~60 kDa.
 I have a 3.3 angstrom native dataset.  The matthews
 number show there are 6
 molecules in the asymmetric unit.
 The structures of the individual domains are already
 known from prokaryotes.
 The sequence identity with the known structures are
 about 30%.
 I have tried molecular replacement using the two
 parts as models
 respectively with CNS, MOLREP, PHASER etc. However I
 always get the solution
 for one domain. I have also tried to fix that domain
 and find the other one.
 But none of the programs can find a solution.
 I am trying to model build the correct sequence of
 one domain using a
 density modified (using CNS), NCS averaged (using
 RAVE) map but the map does
 not look very good. The side chains are not clear.
 That might be due to the
 fact that I am only having a partial model.
 Any suggestion will be appreciated.
 Thanks.
 Ms. Anjali Mehta
 



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Re: [ccp4bb] Suggestion: Wiki -- was:Re: [ccp4bb] need help--Rfree is not decreasing

[Lucas Bleicher]

That would be a great idea. In fact, I keep on my
mailbox dozens of great postings (most of them
summaries) in CCP4 which would be very useful to
everybody if there's an online resource, with
information organized in topics. I would gladly copy
them to this wiki.

Lucas

--- Kay Diederichs [EMAIL PROTECTED]
escreveu:

 So - rather than repeat things that are obvious to
 some people, would it 
 not be good to have a crystallography-FAQ that one
 could point people 
 to? This should be part of a Wiki where we
 crystallographers could 
 collect our wisdom. This would be much more
 systematic, and less 
 volatile, than the postings of this mailing list
 (which to me _is_ a 
 very valuable ressource).
 
 A Wiki is not difficult to set up. Maybe it could be
 part of the CCP4 
 pages? We set up a Wiki for our lab at the beginning
 of the year, and it 
 was a great success, in particular because it works
 the same way as 
 Wikipedia - anybody can contribute. There should be
 some means of 
 controlling write access, but that could simply be
 granted to people 
 who are subscribed to the CCP4 mailing list.
 
 I'd at least volunteer in helping to get a Wiki
 started. And one way to 
 get it filled with articles would be that those
 people who used to write 
 a summary of responses would simply compose a new
 Wiki article, and 
 report to the mailing list that this article exists,
 which could then be 
 expanded by others.
 
 best,
 
 Kay
 
 
 Anastassis Perrakis schrieb:
  Sorry for the cliche, but *the goal of refinement
 is not to reduce R 
  factors, but to produce a good model.*
  
  ARP/wARP uses the 'WEIGHT AUTO' option of REFMAC5
 to get a good geometry.
  You should set the weight to a value that produces
 1-2 and 1-3 distances 
  rms deviations similar to the ARP/wARP job, 
  to be able to compare. The fact that weight is 0.3
 says nothing.
  
  The correct weight can vary wildly from 0.02 to
 0.5, in my experience. 
  for 2.0 data 0.3 sound loose, 0.15-0.2 is what I
 am used to,
  depending on dataset. But, The only way to tell
 what is right is 
  inspecting the geometry and aim for a 'reasonable'
 rms 1-2 distances 
  deviation.
  
  What is 'reasonable',  can cause yet another long
 discussion, but my 
  personal favorite for 1-2 distances rms deviation
 is between 0.015-0.020.
  In Refmac these also give the lowest R factors, in
 my hands.
  
  The invisible side chains is yet another long
 discussion that you can 
  retrieve from the ccp4bb archives.
  Again, my personal preference is to leave them in
 and let them get very 
  high B factors, as long as they do not
  get negative density in difference maps, that I
 presume you are inspecting.
  I dont mind deleting them (but dont like it) and I
 think mutating to ALA 
  is worse since its misleading to users.
  
  Finally, given that you have 2.0 A data you should
 try and model not 
  only waters, but also:
  a. double conformations of side chains
  b. solvent and cryoprotectant molecules; glycerol,
 SO4 etc should be 
  different than waters and easy to model.
  
  ... and I still cant help wondering how people do
 their phd's or 
  post-docs in labs that no-one can explain
  such trivialities. Or why people prefer not to ask
 their colleagues and 
  supervisors, but to mail ccp4bb. 
  Or why do I bother answering such emails on a
 Saturday morning, and then 
  complaining, 
  only to have the likes of Dr. Walsh commenting
 about my humor ;-)))
  I find all these really scary.
  
  Tassos
  
  On 21 Jul 2007, at 0:29, JOE CRYSTAL wrote:
  
  Dear all,
 
 
  I am refining a structure at 2.0 A.  The water
 molecules have been 
  added using arp/warp resulting Rwork/Rfree=21/26%
 (about 370 HOH for 
  360 residues).  After 10 cycles of refmac
 refinement (wt 0.3), 
  Rwork/Rfree went up about 1.5% to 22.5/27.5%.  I
 did some minor 
  adjustments and add/delete water in Coot followed
 by 10 cycles refmac 
  refinement, but Rwork/Rfree are still around
 22.5/27.5%.  I also 
  noticed a few side chains without density.  Will
 setting those atoms 
  to 0 occupancy or high B factor or mutating to
 Ala help decrease Rfree 
  substantially?  If not, is there any better
 strategies to lower down R 
  factors?  I will be very appreciative if you have
 any suggestions or 
  comments to offer.  Thank you in advance. 
 
 
  Best,
 
 
  Joe
  
 
 
 -- 
 Kay Diederichs 
 http://strucbio.biologie.uni-konstanz.de
 email: [EMAIL PROTECTED]  Tel +49 7531
 88 4049 Fax 3183
 Fachbereich Biologie, Universität Konstanz, Box
 M647, D-78457 Konstanz
 
 



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[ccp4bb] SUMMARY: I vs. 2theta plot, image processing

[Lucas Bleicher]

Few, but very informative and useful responses about
2D to I vs. 2theta plot conversion and image
processing.

My original message was:

1) Some data collection and image processing files
have the options to show the intensity distribution
over a user-defined line in the image. Does any
program allow one to trace a line from the beam center
to 
the detector edge and save this intensity distribution
to a file, so one could have I vs. 2theta data (or
even a I vs. pixel data file, which could be easily
converted to a I vs. 2theta file given the
experimental 
setup)?

2) Is there a program which could convert image files
from common 2D detectors (Mar345, MarCCD, RaxisII...)
to a text file with the intensity on each pixel so one
could easily write programs to do things such as in
(1)?

3) If the answer to 2 is No, you should learn how to
handle binary files and image data formats, is there
a tutorial on how to do this (I would prefer C/C++,
but Fortran is OK), or some well-documented open
source code I could study?

==
James Holton wrote:

I recommend Andrew Hammersley's program FIT2D for
doing this.

http://www.esrf.eu/computing/scientific/FIT2D/

You can integrate a 2-D image into a 1-D profile using
the POWDER command.  You want to set up the image
geometry with the GEOM command first.  Then you have
the option to get I vs 2theta in the output. You can
also go from a 1-D profile to a 2-D image with the
SYMFUNC command.

FIT2D can also interconvert a number of image file
formats.  When it can't output the file format you
want, you can usually just export the image data as
binary and slap a new header on it.  For example, if

you read in a Bruker image to FIT2D and want to make
it an ADSC-type image, then you can export the data
(OUTPUT) as binary integers (BIN), using the
filename binary.bin, then you can do this:

head -512c frame_001.img ! header
vi header
head -512c header ! newimage.img
cat binary.bin  newimage.img

Here you are stealing a header from a pre-existing
image frame_001.img.  You can edit the header with a
text editor if you like, but make sure it stays as 512
bytes (you can run the saved text through head -512c
to truncate it).  This will let you display the 
Bruker data frame in ADXV.  You might need to play
around with byte swapping in FIT2D to make it work.

To get binary data into text, I find it most
convenient to use the unix program od (octal dump). 
The dump does not have to be octal and you can
arbitrarily set where in the file to start dumping and
what format 
to dump it.  For example, dumping a MarCCD image goes
something like this:

od -v -t u2 -w2 -j 4096 frame_0001.mccd

Will dump all the 2-byte words in the image, starting
with the first pixel in the image.  The only problem
is if the pixels are byte-swapped.  A quick-and-dirty
way to un-swap bytes is:

od -v -t u1 -w2 -j 4096 frame_0001.mccd | awk '{print
$2*256+$3}'

Will dump as single bytes, and then you convert them
into the equivalent 2-byte value with awk.

The x-y coordinate of the pixel can be worked out from
the sequence.  
For example, if you have a 4096x4096 image,

od -v -t u2 -w2 -j 4096 frame_0001.mccd | awk '{print
x+0,y+0,$2;++x} 
x4096{++y;x=0}'

Will dump x,y,and I for every pixel in the image. 
This output file will be quite large and this is
DEFINITELY not the fastest way in the world to do
this.

-James Holton
MAD Scientist

==
Graeme Winter wrote:

Hi Lucas,

There is a C++ library called DiffractionImage which
may help with #3 if you get that far:

http://www.ccp4.ac.uk/newsletters/newsletter45/articles/DiffractionImage.html

If you get in touch with Francois Remacle I'm sure
he'll send you everything you need.

Cheers,

Graeme 

==
Jon Wright wrote: 

Fit2d is perhaps the 'gold standard' for making powder
diagrams:

http://www.esrf.eu/computing/scientific/FIT2D/

See also:

http://www.datasqueezesoftware.com/

For source code try:

http://cctbx.sourceforge.net/current_cvs/python/iotbx.detectors.html

Good luck,

Jon

==

Thanks a lot,
Lucas Bleicher


   

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[ccp4bb] I vs. 2theta plot, image processing

[Lucas Bleicher]

1) Some data collection and image processing files
have the options to show the intensity distribution
over a user-defined line in the image. Does any
program allow one to trace a line from the beam center
to the detector edge and save this intensity
distribution to a file, so one could have I vs. 2theta
data (or even a I vs. pixel data file, which could be
easily converted to a I vs. 2theta file given the
experimental setup)?

2) Is there a program which could convert image files
from common 2D detectors (Mar345, MarCCD, RaxisII...)
to a text file with the intensity on each pixel so one
could easily write programs to do things such as in
(1)?

3) If the answer to 2 is No, you should learn how to
handle binary files and image data formats, is there
a tutorial on how to do this (I would prefer C/C++,
but Fortran is OK), or some well-documented open
source code I could study?

Thanks,
Lucas Bleicher

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Re: [ccp4bb] pdb-l: Sequence Location in Protein Tertiary Structure

[Lucas Bleicher]

By the way, I'll extend that question: the validation
software Verify3D assigns not only buried state but
also polar fraction and secondary structure, using the
probability of finding given residues in the different
environment defined when combining all this
information to calculate a score of protein regions,
which could identify, for example, sequence
misthreading. The program is rather old (1991) and,
aside from the automated validation site at UCLA
(which just let you upload a PDB and get the scores),
I haven't found a web page for it. Is there available
code to assign residues to one of those environments
and updated probabilities of finding amino acids in
each one?

Lucas

Wei Huang wrote:
 Hi all,

 Do someone know a tool which could identify the
 location of the sequence in
 tertiary structure known protein, that is the
 sequence is on the surface or
 in the
 core? Usually we use visualization tools, such as
 RasMol, VMD, to identify this
 by our eyes. But I don't know whether there are
 tools that we could input PDB
 file and the sequence only, then the computer
 tells us the sequence is on the
 surface or in the core.



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[ccp4bb] change the B-factor for a residue

[Lucas Bleicher]

Is there a program in CCP4 with a command to change
the B-factor of a single residue? I checked the
documentation for pdbset and it seems to assign
B-factors only for the whole molecule.

What I'd like to do is plot a given residue property
in a graphic software using the color by b-factor
feature. I could write a script to directly parse and
modify the PDB file, but things would be easier if I
could just generate a script that used some program
which would handle the B-factor assignment.

Lucas

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Re: [ccp4bb] change the B-factor for a residue

[Lucas Bleicher]

--- Juergen Bosch [EMAIL PROTECTED] escreveu:
 How about Coot ? Click the residue you want to
 change and hit Resdiue 
 Property.

That's how I used to do it, but things start to become
boring when one needs to do it with more than one pdb
file with about 200 residues each. Does coot accept
some kind of in-line command to do this, so I could
automatically generate a script?

Lucas

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[ccp4bb] Ordered His-tags

[Lucas Bleicher]

I remember reading once or twice people requiring
examples of PDBs which contained ordered His-tags.
Someone did a survey on this, which is on the latest
Acta Cristallographica D:

http://journals.iucr.org/d/issues/2007/03/00/en5203/index.html

Lucas

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