[ccp4bb] Postdoc position at the Membrane Protein Lab
Dear All, A position has become available for a Research Associate in the Membrane Protein Laboratory (MPL) for crystallisation, crystallographic and biochemical studies on bacterial antibiotic transporters. The successful candidate will work on improving the crystals and solving the structure of these important proteins, as well as biochemically characterising them. The MPL is located at Diamond Light Source, near Didcot, Oxfordshire. The laboratory is an out-house of Imperial College London and its director is Prof So Iwata. The laboratory is fully equipped for structural studies of membrane proteins and it is also equipped for cell growth and protein purification and has automated crystallisation robots and imaging systems. The laboratory benefits from its location within the Diamond Light Source, and it is close to the ISIS neutron source. The post is funded through a Biotechnology and Biological Sciences Research (BBSRC) Council research grant. You will be responsible for improving membrane protein crystals of bacterial antibiotic transporters and biochemically characterise them within the MPL. The group already has crystals for one of these transporters that diffract to medium resolution. The successful candidate will have a PhD in a biological science, or the equivalent in professional qualifications and experience. You must have experience in molecular cloning and protein purification. Crystallisation, protein crystallography or electron microscopy experience on membrane proteins will be considered as a plus but not essential. For informal enquiries please contact Dr Konstantinos Beis at: konstantinos.b...@imperial.ac.uk Our preferred method of application is online via our website http:// www3.imperial.ac.uk/employment. Please complete and upload an application form as directed. Closing date is the 23rd June. Best, Kostas Dr. Konstantinos Beis RCUK Research Fellow Membrane Protein Lab Diamond Light Source Harwell Science and Innovation Campus Chilton, Didcot Oxfordshire OX11 0DE UK tel: 01235778413 fax: 01235778785 url: http://www3.imperial.ac.uk/people/konstantinos.beis url2: http://www.diamond.ac.uk/Science/MPL/default.htm Or: MPC group, Wolfson Lab, Level 1 Biochemistry Building South Kensington Campus Imperial College London Exhibition Road London SW7 2AZ UK Tel: +44(0)20 7594 1873 +44(0)20 7594 3173 Fax: +44(0)20 7594 3022 P Please consider the environment before printing this email
Re: [ccp4bb] The Total CC in the output of CCP4 OVERLAPMAP
You are in luck - it is the total CC over all grid points used for that Table Eleanor Hailiang Zhang wrote: Hi all: Thanks for all kindly helps with real space CC. Now I have a new question again. In the output of OVERLAPMAP in CCP4, there is a almost last line saying Total...: ### ... 1243 0.9528 0.9249 1244 0.9741 0.8591 1360 0.9483 0.9145 $$ Total: 0.8853 0.8676 BFONT COLOR=#FF!--SUMMARY_BEGIN-- OVERLAPMAP: Normal termination # Now what does the Total CC mean? Is it a single CC generated by integrating over the whole system? Or just an average of each individual CC values? I do need to first one, and hope that's it. Best Regards, Hailiang
Re: [ccp4bb] How to align a sequence to a know profile
chainsaw does just that eleanor 商元 wrote: Hello, everyone, I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Regards, Yuan SHANG
[ccp4bb] beamline technician position at the EMBL in Hamburg, Germany
BEAMLINE TECHNICIAN European Molecular Biology Laboratory, Hamburg, Germany A position is available at the Structural Biology Unit of the EMBL in Hamburg. The Unit utilises synchrotron radiation at the German Synchrotron Research Centre (DESY) for research in structural biology. EMBL operates synchrotron beamlines, which are used by hundreds of external visitors per year as well as local research groups. EMBL is also building an integrated facility for structural biology at the new PETRA III storage ring at DESY, Hamburg, which will include the operation from 2011 of world-class synchrotron radiation beamlines in biological macromolecular crystallography and small angle X-ray scattering, providing an ideal research environment for future challenges in structural biology. The Beamline Technician will be involved in the support of the external visitors at our beamlines in macromolecular crystallography at DORIS and beamlines at PETRA. This includes maintenance and servicing of beamline end-station infrastructure, log-book keeping and direct responsibility for beamline cryogenic equipment. (S)he is expected to actively interact with a broad variety of international visitors and improve the efficiency of the experimental support. The post holder will be expected to take responsibility for the administration of (pre-frozen) crystals shipped to EMBL Hamburg for data collection. The ideal candidate should have a technician or engineering degree in electronics or electro-mechanics, physics technical assistant or a related discipline. Experience in cryogenics, vacuum technology and control electronics is desirable. Skills in Macintosh/PC desktop software are essential; familiarity with control software like LabVIEW, TwinCAD or SPS programming would be an advantage. Knowledge about macromolecular crystallography is a plus. Excellent communication and social skills and a good command of English are required. An initial contract of 3 years will be offered to the successful candidate. This can be renewed, depending on circumstances at the time of the review. Closing date for applications is 13 June 2010 For further information please look at http://www.embl-hamburg.de/aboutus/jobs/jobs_embl_hamburg/2010/w_10_038/index.html To apply, please email a cover letter, CV (in English) and contact information of three professional references quoting ref. no. W/10/038 in the subject line, to applicat...@embl.de General enquiries may be sent to j...@embl.de
[ccp4bb] Ligand present in only one monomer in NCS
Hello, I am solving a structure of an enzyme, which crystallises as a dimer. We have pretty good evidence that this operates as a dimer in vitro, also. We have an inhibitor of this enzyme, which we are keen to visualise by X-ray methods. We seem to have very strong density in which we can model our inhibitor, with good stats and no negative density. However, there is only density in one of the monomers, nothing in the other. The SG is P212121, and although I can postulate why this may have happened (if this is indeed what HAS happened), different solvent channel accessibility etc., I would like to know how common this was and, if possible, some literature regarding this, if the board would be so kind? Regards, Andrew.
[ccp4bb] Post Doc position in Newcastle
Dear BBers There is an ~18 month vacancy in my lab for a postdoc to work on our favourite macromolecular complex, the 'stressosome'. The ideal candidate will know their way around an Akta and be able to solve crystal structures by isomorphous replacement and/or anomalous scattering. Experience of linux system administration and/or electron microscopic methods of single particles would be viewed favourably. Further details, and a link on how to apply for the post can be found here: http://tinyurl.com/25qpweg The closing date is 2nd July 2010 and the position is available immediately. Please note that applications MUST be made through the website and NOT emailed to me direct. Cheers Rick
Re: [ccp4bb] Ligand present in only one monomer in NCS
Hi Andy, I'd say fairly common, and there can be several reasons. One is that the entrance of the active site (in case of crystal soaks) is blocked in some subunits. Also, different affinities in the different active sites, plus allosteric effects, are possibilities to consider. The latest example here I can give you (unpublished yet) is a mutant of an NAD-binding tetrameric enzyme. The crystals were grown by co-crystallisation. Out of the 4 active sites, only 2 of them contain cofactor plus substrate analogue. It is likely that the scientists who do large scale analyses of the PDB using automated programs have done a systematic search in the PDB and could provide you with accurate statistics. I wouldn't know any reference to such work (I am not in that field myself). Fred. ANDY DODDS wrote: Hello, I am solving a structure of an enzyme, which crystallises as a dimer. We have pretty good evidence that this operates as a dimer in vitro, also. We have an inhibitor of this enzyme, which we are keen to visualise by X-ray methods. We seem to have very strong density in which we can model our inhibitor, with good stats and no negative density. However, there is only density in one of the monomers, nothing in the other. The SG is P212121, and although I can postulate why this may have happened (if this is indeed what HAS happened), different solvent channel accessibility etc., I would like to know how common this was and, if possible, some literature regarding this, if the board would be so kind? Regards, Andrew.
Re: [ccp4bb] Ligand present in only one monomer in NCS
Hi, It occurs quite frequently with renin for example, with two molecules in the asu. Depending on the affinity and shape of the inhibitors both, only one or neither of the sites may be occupied. The slight, but significant conformational difference between the two crystallographically independent molecules certainly contribute to this observation. Regards, Zsolt Zsolt Bocskei sanofi-aventis Structure Design and Informatics 16 rue d'Ankara 67000 Strasbourg France tel: +33 632326710 -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of ANDY DODDS Sent: Tuesday, June 01, 2010 12:22 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ligand present in only one monomer in NCS Hello, I am solving a structure of an enzyme, which crystallises as a dimer. We have pretty good evidence that this operates as a dimer in vitro, also. We have an inhibitor of this enzyme, which we are keen to visualise by X-ray methods. We seem to have very strong density in which we can model our inhibitor, with good stats and no negative density. However, there is only density in one of the monomers, nothing in the other. The SG is P212121, and although I can postulate why this may have happened (if this is indeed what HAS happened), different solvent channel accessibility etc., I would like to know how common this was and, if possible, some literature regarding this, if the board would be so kind? Regards, Andrew.
Re: [ccp4bb] Ligand present in only one monomer in NCS
VERY, very common in the Pharma setting where we do hundreds of ligand-bound structures on a given target. Other permutations of this scenario, such as only one monomer's ligand displacing a ligand used for co-crystallization when trying to exchange by soaking, etc. Zsolt and I could share renin stories someday ;) Steve -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Vellieux Frederic Sent: Tuesday, June 01, 2010 6:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Ligand present in only one monomer in NCS Hi Andy, I'd say fairly common, and there can be several reasons. One is that the entrance of the active site (in case of crystal soaks) is blocked in some subunits. Also, different affinities in the different active sites, plus allosteric effects, are possibilities to consider. The latest example here I can give you (unpublished yet) is a mutant of an NAD-binding tetrameric enzyme. The crystals were grown by co-crystallisation. Out of the 4 active sites, only 2 of them contain cofactor plus substrate analogue. It is likely that the scientists who do large scale analyses of the PDB using automated programs have done a systematic search in the PDB and could provide you with accurate statistics. I wouldn't know any reference to such work (I am not in that field myself). Fred. ANDY DODDS wrote: Hello, I am solving a structure of an enzyme, which crystallises as a dimer. We have pretty good evidence that this operates as a dimer in vitro, also. We have an inhibitor of this enzyme, which we are keen to visualise by X-ray methods. We seem to have very strong density in which we can model our inhibitor, with good stats and no negative density. However, there is only density in one of the monomers, nothing in the other. The SG is P212121, and although I can postulate why this may have happened (if this is indeed what HAS happened), different solvent channel accessibility etc., I would like to know how common this was and, if possible, some literature regarding this, if the board would be so kind? Regards, Andrew. Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Far to good r-factors
On Mon, May 31, 2010 at 9:15 PM, Dale Tronrud det...@uoxray.uoregon.edu wrote: One of the great mysteries of refinement is that a model created using high resolution data will fit a low resolution data set much better than a model created only using the low resolution data. It appears that there are many types of errors that degrade the fit to low resolution data that can only be identified and fixed by using the information from high resolution data. Is it such a mystery? Isn't it just a case of overfitting to the experimental errors in the low res data if you tried to use the same parameterization restraint weighting as for the high res refinement? Consequently you are forced to use fewer parameters and/or higher restraint weighting at low res which obviously is not going to give as good a fit. Cheers -- Ian
[ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot
Dear All, I am looking for a ccp4 program that reads in cif-files and converts them into pdb-files, including the CRYST1 card. Can anybody suggest a solution? I didn't find any in ccp4i, e.g. the coordinate utilities. I also tried COOT to read in cif-files (downloaded from the pdb server). For one example it crashed, for others it doesn't colour the bonds properly if Bonds (Colour by Atom) is chosen but shows all bonds in one colour. Is that a known feature? If I save these coordinates in pdb-format and try to read it back, I get an ERROR saying: Wrong ASCII format of an integer. Thanks for any suggestions Christian Engel Mit freundlichen Grüßen / Best regards / Cordialement Dr. Christian Engel Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 020 D-65926 Frankfurt am Main t: +49 69 305 12946 f: +49 69 305 80169 w:www.sanofi-aventis.de 125 Jahre Arzneimittel aus Deutschland von sanofi-aventis * Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias Braun, Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Heinz Riederer *
Re: [ccp4bb] Ligand present in only one monomer in NCS
The rnase structure used as the $CEXAM for CCP4 is another example - a typical coordinate set is 2sar.pdb There one monomer binds the substrate very clearly, whilst the other is blocked by crystal contacts. Eleanor ANDY DODDS wrote: Hello, I am solving a structure of an enzyme, which crystallises as a dimer. We have pretty good evidence that this operates as a dimer in vitro, also. We have an inhibitor of this enzyme, which we are keen to visualise by X-ray methods. We seem to have very strong density in which we can model our inhibitor, with good stats and no negative density. However, there is only density in one of the monomers, nothing in the other. The SG is P212121, and although I can postulate why this may have happened (if this is indeed what HAS happened), different solvent channel accessibility etc., I would like to know how common this was and, if possible, some literature regarding this, if the board would be so kind? Regards, Andrew.
Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot
http://sw-tools.pdb.org/apps/CIFTr/ On Tue, 2010-06-01 at 15:21 +0200, Christian Engel wrote: Dear All, I am looking for a ccp4 program that reads in cif-files and converts them into pdb-files, including the CRYST1 card. Can anybody suggest a solution? I didn't find any in ccp4i, e.g. the coordinate utilities. I also tried COOT to read in cif-files (downloaded from the pdb server). For one example it crashed, for others it doesn't colour the bonds properly if Bonds (Colour by Atom) is chosen but shows all bonds in one colour. Is that a known feature? If I save these coordinates in pdb-format and try to read it back, I get an ERROR saying: Wrong ASCII format of an integer. Thanks for any suggestions Christian Engel Mit freundlichen Grüßen / Best regards / Cordialement Dr. Christian Engel Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 020 D-65926 Frankfurt am Main t: +49 69 305 12946 f: +49 69 305 80169 w:www.sanofi-aventis.de 125 Jahre Arzneimittel aus Deutschland von sanofi-aventis * Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias Braun, Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Heinz Riederer * -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot
Hi Christian, Had exactly the same problem (converting an mmCIF file into a PDB). I located and installed CIFTr . The version I have running here is ciftr-v2.053 . I am afraid I can't remember exactly where I downloaded it from. I think it one of the PDB associated files. Fred. Christian Engel wrote: Dear All, I am looking for a ccp4 program that reads in cif-files and converts them into pdb-files, including the CRYST1 card. Can anybody suggest a solution? I didn't find any in ccp4i, e.g. the coordinate utilities. I also tried COOT to read in cif-files (downloaded from the pdb server). For one example it crashed, for others it doesn't colour the bonds properly if Bonds (Colour by Atom) is chosen but shows all bonds in one colour. Is that a known feature? If I save these coordinates in pdb-format and try to read it back, I get an ERROR saying: Wrong ASCII format of an integer. Thanks for any suggestions Christian Engel */Mit freundlichen Grüßen / Best regards / Cordialement/* Dr. Christian Engel Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 020 D-65926 Frankfurt am Main t: +49 69 305 12946 f: +49 69 305 80169 w:_www.sanofi-aventis.de_ 125 Jahre Arzneimittel aus Deutschland von sanofi-aventis * Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias Braun, Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Heinz Riederer *
[ccp4bb] coot: rotate zone about arbitray point
Dear all, I would like to use Rotate/Translate Zone in coot for a single residue and set the centre of rotation at the nitrogen of the subsequent residue. Is there a why to achieve this with Coot Version 0.6.1? Cheers, Tim P.S.: The Torsion General would be a good start, but it does not seem to work with this twofold conformation in the .res-file of a shelxl-refinement. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Far to good r-factors
This would be a possible explanation, and certainly is a problem with low resolution refinements, but the free R indicates that overfitting is not the problem here. (I'm assuming that the proper choice of test set has been made in this case.) In my experience, for very isomorphous pairs of structures, when a high resolution model is used as the starting point for a low resolution refinement, even the R values before refinement will be very good and that means fitting the noise can't be the cause. Our methods today are simply not as good at fitting low resolution data in the absence of high resolution data as they are in its presence. Dale Tronrud On 06/01/10 04:51, Ian Tickle wrote: On Mon, May 31, 2010 at 9:15 PM, Dale Tronrud det...@uoxray.uoregon.edu wrote: One of the great mysteries of refinement is that a model created using high resolution data will fit a low resolution data set much better than a model created only using the low resolution data. It appears that there are many types of errors that degrade the fit to low resolution data that can only be identified and fixed by using the information from high resolution data. Is it such a mystery? Isn't it just a case of overfitting to the experimental errors in the low res data if you tried to use the same parameterization restraint weighting as for the high res refinement? Consequently you are forced to use fewer parameters and/or higher restraint weighting at low res which obviously is not going to give as good a fit. Cheers -- Ian
Re: [ccp4bb] coot: rotate zone about arbitray point
Tim Gruene wrote: I would like to use Rotate/Translate Zone in coot for a single residue and set the centre of rotation at the nitrogen of the subsequent residue. Is there a way to achieve this with Coot Version 0.6.1? No [1]. Paul. [1] Practically no, but actually, it might be. However it's so involved, creating and deleting dummy atoms, that its not worth mentioning.
Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot
Christian Engel wrote: Dear All, I am looking for a ccp4 program that reads in cif-files and converts them into pdb-files, including the CRYST1 card. Can anybody suggest a solution? I didn't find any in ccp4i, e.g. the coordinate utilities. I also tried COOT to read in cif-files (downloaded from the pdb server). For one example it crashed, for others it doesn't colour the bonds properly if Bonds (Colour by Atom) is chosen but shows all bonds in one colour. Is that a known feature? If I save these coordinates in pdb-format and try to read it back, I get an ERROR saying: Wrong ASCII format of an integer. Dear wwPDB mmCIF coordinate file users, I was rather surprised to read that reading a PDB mmCIF file caused Coot to crash. I was, however, able to reproduce this problem and have made a fix, which is making its way into binaries as we speak. It was due to the mmCIF file apparently making reference to chains for which coordinates (or any other atom or residue attributes) do not exist. Why is that happening? I don't know, but if it came to a choice between a broken mmCIF parser and a bogus mmCIF file, I'd plump for the latter. As to the colours, that is also due, IMHO to a bug^H^H^H issue in the mmCIF file. The atom names and elements in the mmCIF file are not quoted so they result in simple left-hand justified strings - such as N - whereas from the corresponding PDB file one would get an atom name of N and an element of N. These mmCIF simple strings don't match Coot's (or, i imagine, many other macromolecular file-reading program's) expectation of atom names and elements - hence it is not recognised and is represented in grey. Regards, Paul.
[ccp4bb] Linux on SGI O2 Unix Workstation
Hi All, I just obtained a Silicon Graphics O2 Unix workstation from 1996. I want to use it for 3D modelling of protein crystals using Crystal Eyes Stereographics and I'm wondering if anybody knows of any versions of Linux which I could install on it. Thanks, ~Brennan~
Re: [ccp4bb] Linux on SGI O2 Unix Workstation
http://en.wikipedia.org/wiki/SGI_Octane#Available_Operating_Systems just googled linux sgi o2 On Tue, 2010-06-01 at 10:18 -0600, Brennan Bonnet wrote: Hi All, I just obtained a Silicon Graphics O2 Unix workstation from 1996. I want to use it for 3D modelling of protein crystals using “Crystal Eyes Stereographics” and I’m wondering if anybody knows of any versions of Linux which I could install on it. Thanks, ~Brennan~ -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] How to align a sequence to a know profile
Does chainsaw not the opposite? Pruning a coordinate file based on non-conserved residues identified in a MSA? Yuan has a MSA of known structures and a sequence he wants to add to it. I am always keen to learn about alignment programs, it would be great to know how to use chainsaw for this problem. On Tue, Jun 1, 2010 at 02:20, Eleanor Dodson c...@ysbl.york.ac.uk wrote: chainsaw does just that eleanor 商元 wrote: Hello, everyone, I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Regards, Yuan SHANG
Re: [ccp4bb] How to align a sequence to a know profile
3-d coffee and expresso will align sequences without structures with sequences that do have structures in a structure-based sequence alignment: http://www.tcoffee.org/Projects_home_page/expresso_home_page.html perhaps this is along the lines of what Yuan is looking for? __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Tue, 1 Jun 2010, Thomas Juettemann wrote: Does chainsaw not the opposite? Pruning a coordinate file based on non-conserved residues identified in a MSA? Yuan has a MSA of known structures and a sequence he wants to add to it. I am always keen to learn about alignment programs, it would be great to know how to use chainsaw for this problem. On Tue, Jun 1, 2010 at 02:20, Eleanor Dodson c...@ysbl.york.ac.uk wrote: chainsaw does just that eleanor 商元 wrote: Hello, everyone, I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Regards, Yuan SHANG
Re: [ccp4bb] please recommend a crystallization incubator
Here is an incubator about the size of the Ecotherms but much cheaper: http://www.tritechresearch.com/DT2-MP-38.html We have one for insect cell culture that has worked great for several years, and there is no vibration. However for crystallization we have BOD incubators from Fisher. Nat On Mon, May 31, 2010 at 12:48 AM, Ho Leung Ng h...@confometrx.com wrote: I've been quite happy with our refrigerated BOD incubator from Fisher. Relatively inexpensive. ho
Re: [ccp4bb] How to align a sequence to a know profile
I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Hi Yuan, You can use UCSF Chimera's Multalign Viewer tool to do this. Just open your alignment with that tool and use the Edit-Add Sequence menu item to add your sequence to the alignment. UCSF Chimera: http://www.cgl.ucsf.edu/chimera/ Multalign Viewer tool: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/framemav.html specifically the Add Sequence part: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
