Re: [ccp4bb] Do manufacturers change their crystallogenesis screens?

Op 8/24/2011 17:21, Chris Morris schreef: Hi Chris, Yes, I have seen quite a few inconsistencies in screen formulations. Errors in listed conditions include recipe changes, but also typos both in the vendor description and in the database entries. At the moment I'm building a list of all discr

Re: [ccp4bb] sealing tapes

Hi Jean-Luc, We have complied a list of UV compatible cover media and plates. The list is by all means not complete yet, but the best seals we found are all sheets (that does not mean all sheets are UV compatible!). If you want I can send you a PDF file outside of the BB. Flip On 3/7/2011 1

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

Dear Ethan, I would really really like to enhance all my PDB files, but I am concerned I will create a black hole in my hard drive. I hope you can convince me of the safety of your tool, thx Flip On 4/1/2011 8:06, Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the av

Re: [ccp4bb] what to do with disordered side chains

It's nice to see that this discussion pops up every two years or so with exactly the same arguments :) My vote (as always) is for leaving the atoms of disordered side chains in with high B values, the B values are part of the models. Its up to the popular Biologist's visualization software

Re: [ccp4bb] viewing and scoring crystallization drops on the iPad

Indeed Chris :) This is one of the topics we will cover in our user group meeting next September, after the RAMC meeting organised by Allan D'Arcy Flip On 4/18/2011 13:49, Chris Ulens wrote: Formulatrix is reading this as well, so it would be useful to get objective comments from the > 10

Re: [ccp4bb] APBS

Leave it to the crystallographers to be the last on the Planet with text-only email readers Just before the ccp4bb will migrate to google+ :) Flip Op 7/6/2011 10:27, Tim Gruene schreef: Dear Boaz (and others) it immensly improves readability of your emails if you can ask your email clien

Re: [ccp4bb] How to delete loops from Protein for crystallization

Hi Obayed, I would start with doing some limited proteolysis with a few different proteases followed by Mass Spec analysis of the fragments to identify loops that are readily cut. There is lots of info and published protocols, see e.g. http://biowww.net/protocols/proteomics/mass_spectrometry/

Re: [ccp4bb] trouble with protein storage

Hmm, You can try to precipitate it with AmmSO4 and keep it as a suspension at 4C. Flip LEDU Marie-Helene 16 wrote: Hello, Sorry for the unrelated question. We encounter important storage problem of our favorite protein. We can not freeze it without a lost of 50 to 90 %, and can not use g

[ccp4bb]

Nothing. The B value increase is part of the refinement! Flip Vandana Kukshal wrote: i have one Query . after using phenix auto build for building model R factor and R free reduced but B factor is increesed for all the atom .what next i should do to decrease the B factor of atoms.

Re: [ccp4bb] FW: [ccp4]: TDS upon flashcooling

You can also set your cryostream to something like 253K... or even lower with high salt. Better than RT and still no freezing. You need to use one of these new loop covers to prevent drying out. Flip mjvanraaij wrote: why not stay with room temp? many structures have been solved at RT... Ma

Re: [ccp4bb] Crystal rescue

Zhiyi, You can use a thin cap over your cryo loop, just put a drop of mother liquor in the top, place over the loop and make it airtight at the base. Not sure who sells these things though, I guess you can make it from a capillary too. Then remove the cryo stream or put it at a temp above fr

Re: [ccp4bb] X-Ray films

Indiana Jones and the Kingdom of the Crystal Skull? "Nothing shocks me, I'm a scientist". Flip harry powell wrote: Hi Not a question about films for recording X-rays on, but a question about films about X-rays, Crystallography and related subjects! I was wondering what ccp4bbers favourite m

Re: [ccp4bb] Crystallography Near Venice/Padova Italy

Dip. Scienze Chimiche and Istituto di Chimica Biomolecolare del CNR, sezione di Padova Universita di Padova Via Marzolo, 1 I-35131 Padova Copied from http://www.weizmann.ac.il/esf_xtal/ which is the first place to look if you want to find crystallographers in Europe. I think it is quite up-to-d

Re: [ccp4bb] model refinement (corrections, apologies!)

Hi Atul, With an I/sig of 2.3 and 99.9% completeness in the highest resolution shell you could have collected to an even higher resolution it would seem That might help in modeling the solvent molecules. Do you have more crystals? Flip atul kumar wrote: Dear all Thanks for your replie

Re: [ccp4bb] creating new ligand cif file

Hi Paul, Usually I just Sketch the molecule, I make sure that the bond types are OK (single, double, aromatic etc.) and I do an idealization in Sketcher, then use the resulting .cif file in RefMac. Flip Paul Lindblom wrote: Hi all, I need to create a cif file for a new ligand that does not

Re: [ccp4bb] PEG 1000

The meting point of PEG 1000 is around 38C. Obviously, if Sigma has heated the batch to fill the bottles in the first place this is a futile exercise... I'd ask them first. Flip Vellieux Frederic wrote: R.Srinivasan wrote: Dear All, I have got initial crystals in a condition with

Re: [ccp4bb] Protein PI calculators

Hi Lori, If you want to get the contribution of a metal ion you have to take the metal co-ordination into account, so you need to know the fold. A theoretical pI becomes quite useless, so you'd have to do an IEF gel or something like that to get your answer. Flip Lori Horton wrote: Does an

Re: [ccp4bb] attachments

Anyone still on PINE should consider a new email application :) Flip On 7/2/2010 20:29, Tim Gruene wrote: I agree to this. What are the actual reasons against attachments? If one really has a slow network connection and cannot use IMAP instead of POP3 (if I understand correctly, with IMAP one d

Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries

Yep, its green-blue vs grey... Bad choice I guess? Perhaps you can provide a set of examples that work for you? Flip On 7/15/2010 13:20, Kevin Cowtan wrote: Gerard DVD Kleywegt wrote: For a five-minute illustrated introduction to PDBprints (including instructions on how to include them in you

Re: [ccp4bb] First 96 wells plate

Hi, Its been a while since this was posted, but I was going through the "old" entries to see if I missed anything... See http://www.microplate.org/history/det_hist.htm Flip _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, January

Re: [ccp4bb] AKTA prime

Talking about akta's and beyond... Im offered a 2nd hand Pharmacia FPLC, but in order to run it with a PC I'd need a copy of FPLCManager. The software is not sold anymore by Pharmacia --> Amersham --> GE. Would anybody have a copy lying around by any chance? Thx, Flip

Re: [ccp4bb] AKTA prime

, not too many things that can break, etc. There are more 2nd hand systems around, so this might be a good alternative for a new Äkta... Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Flip Hoedemaeker Sent: Wednesday, February 14, 2007 15:30 To

Re: [ccp4bb] human cDNA clones?

I usually buy my IMAGE clones from Geneservice in the UK (http://www.geneservice.co.uk/products/image/index.jsp), if you buy more than 75 clones the price per is GBP 33.75 which is CAD76.62 according to the google exchange rate... Flip -Original Message- From: CCP4 bulletin board [mailto

Re: [ccp4bb] wine coolers for crystallization?

I know of several labs where batteries of wine coolers are used, we as a small lab have one. Works fine. Of course also our rockimager works with peltier-based temp control, its effective, and vibration free. Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] O

Re: [ccp4bb] unsubscribe ccp4bb

The old CCP4 had an "how to unsubscribe" header, can we have that back? Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sarat C Sahu Sent: Friday, March 09, 2007 20:24 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unsubscribe ccp4bb -- Sarat Chand

Re: [ccp4bb] oxidised cys

I've actually seen something like this on disulfides (or at least I think so, I havent seen your density obviously), turned out it was model bias in MR, if I used a different template for MR the feature went away. This was high resolution stuff (~1.0 Å). Flip -Original Message- From: CCP4

Re: [ccp4bb] Refmac and B factors

Yes, it is available in the GUI... Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Peter Adrian Meyer Sent: Wednesday, May 09, 2007 23:28 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac and B factors Simon, REFI BREF OVERALL should do som

[ccp4bb] CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors)

Hi Simon, Well, X-ray crystallography nowadays often, but certainly not always, amounts to running a set of programs with default settings with a few mouse clicks in the GUI. The fun part is knowing when you have to deviate from default, leave the well travelled paths etc. The GUI is excellent

Re: [ccp4bb] CCP4 GUI

attention would be useful to the development team. Cheers, Charlie Flip Hoedemaeker wrote: > Hi Simon, > > Well, X-ray crystallography nowadays often, but certainly not > always, amounts to running a set of programs with default settings with > a few mouse clicks in the GUI. The

Re: [ccp4bb] mtz in windows

Hi Christopher, No that should not be necessary with a binary file format. I just tried this and it works fine. Did your file copy over properly? Is the size the same as on the linux box? Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of c.weiner

Re: [ccp4bb] Fedora core 6 install problem

I now have my own issue with in stalling CCP4 6.0.2 on Fedorea core 6. when I start a job I get this error: ERROR running script can not connect to server port (RunNotification) SERVER_HOST localhost SERVER_PORT 4441 Message: "couldn't open socket: host is unreachable" Any clues? Naturally, I ju

Re: [ccp4bb] Fedora core 6 install problem

il: [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Flip Hoedemaeker Sent: Monday, June 25, 2007 10:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fedora core 6 install problem I now have my own issue with in stalling CCP4 6.0.2 on Fedo

[ccp4bb] Off topic: job description for support engineer

Posted on behalf of Jeremy Stevenson of Formulatrix, please respond directly to him (jeremy at formulatrix.com) Off topic somewhat, but might be interesting for some... Flip Subject: Formulatrix Software and Robotics Support Engineer - Waltham, Massachuse

[ccp4bb] Job posting, Waltham MA, USA, support engineer

Posted on behalf of Jeremy Stevenson of Formulatrix, please respond directly to him (jeremy at formulatrix.com) Off topic somewhat, but might be interesting for some... Flip Subject: Formulatrix Software and Robotics Support Engineer - Waltham, Massachuse

Re: [ccp4bb] Help with reducing crystal mosaicity

You might also want to loook into using parathone for freezing... Or collection at 260K indeed! Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of mesters Sent: Tuesday, July 10, 2007 11:01 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Help with re

Re: [ccp4bb] pymol help

Hi Yangming, If you change the HETATM records of the ligand to ATOM records in the PDB file, you can replace the spheres for a surface representation, for which you can set the transparancy to make it less visible, that might help. Flip -Original Message- From: CCP4 bulletin board [mail

Re: [ccp4bb] Crystal Screens

There are some screens for sale based on experiences of large Structural Genomics consortia, the JCSG (+) screen is an example. Screens like these are often biased towards the type of organism targeted by the consortium (e.g. eukaryotic/prokaryotic) Flip -Original Message- From: CCP4 bul

Re: [ccp4bb] refined vs 'others'

Ive always assumed that "others" in case means the bonds to the hydrogens added in riding positions during refinement... This also explains that there are no torsions! Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: Sunday, N

Re: [ccp4bb] TLSANAL

Hi Jim, I find the graphical representation of the TLS motion determination site (http://skuld.bmsc.washington.edu/~tlsmd/) very helpful. You only have to feed it the final PDB to set up an automated TLS analysis. Im not sure if you can submit your own TLS file... Flip -Original Message

Re: [ccp4bb] heavy metal source

Been Googling a bit, Methyl mercuric acetate is sold by Chemos in Germany, perhaps they have the others too. http://www.chemos-group.com/ Flip From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Joyce, Gordon M.(NIH/NIAID) [F] Sent: Thursday, December 06, 2007 4:32 PM To: CCP4

Re: [ccp4bb] crystallisation robot

? > >>? > >> --> Demetres D. Leonidas, Ph.D.? > >> Structural Biology & Chemistry Group? > >> Institute of Organic and Pharmaceutical Chemistry? > >> The National Hellenic Research Foundation? > >> 48, Vassileos Con

Re: [ccp4bb] Crystal Imaging Systems - possibilities and recommendations

Just a FYI, these imagers can be used (and are used) with external chillers to reach a temperature of 4C in a 22C room. If you do not have the chiller option, you can indeed reach +/- 4 deg from ambient. Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf

Re: [ccp4bb] Vista

Strange, CCP4 and Coot run just fine on my Vista laptop... Have not tried all programs though. Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Scott Pegan Sent: Wednesday, February 20, 2008 22:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Vist

Re: [ccp4bb] Vista

attempt was a desktop installation. This was ~1 month ago. Scott On Wed, February 20, 2008 3:34 pm, Flip Hoedemaeker wrote: > Strange, CCP4 and Coot run just fine on my Vista laptop... Have not tried > all programs though. > > Flip > > -Original Message- > From: CCP4 b

Re: [ccp4bb] Vista

This actually pops up a question on a somewhat related issue, I've recently tried to install Fedora 8 on a virtual PC, but I get caught up with the video display being completely warped. Since I don't see anything I cannot even begin to troubleshoot the issue. Has anybody got a solution for this?

[ccp4bb] running fedora on virual PC 2007 (was RE: [ccp4bb] Vista)

rtual machines tries to boot from CD/DVD? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 21 Feb 2008, Flip Hoedemaeker wrote: > This actually pops up a question on a somewhat related issue, I've recently > tried to insta

Re: [ccp4bb] Protein/DNA microcrystals

Hi Scott, I'd try and set up drops at 20% PEG, then back off by dilution to 15% PEG at different time points (15 min, 30 min 1 hour...) Since equilibration of PEG in hanging drops is much slower than this, you actually need to dilute the drops. You can also consider microbatch. Flip -Origin

[ccp4bb] plate survey

Hi Community, I would like to do a little survey on popular 2-3 drop per 96 well plates, and the pros and cons of these plates. I know that the new Cornings, the MRC and the Intelliplates are used often in the labs I visit (we use 2 drop MRC plates mostly). Perhaps you can comment on optical qua

[ccp4bb] plate survey: summary

All, Some time ago I put up a small survey to find out what are the popular plates nowadays. I got 8 replies, not counting anyone selling plates themselves, not very representatve perhaps, but anyway thanks to all for participating. Among these, the new 3 drop Intelliplates from Art Robbins are

Re: [ccp4bb] MR- Problem-76 % seqeunce identity-no solution

I had the same problem with an even higher %identity once (>80%), eventually resorted to SIRAS phasing with a mercury compound, and I found a case of domain swapping creating a novel dimer interface. Flip

[ccp4bb] Free Imager available....

All, Just wanted to point out that Formulatrix is interested in donating an imager plus software to a lab conducting research to advance the human condition, including cancer and other disease research. More info on http://www.formulatrix.com/donation.shtml Flip

Re: [ccp4bb] Refmac5 open failed

Hi Stsiapanava, It is looking for this file on the F: drive, is this a network drive, or an external disk? Can you confirm that the folders mentioned are present and that you have write access to them? Flip Stsiapanava Alena wrote: Dear CCP4-Experts, I'd like to ask you to help me to solve

Re: [ccp4bb] Help me!!

Or, to avoid spending $63 and then finding out you want to do something else, start here: www.ruppweb.org/Xray/101index.html Flip James Stroud wrote: Whether probing the bulletin boards for advice or probing nature for her structural secrets, the first thing to do is to ask a good question. T

Re: [ccp4bb] small molecule library

A company called ZoBio screens their 2,000 fragment library with NMR, cool technology. Don't know about € www.zobio.com Flip Sridhar Prasad wrote: Zenobia is a good place to look for, they can even customize it your needs. www.*zenobiatherapeutics*.com Sridhar > Date: Wed, 28 Oct 2

Re: [ccp4bb] SAD phasing at home source

Yep, solved a structure at Cu K-alpha once with the sulfur signal, resolution 1.7A and a redundancy of 50 or so did the trick. Actually, one of the sulphurs we found was an ordered SO4 molecule, so if you have that in your crystallisation condition it might be a bonus... Flip Watanabe Nobuhis

Re: [ccp4bb] Crystallization of lysine and arginine rich proteins

Hi Jan, We have tried crystallizing a similar protein without success, later on it turned out that the protein was having a strong interaction with DNA that was not sequence specific. You might have a case like that Flip Jan Rash wrote: Dear All, I have a question regarding the crysta

Re: [ccp4bb] Plastic and glass plates

Hi Teresa, An additonal disadvantage of using plastic plates would be the polarisation of the plastic. Many users use cross-polarisation to image LCP plates. Flip Op 8/29/2012 21:24, Theresa Hsu schreef: Dear all Is there any pros and cons of using plastic plates for LCP crystallization? T

Re: [ccp4bb] What to put on Custom Declaration for shipped samples?

Hi Jim, I remember the same discussion somectime ago on the bb. The consensus was that there is a standard IATA document (IATA special provision A152) for these kinds of shipments, this greatly decreases the risk of destruction of you samples at Customs. See this thread http://www.mail-archiv

Re: [ccp4bb] Crystallization Screens

In general, at Formulatrix we have a lot of these discontinued screens on record, albeit in RM-XML format (for import into RockMaker). I'd be happy to provide .CSV exports of these if needed. Send requests to me offline. Flip On 3/6/2017 11:18, Hernani Silvestre wrote: many thanks! On 6 Mar