Re: [ccp4bb] Comparison of Water Positions across PDBs
For detailed examination of this topic, see: Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. Steiner, T. (2000). Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica. Journal of Molecular Biology 296, 713-735. http://www.ncbi.nlm.nih.gov/pubmed/10669619 best regards, Joel On 30 Oct 2013, at 01:35, Ed Pozharski epozh...@umaryland.edumailto:epozh...@umaryland.edu wrote: http://www.ccp4.ac.uk/html/watertidy.html On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Comparison of Water Positions across PDBs
Well - years ago I wrote a program called watertidy to do just this - but it asigned waters as OH0 OH1 OH2 with a according to what atom it was H bonded too, and those names are not now permitted.. My way now is to read in a completed homologous structure - use SSM to fit it over the new one - extract the HOHs from structure 1 - add them to structure 2 - do some refinement and use COOT to decide which ones are valid - the density fit picture shows wonderful red bars for wrong'uns - then add more again using coot.. Eleanor On 30 October 2013 06:49, Joel Sussman joel.suss...@weizmann.ac.il wrote: For detailed examination of this topic, see: Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. Steiner, T. (2000). Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica. Journal of Molecular Biology 296, 713-735. http://www.ncbi.nlm.nih.gov/pubmed/10669619 best regards, Joel On 30 Oct 2013, at 01:35, Ed Pozharski epozh...@umaryland.edu wrote: http://www.ccp4.ac.uk/html/watertidy.html On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Comparison of Water Positions across PDBs
At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue they are nearest from N to C terminus along each chain. This renumbering started when waters were assigned to macromolecular chains rather than getting a chain id of their own. I have failed to find the rationale explained in any PDB documents - but it could be motivated by this sort of consideration when waters from different chains or entries are to be compared. Having said that I do not know if there are any cases where this approach has successfully matched waters. .. However an associated step which is certainly a help is that, in the case of multiple chains, the crystal symmetry is applied to replace waters with their symmetry equivalent position if it is closer to a different chain. I believe a freely available program implementing a similar approach is WATERTIDY in CCP4 which might be a good place to start. It gives a pretty complete output, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn From: Joel Sussman joel.suss...@weizmann.ac.il To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 30 October 2013, 6:49 Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs For detailed examination of this topic, see: Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. Steiner, T. (2000). Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica. Journal of Molecular Biology 296, 713-735. http://www.ncbi.nlm.nih.gov/pubmed/10669619 best regards, Joel On 30 Oct 2013, at 01:35, Ed Pozharski epozh...@umaryland.edu wrote: http://www.ccp4.ac.uk/html/watertidy.html On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Comparison of Water Positions across PDBs
Dear all, this water discussion is flowing increasingly towards a place where I feel a bit out of my depth. What is the convention for numbering water molecules? Is there preference for: - putting waters into a separate chain (W for water or S for solvent)? - splitting waters according to the peptide chains in the structure? - appending all waters to chain A? Thanks. Andreas On 30/10/2013 11:57, MARTYN SYMMONS wrote: At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue they are nearest from N to C terminus along each chain. This renumbering started when waters were assigned to macromolecular chains rather than getting a chain id of their own. I have failed to find the rationale explained in any PDB documents - but it could be motivated by this sort of consideration when waters from different chains or entries are to be compared. Having said that I do not know if there are any cases where this approach has successfully matched waters. .. However an associated step which is certainly a help is that, in the case of multiple chains, the crystal symmetry is applied to replace waters with their symmetry equivalent position if it is closer to a different chain. I believe a freely available program implementing a similar approach is WATERTIDY in CCP4 which might be a good place to start. It gives a pretty complete output, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] crystals with large solvent content -dehydratation
While there is no systematic study (I think) on this we have observed RH control systems and concentration of solutes can have the same effect - Photosystem 1 crystals were dehydrated by transferring them from 20% to 40% PEG6000 resulting in a smaller unit cell and better diffraction properties - this is a decrease in the vapour pressure above these solutions from 99 to 96.5% RH. We found that we could reproduce the same transition using the HC1 from 99 to 97% in RH. This also applies to cases where glycerol and ethylene glycol have been used. I agree with your assessment that there is a difference between osmotic pressure and hydrostatic pressure but it does seem to depend more on the mole fraction of water in the system - this is directly proportional to the vapour pressure above a solution (Raoult's law). I have always presumed that by removing water molecules in the solvent channels (either by reducing RH surrounding xtals or by replacing them with something else in the channels) will 'exert pressure' on the crystal lattice - unfortunately I have no evidence for this, best wishes, Matt. On 29/10/2013 17:13, Edward A. Berry wrote: I wonder if there is a big difference between dehydrating in a drop, where the amount of mother liquor is essentially unlimited, and dehydrating a mounted crystal in something like the FMS, where there is only a thin film of ML on the surface. In the latter case, once the surface fluid is gone, assuming surface tension prevents air from entering the channels, the tendency for further evaporation will cause reduced hydrostatic pressure in the channels, and the pressure differential will exert a physical force to shrink the crystal (and to oppose further evaporation). If soaking in a droplet with salt at high osmolarity, salt freely enters the channels, so there is no hydrostatic pressure difference betwene inside and outside. With PEG it would depend whether the PEG can enter channels, with large PEG and small channels there would be an osmotic pressure gradient to shrink the crystal. So it would seem that equilibrating at a certain RH in the FMS vs in a droplet could have very different results. is there any data on this? Matthew Bowler wrote: Hi Andre, a very effective method is the use of a humidity control device. It has the great advantage that you can characterize changes that occur and also move straight to data collection. There are several HC1 devices in Europe (developed here at the EMBL and available at Diamond, BESSY and MaxLab) and at least 1 in the USA - there is also the FMS. You can of course also do this in the lab but the disadvantage is that any change induced cannot be observed. The relative humidity (RH) that is in equilibrium with your mother liquor is 99%, you could think about slowly replacing the reservoir solution with increasing salt solutions so as to dehydrate in the drop - this avoids handling the crystal - equations to convert between PEG concentrations and salt concentrations for RH matching can be found here: http://www.esrf.eu/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/forms/equation-4 Below are some links that might help, best wishes, Matt. Website for HC1 experiments at the ESRF: http://www.esrf.eu/UsersAndScience/Experiments/MX/About_our_beamlines/ID14-2/HC1b Calculation website for mother liquor RH equilibria: http://go.esrf.eu/RH On 29/10/2013 16:18, Andre Godoy wrote: Dear all I'm trying to solve a beautiful large crystal that, unfortunately, doesn't go further than 5 A resolution. I believe that in this case, the lack of resolution is due the high solvent content (about 66%). Therefore, my next strategy should be the dehydratation. Yet, I never (sucessfully) did that. I read different approachs, were people equilibrate crystals in dehydratation solution for days, or do more than 20 steps, or add solvents. Since i never had sucess in my trials, I was thinking that someone can suggest a protocol (should I remove all salt?, should I keep the additive concentration?, how much precipitant should I add? how many steps?). crystal condition: 23% PEG 3350, 0.2M NaCl, 0.1M Tris pH 8.5, 3% galactose (orthorhombic crystals, with about 0.6 x 0.6 mm) all the best, Andre Godoy -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.29.04 http://www.embl.fr/ === -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.29.04 http://www.embl.fr/ ===
Re: [ccp4bb] Comparison of Water Positions across PDBs
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Andreas, I am not sure there is a convention, but there has been a decision. When you deposit a structure with the PDB, they place all ligands including water molecules to the respective nearest macromolecular chain. I found this rather annoying the other day as I looked at the polymerase structure and wanted to take a look at the Zn-atoms. Instead of navigating through chain Z, where probably many crystallographers would have put them, I had to check the PDB (text) file for the correct chain and residue number and enter this into the 'goto'-field of coot. If I understand some people correctly, this is not a shortcoming of the PDB-format, but of the software developer developing the software I used. So I am waiting for the next version of coot/mmdb with voice recognition where I can just say Coot, please centre on the next Zn in this structure. Or at least opening a pop-up window saying This is you coot speaking. This structure contains 6 Zn atoms, and I feel that you are interested in looking at their environment. Please click 'yes' to centre on the next Zn-atom I think is most suitable for you to look at ;-) Best, Tim On 10/30/2013 01:09 PM, Andreas Förster wrote: Dear all, this water discussion is flowing increasingly towards a place where I feel a bit out of my depth. What is the convention for numbering water molecules? Is there preference for: - putting waters into a separate chain (W for water or S for solvent)? - splitting waters according to the peptide chains in the structure? - appending all waters to chain A? Thanks. Andreas On 30/10/2013 11:57, MARTYN SYMMONS wrote: At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue they are nearest from N to C terminus along each chain. This renumbering started when waters were assigned to macromolecular chains rather than getting a chain id of their own. I have failed to find the rationale explained in any PDB documents - but it could be motivated by this sort of consideration when waters from different chains or entries are to be compared. Having said that I do not know if there are any cases where this approach has successfully matched waters. .. However an associated step which is certainly a help is that, in the case of multiple chains, the crystal symmetry is applied to replace waters with their symmetry equivalent position if it is closer to a different chain. I believe a freely available program implementing a similar approach is WATERTIDY in CCP4 which might be a good place to start. It gives a pretty complete output, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFScPxSUxlJ7aRr7hoRAi1TAKDrjtWhH5sCw/3kwPimT/0WVE4oWwCgovPM 4bWow+/SfAp46XnoxD5UJXE= =YXln -END PGP SIGNATURE-
Re: [ccp4bb] Comparison of Water Positions across PDBs
Dear Elise, Try the 3Dss server (http://cluster.physics.iisc.ernet.in/3dss/). You can superimpose up to 20 structures and look for invariant waters. Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
Re: [ccp4bb] Unrelated - Emulsiflex C3 leaking
We've had that leak as well some time ago. Dismantle and reassemble it is the trick. Just a slight angle when tightening it will lead to that problem. This is usually the case because of overtughtening the reservoir to the main part of the machine. Keep it always straight when closing it again. Jürgen Sent from my iPad On Oct 29, 2013, at 11:44, Chiara Rapisarda chiara.rapisa...@pasteur.fr wrote: Hi all, sorry for the unrelated e-mail, but we have an emulsiflex C3 and it leaks from the chamber that contains the sample as I show in the figure. The Avestin European support was not very helpful, has anybody experienced a similar leak and has succeeded in fixing it? Chiara Diapositive1.jpg
Re: [ccp4bb] Comparison of Water Positions across PDBs
This is to be answered by PDB people, who definitely read BB :) Would be nice to have a tool common between CCP4/Phenix and the PDB which sorts this out Eugene On 30 Oct 2013, at 12:09, Andreas Förster wrote: Dear all, this water discussion is flowing increasingly towards a place where I feel a bit out of my depth. What is the convention for numbering water molecules? Is there preference for: - putting waters into a separate chain (W for water or S for solvent)? - splitting waters according to the peptide chains in the structure? - appending all waters to chain A? Thanks. Andreas On 30/10/2013 11:57, MARTYN SYMMONS wrote: At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue they are nearest from N to C terminus along each chain. This renumbering started when waters were assigned to macromolecular chains rather than getting a chain id of their own. I have failed to find the rationale explained in any PDB documents - but it could be motivated by this sort of consideration when waters from different chains or entries are to be compared. Having said that I do not know if there are any cases where this approach has successfully matched waters. .. However an associated step which is certainly a help is that, in the case of multiple chains, the crystal symmetry is applied to replace waters with their symmetry equivalent position if it is closer to a different chain. I believe a freely available program implementing a similar approach is WATERTIDY in CCP4 which might be a good place to start. It gives a pretty complete output, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London -- Scanned by iCritical.
[ccp4bb] A photograph of the Arndt-Wonacott rotation camera?
Dear all, Apologies for such a retro and non-biological question, but would anyone have a photograph of an Arndt-Wonacott rotation camera that he/she would be willing to share? I collected data on the first two prototypes in the early seventies, then on one of the first commercial models, but I cannot find any images of this ground-breaking piece of equipement on the Web. I found images for the Enraf-Nonius precession camera and the CAD-4 diffractometer, but not for the A-W rotation camera. This would be for use as visual material in presentations, and I would gratefully acknowledge the source of it. Thank you in advance! With fingers crossed ... . Gerard. -- === * * * 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 * * * ===
[ccp4bb] postdoctoral position available
Dear all, We seek to appoint a Post-doctoral Training Fellow to join the newly established Armenise-Harvard Laboratory of structural biology at the University of Pavia. The group will focus on the molecular characterization of extracellular ligand and receptors involved in synapse formation using a combination of techniques including structural biology, biochemistry and biophysics. More information on http://www.unipv.it/biocry/fornerislab/ The position will be initially available for one year and may be extended upon positive evaluation. The application should include curriculum vitae, publications, a cover letter explaining research interests and fit for the position. Please also include a minimum of two personal references (name, email and phone number). The application should be sent via e-mail to Dr. Federico Forneris (f.forne...@uu.nl). Review of applications will begin immediately and the position will remain open until filled. Best, F. Federico Forneris, PhD --- Crystal and Structural Chemistry Bijvoet Center for Biomolecular Research - Utrecht University Padualaan 8 3584 CH UTRECHT - The Netherlands Tel. +31 (0) 30 253 4179 - Fax +31 (0) 30 253 3940 http://www.crystal.chem.uu.nl/~forneris/ http://www.unipv.it/biocry/fornerislab/
Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?
Dear Gerard - Here is one picture, but I'm afraid it's quite small and not good quality: http://books.google.com/books?id=S9PPHvJ8otMCpg=PA28 I assume the camera is that object with the multiple circles in the left center of panel A? Also, these folks seem to have one in their collection: http://collectionsonline.nmsi.ac.uk/detail.php?t=objectstype=allf=s=arndt+wonacottrecord=0 No image that I could find online, but perhaps they would share one with you? Hope that helps, Matt On 10/30/13 12:05 PM, Gerard Bricogne wrote: Dear all, Apologies for such a retro and non-biological question, but would anyone have a photograph of an Arndt-Wonacott rotation camera that he/she would be willing to share? I collected data on the first two prototypes in the early seventies, then on one of the first commercial models, but I cannot find any images of this ground-breaking piece of equipement on the Web. I found images for the Enraf-Nonius precession camera and the CAD-4 diffractometer, but not for the A-W rotation camera. This would be for use as visual material in presentations, and I would gratefully acknowledge the source of it. Thank you in advance! With fingers crossed ... . Gerard. -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?
Is the prototype shown Figure 1 from U. W. Arndt, J. N. Champness, R. P. Phizackerley and A. J. Wonacott A single-crystal oscillation camera for large unit cells J. Appl. Cryst. (1973). 6, 457-463 http://dx.doi.org/10.1107/S0021889873009210 http://journals.iucr.org/j/issues/1973/06/00/a10549/a10549.pdf what you are looking for? Regards, Mitch http://journals.iucr.org/services/permissions.html -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard Bricogne Sent: Wednesday, October 30, 2013 9:05 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera? Dear all, Apologies for such a retro and non-biological question, but would anyone have a photograph of an Arndt-Wonacott rotation camera that he/she would be willing to share? I collected data on the first two prototypes in the early seventies, then on one of the first commercial models, but I cannot find any images of this ground-breaking piece of equipement on the Web. I found images for the Enraf-Nonius precession camera and the CAD-4 diffractometer, but not for the A-W rotation camera. This would be for use as visual material in presentations, and I would gratefully acknowledge the source of it. Thank you in advance! With fingers crossed ... . Gerard. -- === * * * 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 * * * ===
Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?
There is, of course, a photo in The Rotation Method in crystallography, by Arndt and Wonacott, which currently fetches over $245 on Amazon... On 30 Oct 2013, at 16:05, Gerard Bricogne wrote: Dear all, Apologies for such a retro and non-biological question, but would anyone have a photograph of an Arndt-Wonacott rotation camera that he/she would be willing to share? I collected data on the first two prototypes in the early seventies, then on one of the first commercial models, but I cannot find any images of this ground-breaking piece of equipement on the Web. I found images for the Enraf-Nonius precession camera and the CAD-4 diffractometer, but not for the A-W rotation camera. This would be for use as visual material in presentations, and I would gratefully acknowledge the source of it. Thank you in advance! With fingers crossed ... . Gerard. -- === * * * 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 * * * === Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?
Bob Sweet has a powerpoint presentation but it took a long time to download the file (http://www.google.com/url?sa=trct=jq=esrc=ssource=webcd=27ved=0CEoQFjAGOBQurl=http%3A%2F%2Fcima.chem.usyd.edu.au%3A8080%2FMMSN%2Fevents%2FRAAW_Mar_2005%2FBob_Sweet_v2.pptei=_jRxUqvjGeqrsASg8YDwBAusg=AFQjCNFXctrZtshdnzaF-zyHmg6ELyu_twbvm=bv.55617003,d.cWccad=rja) I have copied the camera and placed it here (https://www.dropbox.com/s/oceo44w5bngmdgh/Picture1.jpg) for easier access. I hope it is the camera.
Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?
A good source for used books is used.addall.com which searches many used book dealers. A copy of this book is listed there for about $60 US and is shipped from the UK. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 30 Oct 2013, Harry Powell wrote: There is, of course, a photo in The Rotation Method in crystallography, by Arndt and Wonacott, which currently fetches over $245 on Amazon... On 30 Oct 2013, at 16:05, Gerard Bricogne wrote: Dear all, Apologies for such a retro and non-biological question, but would anyone have a photograph of an Arndt-Wonacott rotation camera that he/she would be willing to share? I collected data on the first two prototypes in the early seventies, then on one of the first commercial models, but I cannot find any images of this ground-breaking piece of equipement on the Web. I found images for the Enraf-Nonius precession camera and the CAD-4 diffractometer, but not for the A-W rotation camera. This would be for use as visual material in presentations, and I would gratefully acknowledge the source of it. Thank you in advance! With fingers crossed ... . Gerard. -- === * * * 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 * * * === Harry -- ** note change of address **Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] bluetooth monitor
Hi Or you could look at using something like an Apple TV connected to a wall mounted flat screen monitor to stream via wifi (which may be better suited to fast data rates than bluetooth). Roku or Chromecast might be cheaper alternatives to the Apple TV, but I know almost nothing about them. Wireless presentations from iPad to Apple TV work pretty well, and I'm sure there must be more economical solutions out there. On 30 Oct 2013, at 17:20, mesters wrote: Alternatively, several projectors can do that which could be an alternative? Monitors have a too high resolution and that could be a problem. - J .- Am 29.10.13 18:05, schrieb Brett, Thomas: Hi all: I was wondering if anyone had economical suggestions on a bluetooth LED or LCD monitor. I would like to have a wall mounted monitor that one could easily connect laptops and imacs to for structure display, doing tutorials on building into maps, etc. 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/ -- protest.jpgDr. Jeroen R. Mesters Gruppenleiter Strukturelle Neurobiologie und Kristallogenese Institut für Biochemie Universität zu Lübeck Zentrum für Medizinische Struktur- und Zellbiologie Ratzeburger Allee 160, D-23538 Lübeck Tel: +49-451-5004065 Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- Any intelligent fool can make things bigger and more complex. It takes a lot of genius and a lot of courage to move in the opposite direction (Albert Einstein, 1879-1955) If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) -- Disclaimer * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. -- Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?
Dear Daniel, Thank you very much! That is the kind of picture I was hoping for. Thanks to you too, Bob, for your Powerpoint presentation that contains other interesting pictures of the major instruments that made MX possible. Finally, many thanks to the authors of all the other amazingly prompt replies to my message. I hope everyone will enjoy seeing the picture in Daniel's dropbox. Memories of the 3-day week in the UK and of Watergate in the US might come wafting through some people's minds ... . With best wishes, Gerard. -- On Wed, Oct 30, 2013 at 04:49:01PM +, D Bonsor wrote: Bob Sweet has a powerpoint presentation but it took a long time to download the file (http://www.google.com/url?sa=trct=jq=esrc=ssource=webcd=27ved=0CEoQFjAGOBQurl=http%3A%2F%2Fcima.chem.usyd.edu.au%3A8080%2FMMSN%2Fevents%2FRAAW_Mar_2005%2FBob_Sweet_v2.pptei=_jRxUqvjGeqrsASg8YDwBAusg=AFQjCNFXctrZtshdnzaF-zyHmg6ELyu_twbvm=bv.55617003,d.cWccad=rja) I have copied the camera and placed it here (https://www.dropbox.com/s/oceo44w5bngmdgh/Picture1.jpg) for easier access. I hope it is the camera.
Re: [ccp4bb] Comparison of Water Positions across PDBs
Elise - after looking into a related problem for some time, I've come to the conclusion it's a bit harder than it seems. Two obstacles: (1) there is no good coordinate system for partitioning the overall solvent volume (fraction of unit cell not occupied by protein density) into suitable neighborhoods (2) experimental support for water placement in deposited structures varies from sound to wishful thinking - with no single useful credibility metric ( a helpful review : http://www.ncbi.nlm.nih.gov/pubmed/8081736 ) The path I've gone down for (1) is to : (a) compute the distance field from the molecular surface and skeletonize it. This will give you the outer boundary of surrounding solvent (eg if you blew up the molecular surfaces like balloons, the surface defined by where the balloons touch); (b) carve up the resulting volume as appropriate, eg radial shells from the molecular surface for outer regions modeled as bulk solvent, atom-specific expansion of the molecular surface for regions occupied by modeled waters/ions. This is quite a bit of work (or so it seemed) but it enables you to segment the overall solvent volume into regions of interest and then calculate density of ordered waters/ions across structures (bearing in mind that much of modeled solvent may not be real). For sorting out non-bonding contacts there is a very nice and fast class, MAtomNonBond, in Kevin Cowtan's clipper library. For the distance field and skeletonization/medial-axis computation you might want to look at fast-marching implementations. Good luck! Alastair --- On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship
[ccp4bb] Re; A photograph of the Arndt-Wonacott rotation camera?
Gerard, I have the original rotation method book in my office, and it might have the picture that you are looking for. I will check in the morning. -Mark ___ Mark A. Saper, Ph.D. Department of Biological Chemistry, University of Michigan Medical School sa...@umich.edu | +1 (734) 764-3353 On Oct 30, 2013, at 8:00 PM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: A photograph of the Arndt-Wonacott rotation camera?
[ccp4bb] Fwd: [ccp4bb] Add C-terminal amide - solved
Thanks for the help, the issue is solved. Here a short summary in case anybody else has the same problem: 1) Add pointer atom in Coot NH2 and create link to C-terminal residue 2) create cif file with correct link description 3) modify LINK record in PDB to correct residues/ link name 4) refine in Refmac with cif as LIB in Thanks especially to Maike and Augen Bernhard Begin forwarded message: From: Bernhard Lechtenberg blechtenb...@sanfordburnham.orgmailto:blechtenb...@sanfordburnham.org Subject: [ccp4bb] Add C-terminal amide Date: October 29, 2013 6:32:37 PM PDT To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Reply-To: Bernhard Lechtenberg blechtenb...@sanfordburnham.orgmailto:blechtenb...@sanfordburnham.org Hello experts, I am currently working on a structure of a protein-peptide complex. The peptide was synthesized with a C-terminal amide group. What is the best way to add this in Coot and refine in Refmac? I did a search on the web but only found a protocol for CNS not for Coot/Refmac. Thanks for the help. Bernhard Bernhard C. Lechtenberg, PhD Postdoctoral Fellow Riedl Lab Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Road La Jolla, CA 92037, USA Phone: 858.646.3100 x 4216 Email: blechtenb...@sanfordburnham.orgmailto:blechtenb...@sanfordburnham.org
