[ccp4bb] Last beamtime on BM14 before ESRF Upgrade shutdown period
Dear all, the period November - December 2011 is opened for beamtime e-proposal requests at the BM14 MAD MX Beamline (ESRF, Grenoble, France) . This is the last period time before the ESRF Upgrade winter shutdown [Dec-5th 2011 -- April 30th 2012 ]. Thank you to submit your proposal on-line http://www.bm14.eu (“Apply for Beamtime”). We provide travel and subsistence funding to EU-member and EU-associated state users[1]. * * *Beamline features:* * * - Easily tuneable energy over 7 to 17 keV - MarMosaic 225 CCD detector - MD2 Microdiffractometer with mini-Kappa goniometer head - Robotic Sample changer (SPINE standard sample holders are mandatory) - Very low resolution beamstop: permits diffraction to be recorded down to 300 Å - Crystal Humidity Control Device (HC1) as a tool for improving diffraction quality (Upon request: http://www.embl-grenoble.fr/groups/instr/humidifier_page1.html). - Remote data collection. - Opitcs hutch will be fully refurbished at that time. Best regards, Hassan Belrhali (belrhali-at-embl.fr belrh...@embl.fr). [1]* EU-associated state*: Switzerland, Israel, Norway, Iceland and Liechtenstein Turkey, Croatia, the Former Yugoslav Republic of Macedonia and Serbia, Albania and Montenegro, Bosnia Herzegovina (source EC: FP7 Third Country Agreements)
Re: [ccp4bb] Structure problem
Original Message Subject: Structure problem Date: Tue, 13 Sep 2011 08:55:47 + From: #HEW KAI LI KELLY# klh...@e.ntu.edu.sg Hi, I am facing some problems in solving my structure now, so I am wondering if anyone is able to give me any tips and tricks on this matter. My protein-DNA complex structure diffracted to 1.5A. There are 4 missing residues, 2 on each terminal. There is no twinning in the data. The angles, the bonds, the rotamers and the Ramachandran plot are okay too. I am using molecular replacement for the phasing and the sequence homology between my protein and my homologous model is 33%. The electron density map for the protein looks very nice and there is also nice density for the DNA. Rfree converged from the initial 39%. However, Rfree refused to go down any further and it's still around 30-31%. Does anyone have any suggestions for me? Thank you in advance! Warmest Regards, Kelly Hew Hi, pls check out http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement To get more specific help, you'll have to tell us much more - number of residues and bases, spacegroup, ... (at least) everything that would end up in Table 1 of your paper describing the structure, and in the header of the PDB file. HTH, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature smime.p7s. smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] neutron diffraction 'difference' map?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Francis, ad [1]: if you are going for neutron diffraction, you probably want the ligand to have its hydrogens replaced with deuteria, rather than a 'heavy atom derivative' of your ligand. The scattering power for neutrons does not correlate with the weight of the nucleus und deuterium scatters as strongly as O,C, ... (see ITCr, Vol. C, Chapter 4.4) In that case you also do not need a difference map against the X-ray data because the scattering of X-rays by hydrogens can be neglected. ad [1b]: see [1]; remark: since we are doing science as opposed to math or philosophy, there is no 'unambiguity'. There is only a model for the experimental data which - depending on your means of validation - fits the data more or less well. ad [2]: That probably depends on whether your ligand site is fully occupied and whether the ligand is disordered or not. Cheers, Tim On 09/13/2011 09:01 PM, Francis E Reyes wrote: Hi all Suppose you have a high resolution xtal structure (from usual x-ray diffraction) and you wanted to verify the location of a ligand. You can purchase a heavy atom isotope version of the ligand. [1] Is it possible to do a neutron diffraction difference map (where you simply calculated Fobs(heavy) - Fobs(light) to verify the location of the ligand? [1b] Suppose you couldn't measure the diffraction of the light version of the ligand. Can the x-ray data be combined with the neutron diffraction of the heavy atom isotope to unambiguously assign the ligand site? [2] What would be the minimum resolution required from the neutron diffraction? (This is particularly important as you may be unable to grow high diffracting crystals or large crystals) Note that you don't necessarily want to solve the structure of the structure from neutron diffraction from scratch, but rather you want to use it as a tool to verify the location of a ligand binding site. Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOcGZNUxlJ7aRr7hoRAgY1AKC7nvHVe3RwwWnIWHzm9tjbkZcsTgCcCAmW /RGhWn+QQTJ2ZQtTdozVY4E= =XmDf -END PGP SIGNATURE-
[ccp4bb] Refinement with Low resolution data
Dear ccp4, I am refining one structure at low resolution (3.5 A). I solved the structure in space group P622 by molecular replacement. The Rw/Rf after some cycle of rigid body refinement in Refmac5 is 34/37. But when I am trying to refine with Restrain refinement in Refmac the Rw is going down but the Rf is going up. This same happens with the phenix refinement. The protein is quite big 520 residues and one molecule is present in the crystal asymmetric unit. The maps are also not so bad except some region. Please give me suggestion, what should I have to care during low resolution refinement? or is there any other tricks for this types of data? Thanks in advance. Md. Munan Shaik PhD Student Department of Biotehnology School of Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com munan.sh...@unipd.it
[ccp4bb] stereo
Dear Members, Is any one using NVidia NVision 3D Setup with active stereo in linux distribution for crystallographic work? Which one would be the best choice to set up, an active stereo or a passive stereo for crystallographic work? Can anyone shade some details on this? I am planning to buy or build a new workstation with stereo set up. It would be great if someone can give some estimate on this. Many thanks, Hena
Re: [ccp4bb] Refinement with Low resolution data
Hi, did you use refinement strategy suitable for low (3.5A) resolution (secondary structure restraints, Ramachandran plot restraints, proper ADP parameterization, SA, etc etc...)? If you send me the data and model files off-list I will have a look. Pavel On Wed, Sep 14, 2011 at 7:34 AM, Md Shaik munanbt2...@yahoo.com wrote: Dear ccp4, I am refining one structure at low resolution (3.5 A). I solved the structure in space group P622 by molecular replacement. The Rw/Rf after some cycle of rigid body refinement in Refmac5 is 34/37. But when I am trying to refine with Restrain refinement in Refmac the Rw is going down but the Rf is going up. This same happens with the phenix refinement. The protein is quite big 520 residues and one molecule is present in the crystal asymmetric unit. The maps are also not so bad except some region. Please give me suggestion, what should I have to care during low resolution refinement? or is there any other tricks for this types of data? Thanks in advance. Md. Munan Shaik PhD Student Department of Biotehnology School of Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com munan.sh...@unipd.it
Re: [ccp4bb] stereo
I run the Alienware OptX AW2310 on two of our 3D Linux workstations and it looks spectacular. Make sure that you have a Quadro FX Nvidia video card that is on the approved list ( http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html) with 3-pin stereo (3-pin stereo connector required for Linux, it will work without one in Windows through USB) output and not just a normal GeForce Nvidia card or you won't be able to run stereoscopic 3D in Linux. One option that supports both Mac and Linux are the Zalman brand 3D monitors. Some people like them, some people don't. Unless Zalman significantly improved the technology on their monitors (ie: the right eye can see odd numbered rows of pixels and the left eye can see even numbered rows of pixels) you lose a significant amount of resolution from displaying 3D on these. Due to half the pixels being drawn to each eye, the display on the 3D Vision system using a 120 Hz monitor will look crisper and higher quality than the equivalent Zalman monitor when displaying stereoscopic 3D. That being said, this solution is significantly cheaper than the Nvidia system. I've used and seen both and prefer the quality of the Nvidia 3D Vision, but some people are happy with the Zalman setup. It's really up to personal preference as to which you will choose. Cheers, Jim On Wed, Sep 14, 2011 at 10:48 AM, Hena Dutta hdutt...@gmail.com wrote: Dear Members, Is any one using NVidia NVision 3D Setup with active stereo in linux distribution for crystallographic work? Which one would be the best choice to set up, an active stereo or a passive stereo for crystallographic work? Can anyone shade some details on this? I am planning to buy or build a new workstation with stereo set up. It would be great if someone can give some estimate on this. Many thanks, Hena -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov
Re: [ccp4bb] Refinement with Low resolution data
Are you sure of the space group? P622 is much rarer than P6(x)22 where x 0 Phil On 14 Sep 2011, at 15:34, Md Shaik wrote: Dear ccp4, I am refining one structure at low resolution (3.5 A). I solved the structure in space group P622 by molecular replacement. The Rw/Rf after some cycle of rigid body refinement in Refmac5 is 34/37. But when I am trying to refine with Restrain refinement in Refmac the Rw is going down but the Rf is going up. This same happens with the phenix refinement. The protein is quite big 520 residues and one molecule is present in the crystal asymmetric unit. The maps are also not so bad except some region. Please give me suggestion, what should I have to care during low resolution refinement? or is there any other tricks for this types of data? Thanks in advance. Md. Munan Shaik PhD Student Department of Biotehnology School of Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com munan.sh...@unipd.it
Re: [ccp4bb] stereo
Hi, On Wed, Sep 14, 2011 at 9:48 AM, Hena Dutta hdutt...@gmail.com wrote: Dear Members, Is any one using NVidia NVision 3D Setup with active stereo in linux Yes distribution for crystallographic work? Which one would be the best choice to set up, an active stereo or a passive stereo for crystallographic work? Active has better quality, greater 3D viewing area for people not sitting right in front of the monitor, but is more expensive if you have to purchase additional goggles ($70 non-nvidia online retailers - $120 currently from nvidia) Can anyone shade some details on this? I am planning to buy or build a new workstation with stereo set up. It would be great if someone can give some estimate on this. Going with the lowest prices: $300 Quadro 3700 : http://www.google.com/products/catalog?q=quadro+3700cid=5758926893192813358ei=i8FwTpqJGpGkwgXtw9H4CQved=0CAkQgggwAA#scoring=tp $320 Acer GD235HZ : http://www.google.com/products/catalog?q=acer+gd235hzhl=enum=1ie=UTF-8tbm=shopcid=114906938122589343sa=Xei=d8JwTr7TM8WgtwfFuZWJCgved=0CHsQgggwAA#scoring=tp $150 3D Vision kit with the 3 pin mini din VESA to 2.5mm stereo cable : http://www.nvidia.com/object/product_geforce_3D_VisionKit_us.html Total = $770 Passive stereo : $490 (open box) - $550 : Zalman ZM-M240W : http://www.compuvest.com/Search.jsp?Search=ZM-M240Wadvsite=frooglesku=756009288-08dp=3:CVS:51392:0:21 You can use the black RealD 3D movie theater goggles with the Zalman if you need extras. People also sell these online for a $1 + shipping. HTH, Sabuj Many thanks, Hena
Re: [ccp4bb] Refinement with Low resolution data
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Md. Munan Shaik, a couple of aspects you might check: - - first build the model AS MUCH AS POSSIBLE before running the first refinement cycle - - switch off automatic weight determination in refmac and use a low weight (e.g. 0.005) and many cycles of refinement - - check that the geometry does not distort (rmsd angles and bond lengths reported in the refmac log-file must not go too high). if it does, lower the weight even further. if your model stems from higher resolution data and is actually in good agreement with the model you are going at, refinement might ruin the good model if you use inappropriate settings, causing Rfree to go up. Cheers, Tim On 09/14/2011 04:34 PM, Md Shaik wrote: Dear ccp4, I am refining one structure at low resolution (3.5 A). I solved the structure in space group P622 by molecular replacement. The Rw/Rf after some cycle of rigid body refinement in Refmac5 is 34/37. But when I am trying to refine with Restrain refinement in Refmac the Rw is going down but the Rf is going up. This same happens with the phenix refinement. The protein is quite big 520 residues and one molecule is present in the crystal asymmetric unit. The maps are also not so bad except some region. Please give me suggestion, what should I have to care during low resolution refinement? or is there any other tricks for this types of data? Thanks in advance. Md. Munan Shaik PhD Student Department of Biotehnology School of Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com munan.sh...@unipd.it - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOcMiWUxlJ7aRr7hoRAgjmAJ9DGXYXUGHFWW7pJG2weuFMvg8r1ACfUqTq YhxbtdQNuV7rKC/klAKtgjM= =bQQT -END PGP SIGNATURE-
[ccp4bb] Quips about greasy pockets
Hi all, As you may recall, the Protein Data Bank in Europe (PDBe; pdbe.org) regularly produces Quips, short stories about QUite Interesting Pdb Structures (pdbe.org/quips). Quips address biologically interesting aspects of one or more PDB entries, coupled with interactive graphics views and often a mini-tutorial or suggestions for further exploration using PDBe services and resources. Today another Quips episode was released. It is about autotaxins, physiologically important proteins that are pursued as anti-cancer drug targets. This Quips was developed together with scientists from the Netherlands Cancer Institute (Tassos Perrakis and Wouter Moolenaar) to accompany their review paper in Nature Reviews Molecular Cell Biology on autotaxin structure and function that was also published today. - For the Quips story (Autotaxins: inhibiting a greasy pocket), go to: http://pdbe.org/quips?story=Autotaxin - For the review paper (Insights into autotaxin: how to produce and present a lipid mediator), go to: http://www.nature.com/nrm/journal/vaop/ncurrent/full/nrm3188.html --- If you have an interesting structure whose story you would like to tell (with our help) in the form of a Quips episode, please contact us at p...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Pointless problems
Dear All, I am having problems when trying to run Pointless with input from Denzo/Scalepack. (1) Pointless refuses to work from the .sca file. The error message is: CCP4 library signal mtz:File not identified as MTZ (Error) CCP4MTZfile: open_read - File missing or corrupted: rn7e222test.sca or The program run with command: /programs/CCP4/ccp4-6.1.1/bin/pointless has failed with error message child process exited abnormally (when run from ccp4i) (2) Scalepack2mtz refuses to convert a Scalepack file produced using the command: NO MERGE original index (i.e. as instructed by the Pointless instructions). It fails with the rather tactless message: * Resolution Range : 0.002020.00485 ( 22.256 - 14.357 A ) * Sort Order : 0 0 0 0 0 * Space group = 'P 2 2 2' (number 16) SCALEPACK2MTZ: Check your data! And, no my resolution range is not 22.2-14.3 A!! (3) Pointless refuses to work with an .mtz file produced by Scalepack2mtz from a .sca file obtained with the simple NO MERGE instruction (remember the NO MERGE original index instruction is a no-go for Scalepack2mtz). The error message in this case is quite simply: HKLIN is merged and no HKLREF file is defined, SPACEGROUP or REINDEX. I know the orthodox ccp4 reply would be stop whining and use Mosflm!, but is there an alternative if I really want to use Denzo/Scalepack? If not, is there another way to check my point group/spacegroup starting from Denzo/Scalepack? Thanks a lot! Emmanuel
[ccp4bb] Space Group Table
Hello All, Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count on major software packages to honor this mapping if present in a PDB file)? I notice that this web page was authored by a couple of prominent developers. Thank you, James
Re: [ccp4bb] Pointless problems
On Wed, 2011-09-14 at 14:06 -0400, Emmanuel Saridakis wrote: If not, is there another way to check my point group/spacegroup starting from Denzo/Scalepack? If you are trying to choose the screw axes, you can always look at the systematic absences. This script may be useful in extracting the (h00), (0k0),(00l) and such (assuming you used P222 and thus scalepack kept everything): http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Get_systematic_absences_from_.sca_file Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] stereo
Hi, On Wed, Sep 14, 2011 at 10:52 AM, Hena Dutta hdutt...@gmail.com wrote: Hi Sabuj, Can I use LED monitor instead LCD? I heard the color contrast is better. If We haven't tried any, but here's an interesting 120 HZ LED monitor (Acer HS244HQ): http://www.newegg.com/Product/Product.aspx?Item=N82E16824009301nm_mc=OTC-Frooglecm_mmc=OTC-Froogle-_-Monitors+-+LCD+Flat+Panel-_-Acer+America-_-24009301 It comes with active 3D goggles, but it's noted that these only work with the 3D sync signal built into Bluray movies which I think is transmitted off the monitor. Now if this works like 3D DLP link stereo then you don't necessarily need the 3D vision stereo kit/emitter at all. In fact, we have an Infocus IN3116 projector that does 120Hz at 720p and a bunch of $50 DLP link goggles, a quadro 3700 video card in the box, and can do stereo in Windows 7 and Linux using Option Stereo 3 (standard quad buffered stereo). We use a cheap $2 DVI to HDMI converter to connect a long HDMI cable into the projector from the Quadro 3700 and that's it, no super long 3 pin mini din cable is needed. The only downside is that sometimes the left and right eye images are on the wrong sides when stereo is enabled, but most apps (e.g. pymol, chimera, and coot too probably) have an option to swap the eyes when in stereo so that's easily fixed. I buy higher level quadro graphics card (say FX 5600), will it improve the stereo quality? How big difference the prices are? Thanks for your A better card won't improve the stereo quality itself, but will improve surface, vdw, etc renderings with high polygon counts. For building models, most people are looking at wireframes/lines which you can still do for huge macromolecules on an SGI Octane. So yes, the 5600 will work with nvidia 3d vision, it has at least a G8x core (http://en.wikipedia.org/wiki/Nvidia_Quadro) and the stereo connector in the back. If you decide to go with something like that Acer HS244HQ it would be interesting to see if it can be made to work without the nvidia 3d vision kit at all. HTH, Sabuj information. Hena On Wed, Sep 14, 2011 at 11:26 AM, Sabuj Pattanayek sab...@gmail.com wrote: Hi, On Wed, Sep 14, 2011 at 9:48 AM, Hena Dutta hdutt...@gmail.com wrote: Dear Members, Is any one using NVidia NVision 3D Setup with active stereo in linux Yes distribution for crystallographic work? Which one would be the best choice to set up, an active stereo or a passive stereo for crystallographic work? Active has better quality, greater 3D viewing area for people not sitting right in front of the monitor, but is more expensive if you have to purchase additional goggles ($70 non-nvidia online retailers - $120 currently from nvidia) Can anyone shade some details on this? I am planning to buy or build a new workstation with stereo set up. It would be great if someone can give some estimate on this. Going with the lowest prices: $300 Quadro 3700 : http://www.google.com/products/catalog?q=quadro+3700cid=5758926893192813358ei=i8FwTpqJGpGkwgXtw9H4CQved=0CAkQgggwAA#scoring=tp $320 Acer GD235HZ : http://www.google.com/products/catalog?q=acer+gd235hzhl=enum=1ie=UTF-8tbm=shopcid=114906938122589343sa=Xei=d8JwTr7TM8WgtwfFuZWJCgved=0CHsQgggwAA#scoring=tp $150 3D Vision kit with the 3 pin mini din VESA to 2.5mm stereo cable : http://www.nvidia.com/object/product_geforce_3D_VisionKit_us.html Total = $770 Passive stereo : $490 (open box) - $550 : Zalman ZM-M240W : http://www.compuvest.com/Search.jsp?Search=ZM-M240Wadvsite=frooglesku=756009288-08dp=3:CVS:51392:0:21 You can use the black RealD 3D movie theater goggles with the Zalman if you need extras. People also sell these online for a $1 + shipping. HTH, Sabuj Many thanks, Hena
Re: [ccp4bb] Space Group Table
On Wednesday, September 14, 2011 10:16:53 am James Stroud wrote: Hello All, Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count on major software packages to honor this mapping if present in a PDB file)? I'm not sure that's the right question. I think you need to start with the question Is this the list used by PDB files?. And I'm pretty sure the answer is no, if only because the table you link to does not list rhombohedral/hexagonal settings as starting with H or R. See the note on the definition of the PDB field contents: http://www.wwpdb.org/documentation/format33/sect8.html See also many threads over the past several years about inconsistent handling of H3/R3. Ethan I notice that this web page was authored by a couple of prominent developers. Thank you, James -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] glycerol on three-fold axis
Dear colleagues, Has anyone seen glycerol on a three-fold axis? THis is possible as the glycerol can be disordered but I want to know if there is an actual case. Any information would be greatly appreciated. Jackie Vitali
Re: [ccp4bb] stereo
On 09/14/11 13:53, Sabuj Pattanayek wrote: Hi, On Wed, Sep 14, 2011 at 10:52 AM, Hena Duttahdutt...@gmail.com wrote: Hi Sabuj, Can I use LED monitor instead LCD? I heard the color contrast is better. If What is being marketed as LED monitors recently are actually LCD monitors which use LEDs rather than fluorescent lamps for backlighting. So long as your monitor is compatible with the stereo technology you are using, LED backlighting is fine (and more efficient). -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] stereo
On Wed, Sep 14, 2011 at 3:23 PM, Hena Dutta hdutt...@gmail.com wrote: Hi, Isn't that an LCD monitor (Acer HS244HQ)? It's edge LED backlit. I don't know if there are any direct LED backlit 120Hz monitors. Couldn't find much information on those types.
[ccp4bb] refmac and DNA bond angles
I'm running into some geometry problems with my DNA model after refinement with refmac (version 5.5.0109), and would appreciate any feedback. The problem is that the angles for many of the glycosidic bonds are 2 to 4 degrees off of the ideal values, and so are several standard deviations outside what's expected. Our data (from MR) is ~2 Å, and the density is well defined for the DNA. I was thinking that perhaps refmac was not recognizing my DNA and so just taking the poor geometry from one model and enforcing it for the next, but in the log file it does not indicate that a new molecule has been found, and I do not feed in a cif file from previous runs. Another indication that refmac recognizes the DNA bases is that it says it is renaming them. The DNA bases are named DA, DC, DT, DG, and the header of the output pdb file says: MODRES DC B1 Cd RENAME MODRES DC B2 Cd RENAME MODRES DA B3 Ad RENAME MODRES DT B4 Td RENAME (etc...) In the output, strangely (to me), it is actually not renaming them. That is, it is keeping the DC etc names. In coot, I'm measuring the glycosidic bond (O4'-C1'-N9) to be 104.6, whereas in AD.cif, it is listed as 108.4. The bond lengths are fine, and there are no distortions of the protein model. Thanks, Greg
[ccp4bb] JOB POSITION AVAILABLE
*JOB POSITION AVAILABLE*** * * *Postdoctoral Fellow/Researcher *– *Protein Crystallography position *is available for participating in the chemical genomics drug discovery projects targeting GPCRs and stem cells (http://www.cbligand.org/xielab/). Qualifications: PhD (or equivalent working experience) in Biochemistry or Biophysics, good knowledge and experience with protein expression and purification in E. coli and insect cells as well as protein crystallization for X-ray crystallography or NMR studies. Must demonstrated ability to design, execute and analyze experiments independently. Good written, verbal, and interpersonal skills are needed. Salary will be commensurate with experience. Please email your CV and three references to: Prof. XQ (Sean) Xie, Dept. of Pharmaceutical Sciences/Drug Discovery Institute, University of Pittsburgh*, *Pittsburgh, PA 15261. xi...@pitt.edu, http://www.pharmacy.pitt.edu/directory/profile.lasso?Page=425Type=Faculty
Re: [ccp4bb] refmac and DNA bond angles
OK, I updated ccp4 to 6.2.0 (and refmac to 5.6.0117) and now the angles coming out close to the ideal values. Also, I see now the the MODRES in the pdb header from before was tell future refmac runs to rename those residues - which confused the newer refmac version as it thought the DT (renamed Td) were somehow DY. By just deleting these MODRES lines it was fine. On Sep 14, 2011, at 7:10 PM, Gregory Bowman wrote: I'm running into some geometry problems with my DNA model after refinement with refmac (version 5.5.0109), and would appreciate any feedback. The problem is that the angles for many of the glycosidic bonds are 2 to 4 degrees off of the ideal values, and so are several standard deviations outside what's expected. Our data (from MR) is ~2 Å, and the density is well defined for the DNA. I was thinking that perhaps refmac was not recognizing my DNA and so just taking the poor geometry from one model and enforcing it for the next, but in the log file it does not indicate that a new molecule has been found, and I do not feed in a cif file from previous runs. Another indication that refmac recognizes the DNA bases is that it says it is renaming them. The DNA bases are named DA, DC, DT, DG, and the header of the output pdb file says: MODRES DC B1 Cd RENAME MODRES DC B2 Cd RENAME MODRES DA B3 Ad RENAME MODRES DT B4 Td RENAME (etc...) In the output, strangely (to me), it is actually not renaming them. That is, it is keeping the DC etc names. In coot, I'm measuring the glycosidic bond (O4'-C1'-N9) to be 104.6, whereas in AD.cif, it is listed as 108.4. The bond lengths are fine, and there are no distortions of the protein model. Thanks, Greg -- Department of Biophysics Johns Hopkins University 302 Jenkins Hall 3400 N. Charles St. Baltimore, MD 21218 Phone: (410) 516-7850 (office) Phone: (410) 516-3476 (lab) Fax: (410) 516-4118 gdbow...@jhu.edu
Re: [ccp4bb] Structure problem
Just echoing what has been said. I would make sure you have the right space group. It may be worthwhile tyring to find a MR solution in different space groups with different compositions. Another imporatant thing is how complete is your model? Do you have all the protein and DNA modeled in? How many waters (you should see plenty at 1.5 A) How good is the difference map? These are all things that should be checked before panic sets in Cheers
