[ccp4bb] Coot: Residue number conflicts during model building
Dear all, I know I could use your help to work more effectively so here comes my questions. I am building a fairly long polypeptide chain (quite a few hundreds of aa) in Coot. I got the phases from Phenix, which traced much of the main chains for me already, with each fragments assigned with numbers that are apparently mismatched with the linear protein sequence. So, I begin to mutate/fit these Ala fragments (one piece at a time) into correct residues using Coot and also try to correct their numbers by doing "renumber residues". The outcome is that now I have overlapped numbers as I move along, prohibiting me to do real-space refinement effectively. How to get around with this? Thank you! Also, are there any easily accessible programs that could help me build these side-chains based on the very good experimental density map currently at 2.3A? Thanks, Jacob Wong
Re: [ccp4bb] Please help with Raster3D (linux version)
On Tuesday, May 03, 2011 02:00:26 pm jie liu wrote: > Dear All > > I tried to make a stereo picture using Raster3D installed on a linux box with > the following command: > stereo3d -tiff xxx.tif < xxx.r3d > > but got an error message: > stereo3d: normal3d seems to be OK > stereo3d: rendering left eye view > stereo3d: rendering right eye view > stereo3d: joining left and right images > montage: missing an image filename `/usr/tmp/16143_stereo3d.tiff'. > Stereo image size x > mv: cannot stat `/usr/tmp/16143_stereo3d.tiff': No such file or directory I see this problem on one of my machines also. I don't at the moment know why tiff files are a problem, but at least for me it works fine to make a png file instead and then convert it to tiff later if necessary: stereo3d < xxx.r3d > xxx.png convert xxx.png xxx.tiff Meanwhile, thank you for bringing the tiff failure to my attention. I'll see if I can track down a fix. Ethan > > No stereo image of xxx.tif was output, instead, it produced a file called > render.tif in the working directory which is not a stereo one. Interestingly, > the same xxx.r3d input file worked fine with "render", indicating the input > file itself is OK. > > Then I tried to make a PNG image: stereo3d < name.r3d > name.png > it gave the following information: > stereo3d: normal3d seems to be OK > stereo3d: rendering left eye view > stereo3d: rendering right eye view > stereo3d: joining left and right images > Stereo image size 500x500 > > The message looked fine, and the produced picture in the working directory > seemed to have correct image size of 1000X500, but the image showed nothing > except plain grey background. > > Your help is appreciated. > > Jie > -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] Please help with Raster3D (linux version)
Dear All I tried to make a stereo picture using Raster3D installed on a linux box with the following command: stereo3d -tiff xxx.tif < xxx.r3d but got an error message: stereo3d: normal3d seems to be OK stereo3d: rendering left eye view stereo3d: rendering right eye view stereo3d: joining left and right images montage: missing an image filename `/usr/tmp/16143_stereo3d.tiff'. Stereo image size x mv: cannot stat `/usr/tmp/16143_stereo3d.tiff': No such file or directory No stereo image of xxx.tif was output, instead, it produced a file called render.tif in the working directory which is not a stereo one. Interestingly, the same xxx.r3d input file worked fine with "render", indicating the input file itself is OK. Then I tried to make a PNG image: stereo3d < name.r3d > name.png it gave the following information: stereo3d: normal3d seems to be OK stereo3d: rendering left eye view stereo3d: rendering right eye view stereo3d: joining left and right images Stereo image size 500x500 The message looked fine, and the produced picture in the working directory seemed to have correct image size of 1000X500, but the image showed nothing except plain grey background. Your help is appreciated. Jie
Re: [ccp4bb] Dehydration treatments
Israel, Here is a paper that describes a phenomenon like what you have observed: Structure. 2003 Feb;11(2):139-45. Dehydration converts DsbG crystal diffraction from low to high resolution. Heras B, Edeling MA, Byriel KA, Jones A, Raina S, Martin JL. And another review that touches briefly on the idea, among other things: Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1173-80. Epub 2005 Aug 16. Post-crystallization treatments for improving diffraction quality of protein crystals. Heras B, Martin JL. Mike - Original Message - From: "Israel Sanchez" To: CCP4BB@JISCMAIL.AC.UK Sent: Sunday, May 1, 2011 10:32:21 AM GMT -08:00 US/Canada Pacific Subject: [ccp4bb] Dehydration treatments Hi folks, I am currently impressed by the efficiency of dehydration treatments over the diffraction capacity of our crystals in one particular condition. Without any treatment the crystals seldom diffract to 20-30A but in our last synchrotron trip the very same crystals, after been incubated with increasing concentration of low molecular weight PEGs diffracted to 6A. I was wondering if anyone has studied these effects in a systematic way. Does anyone on the ccp4bb knows references or has any experience/pseudo-religious believes that do not care to share with the community about this particular topic? Thank you very much in advance -- Israel Sanchez Fernandez PhD Ramakrishnan-lab MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
[ccp4bb]
On Tue, 2011-05-03 at 18:06 +0100, Ian Tickle wrote: > So Ed, it's not just > relevant to the "Wu&Kabat numbering for antibodies". Obviously, it was meant to be an example of use, not the only example. > The idea that > one would _not_ use consistent numbering (and therefore insertion > codes) across species (viral, fungal, plant and animal so there is > huge sequence variability with insertions & deletions everywhere), > when working with these structures is frankly ludicrous. Personally I don't care one way or the other, but it may be pointed out that if D25 is actually number 37 in a homologous protein, it should be D37. Just as acknowledgement of the (somewhat purist) point of view that the residue number should denote its linear distance from the N-terminus. It's a little different with antibodies, of course, as each individual one is not an entirely inherited gene. Cheers, Ed. -- "Hurry up before we all come back to our senses!" Julian, King of Lemurs
[ccp4bb] INSERTION CODE
Just giving this thread a title. James On May 3, 2011, at 10:06 AM, Ian Tickle wrote: > James, interesting that you chose residue number 32 for your example, > because that is the number of one of the two active-site ASPs in the > aspartic proteinase family (the other is ASP 215) that I (with Tom > Blundell & others) worked on for many years. So Ed, it's not just > relevant to the "Wu&Kabat numbering for antibodies". The idea that > one would _not_ use consistent numbering (and therefore insertion > codes) across species (viral, fungal, plant and animal so there is > huge sequence variability with insertions & deletions everywhere), > when working with these structures is frankly ludicrous. I recall > some programs (FRODO was one) actually required renumbering to the > ordinals, i.e. 1, 2, 3 ... - that is until I fixed it! This caused > endless confusion, not least because there are often other ASPs in the > vicinity of the active site which could easily get renumbered to 32. > For me, it's important that when I refer to 'ASP 32' there's no > possibility that I mean anything other than the active site ASP! > > Cheers > > -- Ian > > On Tue, May 3, 2011 at 5:17 PM, James Holton wrote: >> >> My understanding is that it was introduced for cases where an error in the >> sequence was discovered long after a large body of literature had >> accumulated for the "wrong" sequence. That is, imagine some enzyme where an >> important catalytic active site residue was number "152", and lots of people >> had been talking about this residue for years. Then, when you solve the 3D >> structure, you discover that there is actually a glycine between residues >> "32" and "33", what do you do? Do you change 152 to 153 and put up with all >> the angry letters from enzymologists, telling you that you mislabeled this >> important residue? In case you don't want to do this, the PDB allows you to >> put in a residue "32A". Deletions can happen too, but they are easier to >> deal with from a file format standpoint. >> >> -James Holton >> MAD Scientist >> >> On 5/3/2011 6:27 AM, Jahan Alikhajeh wrote: >> >> Dear Friends, >> I have noticed an issue in a pdb file, the term "insertion code". >> Does anyone know anything about it? what is it used for? >> Thanks in Advance, >> >> >> Jahan Alikhajeh, Ph.D, >> >> Technical Supervisor, >> >> MAN Corporation LTD, >> >> Keshavarz Boulevard, >> >> Ghods Avenue No. 41, >> >> 5th Floor, Tehran, Iran, 14177, >> >> Tel: +982166282841 >> >> Fax: +982166282997 >> >>
[ccp4bb] Postdoctoral position available: Structural biology of human tight junction membrane proteins
Postdoctoral Position Available Laboratory of Professor Robert M. Stroud, Ph.D. Department of Biochemistry and Biophysics University of California San Francisco, USA SUMMARY DESCRIPTION: Structural biology of human tight junction membrane proteins The Stroud Laboratory seeks a postdoctoral fellow to pursue the structural characterization of a family of integral membrane proteins critical to tight junction formation and function. These proteins are widely expressed and are implicated in the pathogenesis of many human diseases, including breast and ovarian cancers, inflammatory bowel disease, inherited deafness, hepatitis virus infection, and renal tubule electrolyte transport disorders. As this work is funded by a NIH PSI Biology grant, the successful candidate will work with top-tier biological collaborators. The successful candidate will have the opportunity to: 1. Express biologically relevant integral membrane proteins in a variety of systems (mammalian, insect, yeast, bacterial) 2. Purify target membrane proteins to homogeneity 3. Crystallize and determine the macromolecular structure of these proteins, both alone, and, where applicable, in complex with their ligand(s) START DATE: Immediately REQUIREMENTS: 1. Experience in the expression of eukaryotic proteins using eukaryotic systems 2. Some experience in protein purification and biochemical characterization 3. A desire to learn about membrane protein biochemistry and macromolecular protein crystallography. APPLICATION: Please send (1) your CV, (2) your resume, describing your relevant skills, and (3) a list of three references to: stroud...@gmail.com
[ccp4bb]
James, interesting that you chose residue number 32 for your example, because that is the number of one of the two active-site ASPs in the aspartic proteinase family (the other is ASP 215) that I (with Tom Blundell & others) worked on for many years. So Ed, it's not just relevant to the "Wu&Kabat numbering for antibodies". The idea that one would _not_ use consistent numbering (and therefore insertion codes) across species (viral, fungal, plant and animal so there is huge sequence variability with insertions & deletions everywhere), when working with these structures is frankly ludicrous. I recall some programs (FRODO was one) actually required renumbering to the ordinals, i.e. 1, 2, 3 ... - that is until I fixed it! This caused endless confusion, not least because there are often other ASPs in the vicinity of the active site which could easily get renumbered to 32. For me, it's important that when I refer to 'ASP 32' there's no possibility that I mean anything other than the active site ASP! Cheers -- Ian On Tue, May 3, 2011 at 5:17 PM, James Holton wrote: > > My understanding is that it was introduced for cases where an error in the > sequence was discovered long after a large body of literature had > accumulated for the "wrong" sequence. That is, imagine some enzyme where an > important catalytic active site residue was number "152", and lots of people > had been talking about this residue for years. Then, when you solve the 3D > structure, you discover that there is actually a glycine between residues > "32" and "33", what do you do? Do you change 152 to 153 and put up with all > the angry letters from enzymologists, telling you that you mislabeled this > important residue? In case you don't want to do this, the PDB allows you to > put in a residue "32A". Deletions can happen too, but they are easier to > deal with from a file format standpoint. > > -James Holton > MAD Scientist > > On 5/3/2011 6:27 AM, Jahan Alikhajeh wrote: > > Dear Friends, > I have noticed an issue in a pdb file, the term "insertion code". > Does anyone know anything about it? what is it used for? > Thanks in Advance, > > > Jahan Alikhajeh, Ph.D, > > Technical Supervisor, > > MAN Corporation LTD, > > Keshavarz Boulevard, > > Ghods Avenue No. 41, > > 5th Floor, Tehran, Iran, 14177, > > Tel: +982166282841 > > Fax: +982166282997 > >
[ccp4bb]
Hi James, The concept of insertion code arose when one species was sequenced and studied and then it turned out that there were both insertions and deletions in the sequence of the analogous molecule for some other species. In analyzing and discussing structure, e.g. the catalytic triad of serine proteases, it is helpful if the residue numbering is aligned between species. In all code using PDB entries it is important to use the chain identifier, residue number, and insertion code to uniquely identify a residue. 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 Tue, 3 May 2011, James Holton wrote: My understanding is that it was introduced for cases where an error in the sequence was discovered long after a large body of literature had accumulated for the "wrong" sequence. That is, imagine some enzyme where an important catalytic active site residue was number "152", and lots of people had been talking about this residue for years. Then, when you solve the 3D structure, you discover that there is actually a glycine between residues "32" and "33", what do you do? Do you change 152 to 153 and put up with all the angry letters from enzymologists, telling you that you mislabeled this important residue? In case you don't want to do this, the PDB allows you to put in a residue "32A". Deletions can happen too, but they are easier to deal with from a file format standpoint. -James Holton MAD Scientist On 5/3/2011 6:27 AM, Jahan Alikhajeh wrote: Dear Friends, I have noticed an issue in a pdb file, the term "insertion code". Does anyone know anything about it? what is it used for? Thanks in Advance, Jahan Alikhajeh, Ph.D, Technical Supervisor, MAN Corporation LTD, Keshavarz Boulevard, Ghods Avenue No. 41, 5th Floor, Tehran, Iran, 14177, Tel: +982166282841 Fax: +982166282997
[ccp4bb]
My understanding is that it was introduced for cases where an error in the sequence was discovered long after a large body of literature had accumulated for the "wrong" sequence. That is, imagine some enzyme where an important catalytic active site residue was number "152", and lots of people had been talking about this residue for years. Then, when you solve the 3D structure, you discover that there is actually a glycine between residues "32" and "33", what do you do? Do you change 152 to 153 and put up with all the angry letters from enzymologists, telling you that you mislabeled this important residue? In case you don't want to do this, the PDB allows you to put in a residue "32A". Deletions can happen too, but they are easier to deal with from a file format standpoint. -James Holton MAD Scientist On 5/3/2011 6:27 AM, Jahan Alikhajeh wrote: Dear Friends, I have noticed an issue in a pdb file, the term "insertion code". Does anyone know anything about it? what is it used for? Thanks in Advance, Jahan Alikhajeh, Ph.D, Technical Supervisor, MAN Corporation LTD, Keshavarz Boulevard, Ghods Avenue No. 41, 5th Floor, Tehran, Iran, 14177, Tel: +982166282841 Fax: +982166282997
Re: [ccp4bb] difference simulated annealing map
Hi, what is the difference simulated annealing map and how can i generate it > - difference map is a Fourier synthesis i*Fo-j*Fc, where i and j are some weights, and Fo and Fc are observed and calculated amplitudes of structure factors; - "difference simulated annealing map" is the above map calculated after a SA run; - "how can i generate it": a possible option: phenix.refine (and phenix.maps) will do it: http://www.phenix-online.org Hope this helps, Pavel.
[ccp4bb] Ultrafiltration membrane filters
Hi All, I was wondering if anyone had troubles with PES (Polyethersulfone) ultrafiltration membrane filters (Vivaspin, Amicon,...) using 5 mM DTT containing buffer. It seems whether or not it is possible for DTT to react with sulfone groups of the membrane and in this way to "crosslink" my cystein rich protein (I can't recover after ultrafiltration neither in the retentate vial nor in the filtrate vial). I was wondering if using regenerated cellulose ultrafiltration membrane (now relatively difficult to find in labs) might be a solution to overcome this problem. Thanks, Seb - __ Dr Sébastien VIOLOT - Maître de conférences Equipe BioCristallographie des Cibles Thérapeutiques Bases Moléculaires et Structurales des Systèmes Infectieux BMSSI - UMR 5086 CNRS - Université Lyon 1 Institut de Biologie et Chimie des Protéines (IBCP) - FR 3302 7, passage du Vercors - 69367 LYON cedex 07 - FRANCE E-Mail: sebastien.vio...@ibcp.fr http://www.ibcp.fr Tel: +33 (0)4 37 65 29 04 http://www.ibcp.fr/rhaser/ Fax: +33 (0)4 72 72 26 16 <>
[ccp4bb] difference simulated annealing map
what is the difference simulated annealing map and how can i generate it haytham wahba Ph.D student Biochemistry Dep UdeM
[ccp4bb]
On Tue, 2011-05-03 at 13:27 +, Jahan Alikhajeh wrote: > term "insertion code". > Does anyone know anything about it? what is it used for? It may be used to follow Wu&Kabat numbering for antibodies. Frankly, it it is something that can be easily avoided (after all, 32A is simply the 33rd residue). -- "Hurry up before we all come back to our senses!" Julian, King of Lemurs
[ccp4bb]
I suggest that you go to the PDB web site and look through the format documentation for the description of ATOM records. Frances Bernstein = 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 Tue, 3 May 2011, Jahan Alikhajeh wrote: Dear Friends, I have noticed an issue in a pdb file, the term "insertion code". Does anyone know anything about it? what is it used for? Thanks in Advance, Jahan Alikhajeh, Ph.D, Technical Supervisor, MAN Corporation LTD, Keshavarz Boulevard, Ghods Avenue No. 41, 5th Floor, Tehran, Iran, 14177, Tel: +982166282841 Fax: +982166282997
[ccp4bb]
Dear Friends, I have noticed an issue in a pdb file, the term "insertion code". Does anyone know anything about it? what is it used for? Thanks in Advance, Jahan Alikhajeh, Ph.D, Technical Supervisor, MAN Corporation LTD, Keshavarz Boulevard, Ghods Avenue No. 41, 5th Floor, Tehran, Iran, 14177, Tel: +982166282841 Fax: +982166282997
[ccp4bb] Postdoctoral position in structural virology
Post Doctoral Position in structural studies of Respiratory Syncytial Virus proteins. A post-doctoral position in protein crystallography is available in the group of Dr Marcel Knossow at the Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, Gif-sur-Yvette, France. The contract will be initially for a period of 1 year, with a net monthly salary of about 1900 €. The Respiratory Syncytial Virus (RSV) is the major causal agent of bronchiolitis in human. We have initiated a structural and biochemical characterization of RSV proteins in collaboration with a group of virologists at INRA (see Tran et al. (2009) J Virol, 83:6363-74). The project will focus on the M2-1 protein, a transcription factor which is part of the ribonucleoprotein complex in which it interacts with the phosphoprotein P. We aim to determine the structure of M2-1 alone and in complex with P. The project also includes the characterization of the interaction of M2-1 with cellular proteins we have recently identified. Ideally the candidate will have experience in protein crystallization and crystallography and an interest in biochemical studies of protein-protein interactions. The lab is located in a multidisciplinary life sciences campus, 40 minutes by direct train from the centre of Paris. The LEBS has all the equipment required for protein purification and characterization by biochemical and biophysical methods. Crystallization robotics and X-ray diffraction equipment are also available in-house or in the campus and we have regular access to synchrotron sources (ESRF at Grenoble or the nearby SOLEIL synchrotron). To apply, please send a CV, a short summary of your research experience and the names and contact information of two referees by e-mail to: Dr. Benoît Gigant (gig...@lebs.cnrs-gif.fr) *** Benoit Gigant LEBS - CNRS Bat 34 1, avenue de la Terrasse 91198 Gif-sur-Yvette Tel 33 1 69 82 35 01 Fax 33 1 69 82 31 29 gig...@lebs.cnrs-gif.fr Web page: http://www.lebs.cnrs-gif.fr/knossow/knossowang.html ***
Re: [ccp4bb] problem with cif file for a new ligand in Coot
On 03/05/11 14:08, Nalam, Madhavi wrote: Hello all: I am trying to generate a cif file for a new ligand using PRODRG server. The server generates cif file without any problem. The problem comes when I try to load the cif file in Coot and try to model the ligand into the electron density. It gives an error message like this.. -- Failed to match (to the dictionary) the following model atom names: XXX "Cl38" "Cl39" That would cause exploding atoms, so the refinement didn't start --- This problem never occurred to me before whenever I generate new cif files. The ligand has two chlorine atoms. I tried to give different three letter codes for the ligand assuming the three letter code I gave may already be in the dictionary and that is why it is giving me the error message. I get the same message irrespective of changing the three letter code. I also tried generating a cif file by running it through Refmac5 (the job fails and gives me a cif file which I used in Coot) and again I ended up with the same message. Check that the dictionary names and the atom elements for the Cl atoms are upper-cased in both the PDB file and the dictionary. Paul.
[ccp4bb] problem with cif file for a new ligand in Coot
Hello all: I am trying to generate a cif file for a new ligand using PRODRG server. The server generates cif file without any problem. The problem comes when I try to load the cif file in Coot and try to model the ligand into the electron density. It gives an error message like this.. -- Failed to match (to the dictionary) the following model atom names: XXX "Cl38" "Cl39" That would cause exploding atoms, so the refinement didn't start --- This problem never occurred to me before whenever I generate new cif files. The ligand has two chlorine atoms. I tried to give different three letter codes for the ligand assuming the three letter code I gave may already be in the dictionary and that is why it is giving me the error message. I get the same message irrespective of changing the three letter code. I also tried generating a cif file by running it through Refmac5 (the job fails and gives me a cif file which I used in Coot) and again I ended up with the same message. Does anyone know what's happening? Thanks and have a nice day, Madhavi
Re: [ccp4bb] ccp4 on Mac Intel
Charles and Guillermo, thanks a zillion. Shame on me, I could't find the scripts! Well, it'll be good to have already v. 6.2 ... ciao, s On May 3, 2011, at 11:26 AM, Charles Ballard wrote: > Hi Sebastiano > > you open an X11 windows, then source > /Applications/ccp4-6.2.0/bin/ccp4.setup-sh . All the paths should then be > set. > > Charles Ballard > CCP4 > > On 3 May 2011, at 09:30, Sebastiano Pasqualato wrote: > >> >> Dear all, >> I have installed ccp4 with the dmg package, and everything is installed >> nicely in the Application folder, and I can get ccp4i working just by >> launching from the ccp4 icon. >> However, I would also like to have the commands working from a X11 terminal, >> to get it working for, say xia2. >> How do I source this ccp4 installation? >> Thanks a lot in advance, >> ciao, >> s >> >> -- >> Sebastiano Pasqualato, PhD >> Crystallography Unit >> IFOM-IEO Campus >> Cogentech - Consortium for Genomic Technologies >> via Adamello, 16 >> 20139 - Milano >> Italy >> >> tel +39 02 9437 5172 >> fax +39 02 9437 5990 >> >> >> >> >> >> > > > -- > Scanned by iCritical. > > -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990
Re: [ccp4bb] ccp4 on Mac Intel
Hi Klaus, that's pretty much the point. With the .dmg install, there are no "setup" files coming. I know I could use fink and Bill Scott's way to install the package, and have everything running, but was wondering if it would have been possible with the .dmg installation, much faster and intuitive. I also have this suggestion from Louis Vanpraet (thank you) Add the following line to the ".profile" file in your home folder alias ccp4i='/Applications/ccp4-6.1.13/bin/./ccp4i' Then you can launch it in any terminal window by executing "ccp4i" but I was more looking in something like the source of the 'setup' files, so that I can have all the commands and not only ccp4i available from the X11 prompt. Thanks, ciao, s On May 3, 2011, at 11:06 AM, Klaus Fütterer wrote: > Dear Sebastiano, > > locate the setup scripts (e.g. ccp4.setup, ccp4.setup-sh) on your system > (must be somewhere in the ccp4 directories), > and source it in your .cshrc or .bshrc files (so that every time you open a > c-shell or bash, the necessary aliases are established). > > For instance in my case the line in .cshrc (I"m using C-shell): > source /sw/share/xtal/ccp4-6.0.2/include/ccp4.setup > > Best, > > Klaus > > === > >Klaus Fütterer, Ph.D. >Reader in Structural Biology > Undergraduate Admissions > > School of Biosciences P: +44-(0)-121-414 5895 > University of BirminghamF: +44-(0)-121-414 5925 > Edgbaston E: k.futte...@bham.ac.uk > Birmingham, B15 2TT, UK W: http://tinyurl.com/futterer-lab > === > > > > > > On 3 May 2011, at 09:30, Sebastiano Pasqualato wrote: > >> >> Dear all, >> I have installed ccp4 with the dmg package, and everything is installed >> nicely in the Application folder, and I can get ccp4i working just by >> launching from the ccp4 icon. >> However, I would also like to have the commands working from a X11 terminal, >> to get it working for, say xia2. >> How do I source this ccp4 installation? >> Thanks a lot in advance, >> ciao, >> s >> >> -- >> Sebastiano Pasqualato, PhD >> Crystallography Unit >> IFOM-IEO Campus >> Cogentech - Consortium for Genomic Technologies >> via Adamello, 16 >> 20139 - Milano >> Italy >> >> tel +39 02 9437 5172 >> fax +39 02 9437 5990 >> >> >> >> >> >> > -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990
Re: [ccp4bb] reproducibility of protein crystals
sometimes， a little bit change of concentration of your precipitate or pH buffer can affect your crystal. My suggestion is setup a appropriate gradient of your precipitate and additive.
[ccp4bb] ccp4 on Mac Intel
Dear all, I have installed ccp4 with the dmg package, and everything is installed nicely in the Application folder, and I can get ccp4i working just by launching from the ccp4 icon. However, I would also like to have the commands working from a X11 terminal, to get it working for, say xia2. How do I source this ccp4 installation? Thanks a lot in advance, ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990
