[ccp4bb] AW: [ccp4bb] 'Mushroom' shipping dewar for Rigaku pucks
Hi Todd, In case no one answered: We have several of those MVE dry shippers and sometimes use them to store Rigaku pucks. The racks do not fit in nicely. You have to use some force to get them into the shipper, but it works. Cheers, Dirk --- Dr. Dirk Reinert Boehringer Ingelheim Pharma GmbH Co. KG A Leitstrukturfindung Tel.: +49 (7351) 54-97892 Fax: +49 (7351) 83-97892 mailto:dirk.rein...@boehringer-ingelheim.com Boehringer Ingelheim Pharma GmbH Co. KG, Sitz: Ingelheim am Rhein; Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender), Ralf Gorniak, Felix Gutsche, Mark Hagmann, Dr. Martin Wanning; Vorsitzender des Aufsichtsrates: Engelbert Tjeenk Willink; Sitz: Ingelheim am Rhein; Registergericht Mainz: HR B 23260 Diese E-Mail ist vertraulich zu behandeln. Sie kann besonderem rechtlichen Schutz unterliegen. Wenn Sie nicht der richtige Adressat sind, senden Sie bitte diese E-Mail an den Absender zurück, löschen die eingegangene E-Mail und geben den Inhalt der E-Mail nicht weiter. Jegliche unbefugte Bearbeitung, Nutzung, Vervielfältigung oder Verbreitung ist verboten. / This e-mail is confidential and may also be legally privileged. If you are not the intended recipient please reply to sender, delete the e-mail and do not disclose its contents to any person. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Todd Geders Gesendet: Dienstag, 23. März 2010 23:40 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] 'Mushroom' shipping dewar for Rigaku pucks Greetings, We're searching for a 'mushroom' shipping dewar (i.e. rounded sites and domed lid) to keep FedEx from laying our dry shipper on its side despite giant arrows and signs stating otherwise. From my look at descriptions and specifications, I believe the MVE SC 4/3V dry shipper dewar and 'minimoover' protective carton will hold a single Rigaku ACTOR storage rack of pucks. Since no one local has this particular dewar, can anyone tell me if they've shipped Rigaku (or ALS) pucks in a MVE SC 4/3V dry shipper? Thanks in advance, Todd Geders University of Minnesota Dept. of Medicinal Chemistry 308 Harvard St. SE, #8-101WDH Minneapolis, MN 55455 Office 2-163 WDH / Lab 2-160 WDH Phone: 612-624-2448
[ccp4bb] N-term sequencing facility
Hi all, can anyone recommend an N-terminal sequencing facility in Germany, or nearby in Europe, which does seqquencing of PVDF blotted protein? Perhaps replies off-board are best and I can post a summary anyone interested. Thanks in advance, Tim Keys PhD Student Medizinische Hochschule Hannover Zelluläre Chemie, OE 4330 Zentrum Biochemie Carl-Neubergstr. 1 30625 Hannover
Re: [ccp4bb] 2,3-butanediol
One thing I found with 2,3-Butanediol was for some crystallizations you can make it up a cryo solution with it at 12% and then put a thin layer it on top of the crystal droplet in a sitting drop well. Then you can loop the crystal and pull it up through the cryo layer - then out and to N2(l). Just how brief this is depends on your dexterity and also how well the crystal is engaged in the loop. My crystals were not very happy about the cryo but I could make it brief enough to get them out intact. Good luck, Martyn Martyn Symmons MBU Cambridge - Original Message From: Sean Seaver s...@p212121.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 24 March, 2010 18:47:38 Subject: Re: [ccp4bb] 2,3-butanediol Dear all, I would like to know which is the more suitable method of using 2,3-Butanediol as cryoprotectant? Addition in to reservoir buffer or crystal soaking or both can be tried? Cheers Gauri -- I am sure both could be tried, but have found quite few papers mentioning brief soaking with 2,3-butanediol: Purification, crystallization and X-ray diffraction analysis of the extracellular part of the human Fc receptor for IgA, Fc[alpha]RI (CD89) http://scripts.iucr.org/cgi-bin/paper?cnor=bw5002 5-10 seconds Purification, crystallization and X-ray analysis of Hibiscus chlorotic ringspot virus http://scripts.iucr.org/cgi-bin/paper?cnor=gr2202 described as 'briefly' Crystallization and preliminary X-ray analysis of recombinant human acid [beta]-glucocerebrosidase, a treatment for Gaucher's disease http://scripts.iucr.org/cgi-bin/paper?cnor=pu0086 described as 'briefly' Crystallization and preliminary X-ray crystallographic studies of recombinant human betaine-homocysteine S-methyltransferase http://scripts.iucr.org/cgi-bin/paper?cnor=gr2115 'quickly transferred' Purification, crystallization and X-ray analysis of Hibiscus chlorotic ringspot virus http://scripts.iucr.org/cgi-bin/paper?cnor=pu0115 5% increments from 5 to 30% for 3 min at each step Hope that helps, Sean
[ccp4bb] summary: Display X-ray images in windows
Thanks to everyone who answered. There are many ways to display the images. Summarized here are the answers: - adxv http://www.scripps.edu/~arvai/adxv.htmlhttp://www.scripps.edu/%7Earvai/adxv.html Run it with the option -nopixmap if you are using it inside an NX client - - There is also BDXV: an open-source viewer for ADSC-style *.img files being developed by the BSCB here at ALS: http://bcsb.als.lbl.gov/wiki/index.php/BDXV You will need GTK installed for this to work. - imosflm works very nicely indeed on windows, and needs no third-party package. - use idiffdisp - As I recently learnt from Andy Arvai, the -nopixmap is not needed if the (free) NX server has AGENT_EXTRA_OPTIONS_X=-defer 0 in its node.conf . - I think its's basically a TIF format and any program should work. I am using photoline32.
Re: [ccp4bb] R merge and R init
What XPREP (and some other programs) calls Rint is the same as Rmerge and is given by 100Sum|I-I|/Sum(I) where the sums are calculated over all reflections with more than one equivalent (symmetry equivalents and identical indices), I is the intensity of an individual reflection and I is the mean intensity of a group of equivalents. As Manfred Weiss, Kay Diederichs and others have pointed out, it would be better to quote R-values corrected for the multiplicity of observations so that they do not increase as you add data, but if your reviewer wants Rmerge (alias Rsym or Rint) he or she should be given it. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 24 Mar 2010, Muhammed bashir Khan wrote: Dear All; I have a crystal structure collected on in house X-ray facility from Bruker using Xprep. I submitted the paper but the reviewer ask for the R merge. As I can't access to the computer at the moment its crashed out. But I have the prp file which have the R init values. My question is!!! 1)Can I use the R init value instead of Rmerge? 2)If yes how it has been calculated, I mean the mathematical formula so that I can write below the table. Thank you very much for the help in advance Sincerely Bashir -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Phone: +43(1)427752224 Fax: +43(1)42779522
[ccp4bb] Calculation of the net charge of an electrostatic surface for secondary structural elements
Dear CPP4 community, I am in search of a program that will calculate the net charge of an electrostatic surface formed by individual secondary structural elements (versus the entire protein) of a structure: for example, the net charge of the electrostatic surface of helices 2 and 3 versus, say, helices 3 and 4 of the same protein. Thanks in advance, Rebecca
Re: [ccp4bb] ccp4 vs. phenix special position atoms
Hi Pavel, you should add to the explanation what /==1 and !=1 are, as the majority of people don't know. / == : equal != : not equal Maia / / Pavel Afonine wrote: Hi Regina, this subject was discussed on PHENIX bulletin board some time ago: http://www.phenix-online.org/pipermail/phenixbb/2009-December/003074.html I think this answers your question; please let me know otherwise. Also, I'm not sure what you mean by (except that refinement will fail if the special position atoms are not a separate group in refinement). If something fails in phenix.refine then I would to know about it so I (or someone else) can fix it asap. We can discuss it off-list. Pavel. On 3/23/10 1:37 PM, Regina Kettering wrote: Hello all. I have a refinement that includes atoms at special positions, am unsure how to delineate them in CCP4 vs. PHENIX programs. According to the information, for CCP4 you can reduce the occupancy by the appropriate amount, depending on the axis (2-fold to 0.5, 3-fold to 0.33, etc). However, I have not been able to determine whether PHENIX uses this same convention (except that refinement will fail if the special position atoms are not a separate group in refinement). My refinement uses PHENIX TLS, so I would rather continue using PHENIX. Thanks in advance. Regina Kettering
Re: [ccp4bb] Calculation of the net charge of an electrostatic surface for secondary structural elements
Hello Rebecca,
this is merely a guess, but I think, it should work.
As you calculate the electrostatic surface potential in pymol, it uses apbs.
apbs, if I remember correctly creates an intermediate PDB-file where the
B-factor column is replaced with the partial charge of that atom.
So if you can get hold of that file you can use a text editor to cut out the
helices of interest into separate files and use shell commands to sum up the
B-factor columns.
The following (all in one line, in case any mail program splits the line) adds
up the B-values in the PDB-file:
grep ^ATOM helix.pdb|cut -c61-66|awk '{pcharge += $1}END{print pcharge}'
Having said that I would be curious to hear what the community has to say about
how trustful and meaningful such calculations actually are, because I have
always wondered about this since I looked at my first GRASP surface.
Tim
On Thu, Mar 25, 2010 at 11:03:29AM -0400, Page, Rebecca wrote:
Dear CPP4 community,
I am in search of a program that will calculate the net charge of an
electrostatic surface formed by individual secondary structural elements
(versus the entire protein) of a structure: for example, the net charge
of the electrostatic surface of helices 2 and 3 versus, say, helices 3
and 4 of the same protein.
Thanks in advance,
Rebecca
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
signature.asc
Description: Digital signature
[ccp4bb] Editing mesh in pymol?
Hi everybody, can anybody tell me how to increase the number of lines in a mesh, when I generated a electron density map in pymol? My mesh has to much space between the lines. The command min mesh spacing doesn't work, though I'm not sure, if this the right command at all. Thanks, P.
Re: [ccp4bb] Editing mesh in pymol?
One option is to use the map_double command to make a finer mesh, e.g., map_double mymap.map, -1 The maps produced by CCP4 by default are typically too coarse. Cheers. On 3/25/2010 12:00 PM, Paul Lindblom wrote: Hi everybody, can anybody tell me how to increase the number of lines in a mesh, when I generated a electron density map in pymol? My mesh has to much space between the lines. The command "min mesh spacing" doesn't work, though I'm not sure, if this the right command at all. Thanks, P.
[ccp4bb] A postdoc position is available
A postdoc position in membrane protein structural biology is available in the Biomolecular Research Laboratory (BMR) at the Paul Scherrer Institute, Switzerland. The successful candidate will work on the production, characterization, crystallization and structure determination of the serotonin receptors in different conformational states by X-ray crystallography. The project is funded by our external industrial partner, Heptares Therapeutics Ltd. The successful candidate will benefit from the BMR high throughput cloning and protein expression platform to speed up the cloning, expression, purification and crystallization steps. The protein crystallography beamlines of the Swiss Light Source (SLS) at PSI also provide excellent conditions for carrying out crystallographic work. Both Xiao-Dan Li and Gebhard Schertler have extensive experience in the structure determination of membrane proteins using X-ray crystallography as well as electron microscopy. Candidates with a background in biological/chemical sciences and with a thorough knowledge of the basic techniques of molecular biology, biochemistry and biophysics are encouraged to apply. Experience in mammalian protein expression systems, purification, characterization and structure determination of membrane proteins is highly desirable. Being an enthusiastic researcher and a good team player will help to ensure your success in this exciting field of study. The contract will initially be for 2 years with the possibility of a one year extension. Applications including full curriculum vitae and the names of 3 academic referees should be sent to: Xiao-Dan Li, xiao...@psi.ch and Gebhard Schertler , gebhard.schert...@psi.ch.
Re: [ccp4bb] AW: [ccp4bb] 'Mushroom' shipping dewar for Rigaku pucks
Uups: We're using MVE SC 4/2V. Dirk Original-Nachricht Datum: Thu, 25 Mar 2010 08:33:40 +0100 Von: Dirk Reinert dirk.rein...@boehringer-ingelheim.com An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] AW: [ccp4bb] \'Mushroom\' shipping dewar for Rigaku pucks Hi Todd, In case no one answered: We have several of those MVE dry shippers and sometimes use them to store Rigaku pucks. The racks do not fit in nicely. You have to use some force to get them into the shipper, but it works. Cheers, Dirk --- Dr. Dirk Reinert Boehringer Ingelheim Pharma GmbH Co. KG A Leitstrukturfindung Tel.: +49 (7351) 54-97892 Fax: +49 (7351) 83-97892 mailto:dirk.rein...@boehringer-ingelheim.com Boehringer Ingelheim Pharma GmbH Co. KG, Sitz: Ingelheim am Rhein; Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender), Ralf Gorniak, Felix Gutsche, Mark Hagmann, Dr. Martin Wanning; Vorsitzender des Aufsichtsrates: Engelbert Tjeenk Willink; Sitz: Ingelheim am Rhein; Registergericht Mainz: HR B 23260 Diese E-Mail ist vertraulich zu behandeln. Sie kann besonderem rechtlichen Schutz unterliegen. Wenn Sie nicht der richtige Adressat sind, senden Sie bitte diese E-Mail an den Absender zurück, löschen die eingegangene E-Mail und geben den Inhalt der E-Mail nicht weiter. Jegliche unbefugte Bearbeitung, Nutzung, Vervielfältigung oder Verbreitung ist verboten. / This e-mail is confidential and may also be legally privileged. If you are not the intended recipient please reply to sender, delete the e-mail and do not disclose its contents to any person. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Todd Geders Gesendet: Dienstag, 23. März 2010 23:40 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] 'Mushroom' shipping dewar for Rigaku pucks Greetings, We're searching for a 'mushroom' shipping dewar (i.e. rounded sites and domed lid) to keep FedEx from laying our dry shipper on its side despite giant arrows and signs stating otherwise. From my look at descriptions and specifications, I believe the MVE SC 4/3V dry shipper dewar and 'minimoover' protective carton will hold a single Rigaku ACTOR storage rack of pucks. Since no one local has this particular dewar, can anyone tell me if they've shipped Rigaku (or ALS) pucks in a MVE SC 4/3V dry shipper? Thanks in advance, Todd Geders University of Minnesota Dept. of Medicinal Chemistry 308 Harvard St. SE, #8-101WDH Minneapolis, MN 55455 Office 2-163 WDH / Lab 2-160 WDH Phone: 612-624-2448 -- GMX.at - Österreichs FreeMail-Dienst mit über 2 Mio Mitgliedern E-Mail, SMS mehr! Kostenlos: http://portal.gmx.net/de/go/atfreemail
Re: [ccp4bb] Calculation of the net charge of an electrostatic surface for secondary structural elements
Le 25 mars 2010 à 16:43, Tim Gruene a écrit :
Hello Rebecca,
this is merely a guess, but I think, it should work.
As you calculate the electrostatic surface potential in pymol, it uses apbs.
apbs, if I remember correctly creates an intermediate PDB-file where the
B-factor column is replaced with the partial charge of that atom.
So if you can get hold of that file you can use a text editor to cut out the
helices of interest into separate files and use shell commands to sum up the
B-factor columns.
The following (all in one line, in case any mail program splits the line) adds
up the B-values in the PDB-file:
grep ^ATOM helix.pdb|cut -c61-66|awk '{pcharge += $1}END{print pcharge}'
Having said that I would be curious to hear what the community has to say
about
how trustful and meaningful such calculations actually are, because I have
always wondered about this since I looked at my first GRASP surface.
Tim
It depends on what you want to do with the information. If you want something
qualitative, like to decide whether a helix is more or less negative than
another, it may be enough. But that's about all you can get from this approach.
The coordinate file that you mention (in pqr format in fact) it's not unique
and is not produced by APBS, but by other tools, such as pdb2pqr. That file
will include charges and atom radii as derived from a particular force field.
For surface representations, the PARSE force-field is a simple and perhaps good
representation. In this force field the charges and atom radii are not the same
than in other force fields, like CHARMM or AMBER. From this pqr file, APBS
solves the Poisson-Boltzmann equation under certain conditions. Those include,
for example, the presence of counter-ions in the implicit solvent. So, the
results depend on the way you pose the problem, something that standard plugin
users perhaps/probably don't do.
In any case, I must confess that I don't understand what a net charge of an
electrostatic surface means. In my mind, a net charge is a property of a
molecule not of a surface. Actually, I would say that electrostatic surface
is a shorcut for something like a surface-mapped electrostatic potential. The
electrostatic potential is not restricted to the molecular surface and its
representation as an isosurface is often more informative than its mapping to a
particular surface.
These calculations can be very useful, for example to study binding properties,
provided they are carried out carefully.
Best,
-- Miguel
Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2
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[ccp4bb] structures with distinct substrate conformations
My literature search is not going so well. can anyone think of examples of the same substrate (not oxidized/reduced, intermediates or analogs) bound to the same enzyme (not mutants) binding site, but with one moiety adopting a drastically different conformation between different structures/datasets with unambiguous density? --- --- Brock Schuman, Graduate Student Department of Biochemistry Microbiology University of Victoria
