Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Dear All, Thanks for your suggestions! I ended up using the areaimol program in ccp4. My next question: Given a list of accessible surface area, is there a generally accepted value of ASA above which a residue classifies as a surface residue, while below this number it is an interior residue? Thanks! and all the best, --Buz On Nov 2, 2010, at 10:56 AM, Tim Gruene wrote: Hello Buz, I do not know what you mean by 'linear map', but according to its manual, the ccp4-program surface writes a list of accessible are per atom per residue, which you could convert into the total fraction per residue with not too much effort. Is this what you are looking for? Cheers, Tim On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
[ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz
[ccp4bb] Advice on Over-expressing and Purifying Metalloproteins
Dear all, I am trying to purify a metalloprotein (a hydrogenase) using affinity chromatography. I have produced two tagged versions of the enzyme: one with an N-terminal 6x histidine affinity tag, and the other with a C-terminal 6x his-tag. The tagged proteins are both tied to an IPTG-inducible promoter. When trying to express and purify the N-terminal tagged protein, I have found that almost all of the expressed protein goes into inclusion bodies when the culture is grown at 37 or at 30 degrees C. When the culture is grown at 20 degrees C, a small amount of protein can be found in the cell extract. Unfortunately, as the enzyme has several oxygen-sensitive metal clusters, we do not believe that the protein can be refolded from the inclusion bodies. Could you offer some advice on how to express and purify this protein and reduce the quantity of protein found in inclusion bodies? Thanks! and all the best, --Buz
[ccp4bb] Summary of Extracting Amino Acid Sequence from PDB File
Dear All, Thanks to everyone who replied to my query about extracting an amino acid sequence from a PDB file! Here is a summary of responses of my query; 1. Use SwissPDBViewer 2. Use Pymol 1.2 load $TUT/1hpv.pdb save 1hpv.fasta # or by selection save 1hpv_A.fasta, chain A 3. With Phenix, you can use the phenix.print_sequence tool to output the sequence in FASTA format. 4. If the PDB file is in the PDB, you can download the primary sequence from here. 5. Use MOLEMAN2 6. Use PDBSET (part of CCP4) All the best, ---Buz
[ccp4bb] Extracting Amino Acid Sequence from PDB File
Hi All, Does anyone know of a program that can extract the amino sequence of a protein from a PDB file and output it as a FASTA file? Thanks! and all the best, --Buz
Re: [ccp4bb] Extracting Amino Acid Sequence from PDB File
Thanks Mark! --buz On Aug 13, 2009, at 5:45 PM, Dr. Mark Mayer wrote: try PDBSET (ccp4) Hi All, Does anyone know of a program that can extract the amino sequence of a protein from a PDB file and output it as a FASTA file? Thanks! and all the best, --Buz -- +++ Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://snb.nichd.nih.gov/index.htm Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892
[ccp4bb] Protein Sequence Analysis Software
Dear all, I'm sorry for the somewhat non-ccp4 related questions, but here goes; 1. Could anyone recommend a good mailing list for bioinformatics related problems, where I might be able to re-ask question 2. 2. Does anyone know of some good software for visualization of the domain analysis of the primary sequence of a protein? What I would like to do is search a protein sequence, or most preferably, a multiple alignment of protein sequences for conserved domains against the pfam database, and then visualize the results. Preferably, I would like a output to be in a vector format. Thanks! and all the best, --Buz
Re: [ccp4bb] Adding Non-natural Base to RNA Model in Coot
Hi Paul, Thanks for your help on this! I've finished sketching up 2AP in sketcher. However, I'm sure that several of the bond lengths in the nucleotide base are now non-ideal. Is there a way to idealize them before importing them into coot? Thanks! and all the best, --Buz On Mar 28, 2009, at 8:37 AM, Paul Emsley wrote: Buz Barstow wrote: Dear All, I'd like to add substitute a natural base (adenine) for a non- natural base (2-aminopurine), in a molecular model of an RNA molecule. I'd like to do this with CCP4 and Coot. Could I ask for some help please? The CCP4 way would be to use sketcher and search for aminopurines. You will find 2,6-diaminopurine (1AP). Load this up and delete the 6-amino group to convert to 2-aminopurine. Save the coordinates and dictionary (give it a new name). Fire up coot and File - Import CIF dictionary... Centre on the residue you want to substitute Extensions - Modelling - Replace residue - 1AP (or whatever you called it). (If you have a map loaded when you do this, it will try to fit to that as a final step) Paul.
Re: [ccp4bb] Adding Non-natural Base to RNA Model in Coot
Hi Bill, Sorry if my first message was confusing. I do want to convert from A to 2AP. I'm working on following Paul Emsley's suggestions. Thanks! and all the best, --Buz On Mar 28, 2009, at 11:48 AM, William Scott wrote: On Sat, March 28, 2009 5:37 am, Paul Emsley wrote: Buz Barstow wrote: Dear All, I'd like to add substitute a natural base (adenine) for a non- natural base (2-aminopurine), in a molecular model of an RNA molecule. I'd like to do this with CCP4 and Coot. Could I ask for some help please? The CCP4 way would be to use sketcher and search for aminopurines. You will find 2,6-diaminopurine (1AP). Load this up and delete the 6-amino group to convert to 2-aminopurine. Save the coordinates and dictionary (give it a new name). Fire up coot and File - Import CIF dictionary... Centre on the residue you want to substitute Extensions - Modelling - Replace residue - 1AP (or whatever you called it). (If you have a map loaded when you do this, it will try to fit to that as a final step) Paul. I may be mistaken, but I thought he was asking how to mutate from 2AP to A. (If you use simple mutate, you get a menu of 20 amino acids to choose from.) Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
[ccp4bb] Adding Non-natural Base to RNA Model in Coot
Dear All, I'd like to add substitute a natural base (adenine) for a non-natural base (2-aminopurine), in a molecular model of an RNA molecule. I'd like to do this with CCP4 and Coot. Could I ask for some help please? Thanks! and all the best, --Buz
[ccp4bb] Software for Drawing Protein Secondary Structure
Dear All, Does anyone know of a program that is capable of drawing the secondary structure of a protein molecule? I'd really like to be able to take a protein molecule, and draw the secondary structure out along a line, indicating the positions of secondary structural elements like sheets and helices. Thanks! and all the best, --Buz
Re: [ccp4bb] Activity of a mutant enzyme compared to wild type - puzzle
Hi Subbu, Here's my two cents. Your project sounds really interesting. You mentioned in your email that the active site and associated waters in the active site of the wild type and mutant enzymes are identical. It's worth noting that even very small (on the 1/10th of an angstrom level) structural perturbations can have impacts on protein function. When high pressure is applied to some enzymes, their activities can be affected by factors of 2 or 4, or perhaps even more. The structural deformations due to high pressures (1000 x atmospheric) are often on the sub-angstrom level. If you have sufficient crystals, I might be tempted to re-solve the mutant and wild type structure a few times with fresh data, and get a feel for how much error exists is in the position of key residues. This might tell you how close the geometry of the two active sites really are. Good luck! and all the best, --Buz On Jun 11, 2008, at 8:21 PM, Narayanan Ramasubbu wrote: Dear all: I have a single residue mutant whose enzyme activity is about 50% of the wild type. Interestingly, the mutation is in a region that involves a secondary site but not the active site. The two structures with or without ligands fit well (0.18 A) and the metal binding and cofactor binding sites are all preserved in the mutant. The one difference noticed is that the ligand does not fill the active site (partially occupied subsites) unlike the wild type where all the subsites are occupied. Water structure around the actives site residues are identical. I looked at the electrostatics and both surfaces look similar (not an expert). There are some residues whose sides chains show some positional disorder and these residues are at the edges of the active site. The resolution of the both data sets are 1.5A. The mutant enzyme was derived by MR. One another possibility that I want to look at is to compare the compactness of the two enzyme structures. What is the best way to compare that? I am wondering whether the breathing that was mentioned for some enzymes might be playing a role in the mutant enzyme. Also, I would appreciate comments on other possible explanations for this unusual (?) behavior. Thanks a lot Subbu
Re: [ccp4bb] Installing coot on MacOSX 10.5
Hi Bill, Thanks for your advice! Ruby now installs on my machine, as does Coot (which is what I really wanted). Unfortunately, coot is unhappy with my X11 install. When I run coot, I get the following error: dyld: Library not loaded: /usr/X11/lib/libfontconfig.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 5.0.0 or later, but libfontconfig.1.dylib provides version 3.0.0 Trace/BPT trap I'm using X11 version 2.1.1 (xorg-server 1.3.0-apple5) - the version that came with OS X 10.5.2. Is there a way to get coot to look at an updated version of the library. Thanks! and all the best, --Buz On Apr 17, 2008, at 3:39 PM, William Scott wrote: Dear Chris et al, My guess is something needs ruby built as a build-time dependency, but coot doesn't require it. In any case, I've got the latest version of ruby built and anyone who needs it can download it from one of my servers as described on this page: http://tinyurl.com/h2lzq That saves you the overhead of compiling stuff. You can just download precompiled debian packages and have fink unpack them for you. HTH, Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Apr 17, 2008, at 11:51 AM, Chris Richardson wrote: On 17 Apr 2008, at 6:07 PM, Buz Barstow wrote: I'm having trouble installing coot on MacOSX 10.5.2 on my MacBook Pro (Core Duo model). I would like to install coot using fink, but am getting stuck when it comes to installing ruby. Has anyone else experienced this problem? I've spent the afternoon doing a clean rebuild of a fink installation on an iMac (Core 2 Duo) running Tiger 10.4.11, and the process also died at updating ruby. Poking around on Google yields several people with the same problem, but none with a solution. The fink-devel mailing list saw the problem yesterday, so a fix may be forthcoming soon. Regards, Chris The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Installing coot on MacOSX 10.5
Hi Bill Up until a moment ago, my installed fink packages (matching librsvg2) were; librsvg2 2.9.5-11 SAX-based render library for SVG files librsvg2-bin 2.9.5-11 SAX-based render library for SVG files i librsvg2-gtk 2.9.5-11 Enable GTK to use SVG data librsvg2-mozilla 2.9.5-1011 Mozilla plugin for SVG files librsvg2-mozilla-dev 2.9.5-1011 Mozilla plugin for SVG files i librsvg2-shlibs 2.9.5-11 SAX-based render library for SVG files I installed librsvg2 and librsvg2-bin, but still experience the same problems with coot, even after restarting x11. Thanks! and all the best, --Buz On Apr 17, 2008, at 5:47 PM, William Scott wrote: I have i librsvg22.9.5-11SAX-based render library for SVG files i librsvg2-gtk2.9.5-11Enable GTK to use SVG data i librsvg2-shlibs 2.9.5-11SAX-based render library for SVG files Do you have all of those installed? If not, the package is missing a dependency and I should fix it. Let me know if that cures the problem. Sorry Bill On Apr 17, 2008, at 2:34 PM, Buz Barstow wrote: Hi Bill, Thanks a lot for your advice. Coot now installs and runs, however, I do get some warnings; ** (coot:20738): WARNING **: Error loading pixmap file: /sw/share/ coot/pixmaps/connect-to-ccp4.svg ** (coot:20738): WARNING **: Error loading pixmap file: /sw/share/ coot/pixmaps/connect-to-oca.svg
[ccp4bb] Calculation of Selection Volumes
Dear All, I'd like to find a way to calculate the volume of an arbitrary selection of atoms in a protein structure. Could anyone suggest a program that could perform this task, ideally, one that could be called from inside pymol and calculate the volume of a pymol selection? Thanks! and all the best, --Buz
[ccp4bb] Crystallographic Experiment with NADH and a Flavoprotein
Dear All, I'm planning an experiment to study the oxidation of NADH by a flavoprotein at cryogenic temperatures to facilitate collection of X- ray diffraction data. In planning this experiment, I have seen a few obstacles that I am looking for help in overcoming. 1. There are no structures in the PDB that are complexed with NADH or NAD2H. Has anyone ever attempted to solve a structure complexed with NADH or NAD2H, especially at cryogenic temperatures, and if so, what are the difficulties? Does NAD+ de-bind from the protein too fast to permit data collection? 2. NADH oxidation typically takes less than a second by a flavoprotein at room temperature. Is there an NADH or NAD2H analog that has a much longer half time for oxidation by a flavoprotein, for example tens of minutes, rather than tenths of a second, and can this analog still be oxidized at cryogenic temperatures, with a reasonable half time, of several hours or so? Thanks! and all the best, --Buz
