[ccp4bb] ROSETTA for MR model generation
Dear all, I was wondering if anybody has used the ROSETTA software to generate a MR model that could subsequently being used successfully for a MR solution case. The sequence of the protein we work with is relatively small, ~ 85 residues. Crystallization is not very reproducible. Resolution is 1.9 A. Crystals are extremely rare. I would be grateful for any hints and will send a summary of all personally sent comments to the list. Thank you and have a nice day Kornelius -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349
Re: [ccp4bb] ROSETTA for MR model generation
Hello, I know at least the following papers on this topic: --- High resolution protein structure prediction and the crystallographic phase problem http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2504711/ Prospects for de novo phasing with de novo protein models http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631639/ --- I think it worked on several of their cases, better on small proteins if I remember well. Regards, F. Kornelius Zeth wrote: Dear all, I was wondering if anybody has used the ROSETTA software to generate a MR model that could subsequently being used successfully for a MR solution case. The sequence of the protein we work with is relatively small, ~ 85 residues. Crystallization is not very reproducible. Resolution is 1.9 A. Crystals are extremely rare. I would be grateful for any hints and will send a summary of all personally sent comments to the list. Thank you and have a nice day Kornelius -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349
Re: [ccp4bb] ROSETTA for MR model generation
Hello Kornelius, In 2 or 3 cases I successfully used a homology model for molecular replacement using a model generated from the PHYRE server http://www.sbg.bio.ic.ac.uk/~phyre/. I know it is not the same as ROSETTA but if there is some sequence homology you might be lucky... Best regards Eike Am 25.08.10 10:13 schrieb Kornelius Zeth unter kornelius.z...@tuebingen.mpg.de: Dear all, I was wondering if anybody has used the ROSETTA software to generate a MR model that could subsequently being used successfully for a MR solution case. The sequence of the protein we work with is relatively small, ~ 85 residues. Crystallization is not very reproducible. Resolution is 1.9 A. Crystals are extremely rare. I would be grateful for any hints and will send a summary of all personally sent comments to the list. Thank you and have a nice day Kornelius -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349
[ccp4bb] NAD cif in Jligand
Dear all, I'm trying using Jligand for generating a new ligand describition. Have to say I'm using it for the first time, but so far it look very nice. I trying to optimize a new lib file for a modified NAD molecule. I'm using a nad_ebi.cif file of NAD supplied by Garib a while ago which works fine in Refmac. Now I working on a hydroxylated molecule of NAD (NADOH), OH group at C6N of the nicotinamid ring of NAD. what I have done: starting jligand importing the nad_ebi.cif file showing hydrogens changing atom type and name of H6N to O6N of the nad_ebi.cif file change the ligand ID to XAD regularize XAD (ligand regularize XAD) and I am always ending up with a screwed up nicotinamid ring! the C5N carbon atom is moving out of the aromatic ring. I tried to change the bond type to aromatic and/or delocated of the nicotinamid ring but it is always the same result. Am I doing something very bad here? Please could you advice me how to get it right?? It is worse when I start with the original NAD dictionary directly within Jligand ! Please try out for yourself, any help is much appreciated Many thanks for your help Stefan
Re: [ccp4bb] turn granular to crystal
Hi, Did you use detergent? It seems look like detergent crystals. 2010-08-25 yybbll 发件人： rui 发送时间： 2010-08-25 20:37:18 收件人： CCP4BB 抄送： 主题： [ccp4bb] turn granular to crystal Hi, All, I'm trying to crystallize a soluble protein and got something like granular, they are rounded shaped and not so regular and also don't have sharp edges. See the attached pic. The current condition is PEG4000 and pH around 5. How can I improve this condition? Thanks a lot.
Re: [ccp4bb] ROSETTA for MR model generation
Hi Kornelius, A possible solution at this resolution would be to use Arcimboldo which localizes model fragments such as small helices with Phaser and then does density modification with SHELXE. See: Nature Methods 6:651-3. Crystallographic ab initio protein structure solution below atomic resolution Peter. On Wed, Aug 25, 2010 at 10:13 AM, Kornelius Zeth kornelius.z...@tuebingen.mpg.de wrote: Dear all, I was wondering if anybody has used the ROSETTA software to generate a MR model that could subsequently being used successfully for a MR solution case. The sequence of the protein we work with is relatively small, ~ 85 residues. Crystallization is not very reproducible. Resolution is 1.9 A. Crystals are extremely rare. I would be grateful for any hints and will send a summary of all personally sent comments to the list. Thank you and have a nice day Kornelius -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349 -- Peter
[ccp4bb] Crystallization of low solubility proteins from glycerol-containing solutions
Does anyone have practical experience crystallizing low solubility proteins from solutions containing significant (10-20%) glycerol? We can get small crystals by mixing 4:1 ratios of protein to well solution, but the drops do not concentrate back to the well solution volume as anticipated, even if the well solution is brought to 10-20% glycerol as well to balance osmolarity. Concentration of the protein further to reduce the protein:well solution ratio may not be practical (it crashes out) even in 20% glycerol. Unfortunately, glycerol seems to be required to maintain protein solubility, so that may not be practical to remove either. One thought is to add additional osmolyte to the well solution to draw down the drop volume once small crystals form, a kind of a "macro-seeding" approach, but I am not aware of a systematic way of doing this. Anyway, I am almost certain I am trying to re-invent the wheel,as someone has probably done something similar. Any suggestions would be appreciated. Cheers, -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] turn granular to crystal
I would try the following approach, some of which you may have done already: Broad pH screen, by 0.5 pH units to see if you are in the pH sweet spot. Finer PEG-4000 screen at the pH identified in the pH screen--the precipitate in the well would alert me to consider that either PEG-4000 is too high, or protein is insufficiently pure Try some of your best conditions at 4 deg C instead of RT, or some other intermediate temperature if you have the capability. (For me, the 4 deg C often makes a big difference; I've had minimal luck with intermediate temps.) Try an additive screen with 5-10% PEGS, polyols, and liquids (don't forget DMSO, DMF, MPD, as well as EG, glycerol or glucose, etc.), or 0.1-0.2 M salts. Whatever you have on hand, or more thorough march through the Hampton Research additives. If anything improves crystal form, try more (or less), or combine additives. At some point, try "reversing" your protein/precipitant ratios. You will typically have more luck in the higher protein/lower precipitant part of the crystallization phase diagram than the reverse. Screens are usually at the higher precipitant/lower protein part of the crystallization phase diagram. Cheers. On 8/25/2010 8:37 AM, rui wrote: Hi, All, I'm trying to crystallize a soluble protein and got something like granular, they are rounded shaped and not so regular and also don't have sharp edges. See the attached pic. The current condition is PEG4000 and pH around 5. How can I improve this condition? Thanks a lot. -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
[ccp4bb] EMBL Interdisciplinary Postdocs
Dear All, We have an opening for a postdoctoral position within the EMBL interdisciplinary postdocs initiative (EIPOD). The project on 'Combined computational methods for macromolecules' aims at interpretation of macromolecular crystallography data at a resolution from 4 to 10 A, making use of crystallographic and electron microscopy image analysis methods. At the same time the project aims at an enhanced interpretation of electron microscopy data by making use of advanced crystallographic modelling tools. The deadline for applications is August 31, and for further details please refer to http://www.embl-hamburg.de/training/postdocs/eipod/index.html and http://www.embl-hamburg.de/training/postdocs/eipod/app2010/lamzin.pdf Best regards, Victor
Re: [ccp4bb] Crystallization of low solubility proteins from glycerol-containing solutions
Hi Roger, I crystallized a protein that started in solution with 250 mM NaCl, 50% glycerol, and 50 mM Arg+Glu. I initially used traditional microbatch under paraffin oil to get crystallization hits (where protein and screen are 1:1; glycerol ends up at 25%). Then, I found that setting up sitting drops like a microbatch worked even better (where protein and screen are 1:1 and the well solution is the protein buffer and screen also 1:1). Best thing about it was the crystals were already cryoprotected and ready to put on the beam. See Del Campo Lambowitz Acta Cryst. (2009). F65, 832–835. If you have any questions let me know. Best, Mark Research Associate Lambowitz Laboratory UT Austin
Re: [ccp4bb] Crystallization of low solubility proteins from glycerol-containing solutions
Dear Roger, Since you already have initial crystallisation conditions and crystals you could try dialysis buttons to further reduce the glycerol content (and hence get bigger crystals). They are available e.g. from Hampton, the minimum volume is 5 mul and I find they require a little skill to set up. Good luck, Tim On Wed, Aug 25, 2010 at 10:19:13AM -0400, Roger Rowlett wrote: !DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN html head meta http-equiv=content-type content=text/html; charset=ISO-8859-1 /head body bgcolor=#ff text=#00 font face=VerdanaDoes anyone have practical experience crystallizing low solubility proteins from solutions containing significant (10-20%) glycerol? We can get small crystals by mixing 4:1 ratios of protein to well solution, but the drops do not concentrate back to the well solution volume as anticipated, even if the well solution is brought to 10-20% glycerol as well to balance osmolarity. Concentration of the protein further to reduce the protein:well solution ratio may not be practical (it crashes out) even in 20% glycerol. Unfortunately, glycerol seems to be required to maintain protein solubility, so that may not be practical to remove either.br br One thought is to add additional osmolyte to the well solution to draw down the drop volume once small crystals form, a kind of a macro-seeding approach, but I am not aware of a systematic way of doing this. Anyway, I am almost certain I am trying to re-invent the wheel,as someone has probably done something similar. Any suggestions would be appreciated.br br Cheers,br /fontbr div class=moz-signature-- br font face=Verdana hr Roger S. Rowlettbr Professorbr Department of Chemistrybr Colgate Universitybr 13 Oak Drivebr Hamilton, NY 13346br br tel: (315)-228-7245br ofc: (315)-228-7395br fax: (315)-228-7935br email: a class=moz-txt-link-abbreviated href=mailto:rrowl...@colgate.edu;rrowl...@colgate.edu/abr /font /div /body /html -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Crystallization of low solubility proteins from glycerol-containing solutions
Have you tried to use glycerol or ethylene glycol as the precipitant? What happens when you go to 50% or higher concentrations? _ From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Roger Rowlett Sent: Wednesday, August 25, 2010 9:19 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Crystallization of low solubility proteins from glycerol-containing solutions Does anyone have practical experience crystallizing low solubility proteins from solutions containing significant (10-20%) glycerol?
[ccp4bb] Faculty position in Structural Biology at UT Southwestern Medical Center
The Structural Biology Laboratory at UT Southwestern Medical Center currently has an opening at the Research Assistant Professor level for a highly motivated individual who enjoys working in a collaborative, multi-disciplinary setting. A Ph.D. in biochemistry, chemistry, physics or a related field is required. Experience in structural biology, particularly X-ray crystallography and protein expression/ purification is also required. Facility with related techniques such as NMR or cryo-EM spectroscopy, small-angle X-ray scattering, isothermal titration calorimetry or analytical ultracentrifugation is highly desirable. Demonstrable experience in all areas of X-ray crystallography, including crystal growth and sample preparation, data collection on home and synchrotron sources, structure determination and refinement is required, and familiarity with the latest software is necessary. Job requirements include a significant amount of both formal and informal teaching, and travel to a synchrotron source with students may be required several times per year. Salary is competitive and commensurate with experience and qualifications. About the Structural Biology Laboratory The Structural Biology Laboratory (Diana Tomchick, Director) is a platform that allows researchers with different expertise to come together in a collaborative setting and tackle biological problems in a comprehensive way. We use a multitude of experimental approaches, mostly X-ray crystallography, but also NMR spectroscopy, complemented by a plethora of biophysical and molecular-biological techniques. State-of-the-art equipment is shared between the members in the Structural Biology community at UT Southwestern and consists of one Rigaku FR-E SuperBright high brilliancy X-ray generator equipped with one set of high-resolution and one set of high-intensity X-ray optics, two imaging-plate X-ray detectors (one R-Axis IV++ and one R-Axis IV), two X-Stream crystal cooling devices, and one automated sample- mounting device (ACTOR) for the unattended screening of crystals; a Fluidigm microfluidics crystallization robot and imaging system; a Phoenix crystallization robot, plus two Desktop Minstrel imaging systems and a Gallery-160 Plate Hotel; 30 days per year of beamtime at beamlines 19ID and 19BM at the Advanced Photon Source (APS), Argonne, IL; several NMR spectrometers (one 800 MHz, three 600 MHz, two 500 MHz), cryo-probes and robotic sample changer. These facilities are supplemented by a variety of biophysical instruments supporting the study of macromolecules using CD, dynamic light scattering, analytical ultracentrifugation, stopped-flow kinetics, isothermal titration calorimetry and mass spectrometry. The medical center has three degree-granting institutions: UT Southwestern Medical School, UT Southwestern Graduate School of Biomedical Sciences and UT Southwestern School of Health Professions. Nearly 4,200 students are trained each year in graduate and allied health programs, as residents and post doctoral fellows. Funding from the NIH, foundations, individuals and corporations provide more than $360 million annually for over 3,500 research projects. Our faculty is comprised of many distinguished members, including: four Nobel laureates, three of whom are active faculty members; 18 members of the National Academy of Sciences; and 18 members of the Institute of Medicine. Interested applicants should submit a curriculum vita and three letters of reference by September 30, 2010 to Diana Tomchick, Chair, Biophysics Search Committee, UT Southwestern Medical Center. recruit...@utsouthwestern.edu UT Southwestern is an Equal Opportunity/Affirmative Action Employer. Women and minority candidates are encouraged to apply. For further inquiries, please contact: Diana Tomchick Department of Biochemistry, Rm. ND10.214B UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390-8816 Tel. +1 214 645 6383 Email: diana.tomch...@utsouthwestern.edu http://www8.utsouthwestern.edu/utsw/cda/dept16358/files/16776.html http://www3.utsouthwestern.edu/sbl/ Some recent publications: Scheuermann T.H. et al. (2009). Artificial ligand binding within the HIF2a PAS-B domain of the HIF2 transcription factor. PNAS, 106:450-455. Davis L. et al. (2009). Localization and structure of the ankyrin- binding site on b2-spectrin. J. Biol. Chem., 284:6982-6987. Yu, B. et al. (2010). Structural and energetic mechanisms of cooperative autoinhibition and activation of Vav1. Cell, 140:246-256. Shin O-H. et al. (2010). Munc13 C2B domain is an activity-dependent Ca2+ regulator of synaptic exocytosis. Nat Struct Mol Biol 17:280-288. Tian W. et al. (2010). Structural and functional analysis of the YAP- binding domain of human TEAD2. PNAS, 107:7293-7298. Luong P. et al. (2010). Kinetic and structural insights into the mechanism of AMPylation by
[ccp4bb] problems loading electron density
Hi all, I am having problems opening an electron density map on chimera as well as in pymol( tried mtz and xplor formats). Chimera gives a error in line 2 ANOMalous=false message or bad MRC grid size message,where as pymol just gives a error reading map message. Any help will be appreciated. Thanks in advance Rakesh
Re: [ccp4bb] problems loading electron density
Dear Rakesh, at least for pymol you have to convert the mtz-file into a ccp4-map. The program 'fft' does this from the ccp4i. Give the output file the name extension .ccp4, than it's recognised by the default filter in pymol. Tim On Wed, Aug 25, 2010 at 11:56:17AM -0400, Rakesh Joshi wrote: Hi all, I am having problems opening an electron density map on chimera as well as in pymol( tried mtz and xplor formats). Chimera gives a error in line 2 ANOMalous=false message or bad MRC grid size message,where as pymol just gives a error reading map message. Any help will be appreciated. Thanks in advance Rakesh -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] LIGPLOT or similar
Dear All, Having just installed LIGPLOT under Windows, I find it rather convoluted to run. It has to be run via de command line window, and I try to avoid Windows as much as I can anyway. I also tried to install the Unix version on MacOSX, but was not able to get it running properly, probably at least partly due to my relative lack of informatics skills... Is there an alternative program that does the same (pref. with MacOSX version)? For the LIGPLOT developers, ideal would be a MacOSX installer (dmg) - I think it would lead to more use of your program. Greetings, Mark van Raaij
Re: [ccp4bb] Crystallization of low solubility proteins from glycerol-containing solutions
Dear Roger, We have had success using the non-detergent sulphobetaines (NDSBs) to improve solubility of protein samples. For a couple of projects they have proved crucial for concentrating the protein to a reasonable level for crystallization (e.g. PMID: 18765907). Be careful since there is a big variation in price dependent on which particular one you use. Use them at ~200-300 mM and you may even be able to get rid of the glycerol. You may have to incubate the protein with the NDSBs overnight before concentration to get the full effect. Good luck Tom Walter Original message Date: Wed, 25 Aug 2010 10:19:13 -0400 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Roger Rowlett rrowl...@colgate.edu) Subject: [ccp4bb] Crystallization of low solubility proteins from glycerol-containing solutions To: CCP4BB@JISCMAIL.AC.UK Does anyone have practical experience crystallizing low solubility proteins from solutions containing significant (10-20%) glycerol? We can get small crystals by mixing 4:1 ratios of protein to well solution, but the drops do not concentrate back to the well solution volume as anticipated, even if the well solution is brought to 10-20% glycerol as well to balance osmolarity. Concentration of the protein further to reduce the protein:well solution ratio may not be practical (it crashes out) even in 20% glycerol. Unfortunately, glycerol seems to be required to maintain protein solubility, so that may not be practical to remove either. One thought is to add additional osmolyte to the well solution to draw down the drop volume once small crystals form, a kind of a macro-seeding approach, but I am not aware of a systematic way of doing this. Anyway, I am almost certain I am trying to re-invent the wheel,as someone has probably done something similar. Any suggestions would be appreciated. Cheers, -- -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] LIGPLOT or similar
Hi Mark, MOE from ChempComp does something similar, but I think it is not for free. Regards Christian Am Mittwoch 25 August 2010 19:51:08 schrieben Sie: Dear All, Having just installed LIGPLOT under Windows, I find it rather convoluted to run. It has to be run via de command line window, and I try to avoid Windows as much as I can anyway. I also tried to install the Unix version on MacOSX, but was not able to get it running properly, probably at least partly due to my relative lack of informatics skills... Is there an alternative program that does the same (pref. with MacOSX version)? For the LIGPLOT developers, ideal would be a MacOSX installer (dmg) - I think it would lead to more use of your program. Greetings, Mark van Raaij
Re: [ccp4bb] LIGPLOT or similar
Hello Mark, if you would describe the error message you get from the UNIX version of LIGPLOT, someone on the list might be able to help you while you have to wait for and apple installer version or the (commercial) alternatives. Looking at the pictures about ligplot I found on the web and considering what I learned about pymol recently you might also be able to produce pictures with similar information content with pymol, although the pictures would be neatly rendered. Best wishes, Tim On Wed, Aug 25, 2010 at 07:51:08PM +0200, Mark J van Raaij wrote: Dear All, Having just installed LIGPLOT under Windows, I find it rather convoluted to run. It has to be run via de command line window, and I try to avoid Windows as much as I can anyway. I also tried to install the Unix version on MacOSX, but was not able to get it running properly, probably at least partly due to my relative lack of informatics skills... Is there an alternative program that does the same (pref. with MacOSX version)? For the LIGPLOT developers, ideal would be a MacOSX installer (dmg) - I think it would lead to more use of your program. Greetings, Mark van Raaij -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] LIGPLOT or similar
Mark, you might want to try PDBsum (http://www.ebi.ac.uk/pdbsum/), it will generate a LIGPLOT output for a given PDB code entered, which can be downloaded as high resolution .pdf or .ps Best, Javier On Wed, Aug 25, 2010 at 2:49 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Hello Mark, if you would describe the error message you get from the UNIX version of LIGPLOT, someone on the list might be able to help you while you have to wait for and apple installer version or the (commercial) alternatives. Looking at the pictures about ligplot I found on the web and considering what I learned about pymol recently you might also be able to produce pictures with similar information content with pymol, although the pictures would be neatly rendered. Best wishes, Tim On Wed, Aug 25, 2010 at 07:51:08PM +0200, Mark J van Raaij wrote: Dear All, Having just installed LIGPLOT under Windows, I find it rather convoluted to run. It has to be run via de command line window, and I try to avoid Windows as much as I can anyway. I also tried to install the Unix version on MacOSX, but was not able to get it running properly, probably at least partly due to my relative lack of informatics skills... Is there an alternative program that does the same (pref. with MacOSX version)? For the LIGPLOT developers, ideal would be a MacOSX installer (dmg) - I think it would lead to more use of your program. Greetings, Mark van Raaij -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iD8DBQFMdWXHUxlJ7aRr7hoRAhulAKC332MIxmaHPVu8lnhL6dL0GyYE0wCffnJ2 6juBxgbS93ld7NV6ALKcDm0= =GHc4 -END PGP SIGNATURE- -- Javier M. Gonzalez, PhD. University of Maryland Baltimore Department of Pharmaceutical Sciences X-Ray Crystallography Shared Service (UMXSS) 20 Penn St., HSFII, Rm 514 Phone/Fax: 410-7061124/410-7060886 21201 Baltimore, MD http://www2.pharmacy.umaryland.edu/psc/xray/
[ccp4bb] Local real-space refinement by phenix
Hi there: As I understand, phenix.refine do real-space refinement locally (by DiffMap), but from the documentation, I didn't find the keywords to specify the residue range to be refined. Thanks for any help! Best Regards, Hailiang
Re: [ccp4bb] Local real-space refinement by phenix
Hi Hailiang, phenix.refine does local real-space refinement indeed. Here are the details about the algorithm: http://cci.lbl.gov/~afonine/rsr.pdf Slide #10 shows how to use it. Although it works fine in its present shape, there are still some things that need to be improved and some limitations to remove (work in progress). Pavel. P.S.: Second reminder: there is PHENIX mailing list to use for PHENIX related questions. On 8/25/10 1:58 PM, Hailiang Zhang wrote: Hi there: As I understand, phenix.refine do real-space refinement locally (by DiffMap), but from the documentation, I didn't find the keywords to specify the residue range to be refined. Thanks for any help! Best Regards, Hailiang
Re: [ccp4bb] Local real-space refinement by phenix
I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. What have people got against sending purely Phenix questions to the Phenix list? George PS. Since there is no SHELX list, if you have a specifically SHELX question you should just email me directly, as in fact most users do. Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 25 Aug 2010, Hailiang Zhang wrote: Hi there: As I understand, phenix.refine do real-space refinement locally (by DiffMap), but from the documentation, I didn't find the keywords to specify the residue range to be refined. Thanks for any help! Best Regards, Hailiang
Re: [ccp4bb] Local real-space refinement by phenix
On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) All the best! Pavel.
Re: [ccp4bb] Local real-space refinement by phenix
Just realized there is a seperate phenix bb. Sorry guy... I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. What have people got against sending purely Phenix questions to the Phenix list? George PS. Since there is no SHELX list, if you have a specifically SHELX question you should just email me directly, as in fact most users do. Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 25 Aug 2010, Hailiang Zhang wrote: Hi there: As I understand, phenix.refine do real-space refinement locally (by DiffMap), but from the documentation, I didn't find the keywords to specify the residue range to be refined. Thanks for any help! Best Regards, Hailiang
[ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards, Hailiang
Re: [ccp4bb] Local real-space refinement by phenix
Are you suggesting ccp4 is collapsing and people are coming back to the original source? Garib On 25 Aug 2010, at 22:17, Pavel Afonine wrote: On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) All the best! Pavel.
Re: [ccp4bb] Local real-space refinement by phenix
Hey Garib, LOL... no of course, I was just saying that I'm a bit allergic to re-naming well established things, and some other people may be too -:) Why don't we rename you Mr. Refmac -:) ? Pavel. On 8/25/10 2:25 PM, Garib Murshudov wrote: Are you suggesting ccp4 is collapsing and people are coming back to the original source? Garib On 25 Aug 2010, at 22:17, Pavel Afonine wrote: On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) All the best! Pavel.
Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
Why you do not use coot? It does exactly what you want. regards Garib On 25 Aug 2010, at 22:33, Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards, Hailiang
[ccp4bb] homology modeling
Hello, I've been using an the on-line homology modeling program Jigsaw-3D, and would like to run it on my own Linux box, but it requires CHARM, which I am unvailable to get because I am currently looking for a faculty position... does anyone know of an open source energy minimization program that can be substituted for CHARM (will GROMOS from SWISS PROT work?). Also is their any open source homology modeling program that includes solvent interactions in the minimization (it seems they all require $$, at least the good one's). Thanks in advance. Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
Re: [ccp4bb] Local real-space refinement by phenix
On 25 Aug 2010, at 22:17, Pavel Afonine wrote: On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) If 70+ years correspond to almost one generation ago, Russians must live very long and have children awfully late! Perhaps this is why they can accumulate such wisdom ... . With best wishes, Gerard. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
Hi Garib: Actually I tried coot real space refine zone, but the model seems not sliding into the best density map (I also tried dragging it around, but still not working fine). Then I found some comments saying minimizing the difference between 2mFo-DFc and Fc may be better, thats why I am asking for this. Best Regards, Hailiang Why you do not use coot? It does exactly what you want. regards Garib On 25 Aug 2010, at 22:33, Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards, Hailiang
Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
I mean the density of 2mFo-DFc or Fc maps. On Wednesday 25 August 2010 03:13:53 pm Hailiang Zhang wrote: Hi Garib: Actually I tried coot real space refine zone, but the model seems not sliding into the best density map (I also tried dragging it around, but still not working fine). Then I found some comments saying minimizing the difference between 2mFo-DFc and Fc may be better, thats why I am asking for this. Wait a minute. If you are minimizing a residual based on differences between Fo and Fc (never mind the precise coefficients), how is this real space refinement? (puzzled) Ethan Best Regards, Hailiang Why you do not use coot? It does exactly what you want. regards Garib On 25 Aug 2010, at 22:33, Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards, Hailiang -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
On Wednesday 25 August 2010 03:19:53 pm zhan...@umbc.edu wrote: I mean the density of 2mFo-DFc or Fc maps. I still don't understand. Real space refinement will minimize a fit of model to density in whatever map you give it. It's up to you which coefficients are used to calculate the map you are refining against. Ethan On Wednesday 25 August 2010 03:13:53 pm Hailiang Zhang wrote: Hi Garib: Actually I tried coot real space refine zone, but the model seems not sliding into the best density map (I also tried dragging it around, but still not working fine). Then I found some comments saying minimizing the difference between 2mFo-DFc and Fc may be better, thats why I am asking for this. Wait a minute. If you are minimizing a residual based on differences between Fo and Fc (never mind the precise coefficients), how is this real space refinement? (puzzled) Ethan Best Regards, Hailiang Why you do not use coot? It does exactly what you want. regards Garib On 25 Aug 2010, at 22:33, Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards, Hailiang -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
Ethan, I still don't understand. Real space refinement will minimize a fit of model to density in whatever map you give it. It's up to you which coefficients are used to calculate the map you are refining against. This is true. However, I guess, the way it is implemented in Coot is a bit different (Paul, please correct me if I'm wrong). Compare slides #4 and #5: http://cci.lbl.gov/~afonine/rsr.pdf Pavel.
Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
I think Paul (Emsley) is better qualified to answer to this question. However 1) coot uses 2mFo-DFc maps 2) you should be able to feed any map you want to coot so it is nice place for experimenting this kind of calculation 3) You may try to relax gemetry 4) Usually if the model does not fit into electron density and programs do not want to correct it then there may be some fundamental problem in this part of the model a) multiple conformation b) out of register errors c) pepflip or something like that. If it is extremely necessary we can add such option in ccp4. Regards Garib On 25 Aug 2010, at 23:13, Hailiang Zhang wrote: Hi Garib: Actually I tried coot real space refine zone, but the model seems not sliding into the best density map (I also tried dragging it around, but still not working fine). Then I found some comments saying minimizing the difference between 2mFo-DFc and Fc may be better, thats why I am asking for this. Best Regards, Hailiang Why you do not use coot? It does exactly what you want. regards Garib On 25 Aug 2010, at 22:33, Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards, Hailiang
Re: [ccp4bb] (non-crystallographic content ALERT)
I don't see what George's attempt to point out that pure-phenix questions should be asked in phenix bb (and the point itself may be subject to different opinions) has to do with renaming Moscow streets and subway stations (unless you thought that the proposition to rename ccp4bb is serious). You do realize that most of the renamed streets existed prior to 1917 and were renamed by Bolsheviks at some point to honor the ideology and group of people who committed the most massive atrocity in the history of humankind? The comprehensive list of renamed streets can be found here http://onlinelibrary.wiley.com/doi/10./j.1467-9434.2005.00371.x/abstract and except for occasional writer with anti-monarchy leanings or anarchist we are talking about representatives of the first class mass murder machine. I sincerely hope you are not allergic to changing Dzerzhinsky square back to Lubyanka (which name people used anyway). Cheers, Ed. On Wed, 2010-08-25 at 14:38 -0700, Pavel Afonine wrote: Hey Garib, LOL... no of course, I was just saying that I'm a bit allergic to re-naming well established things, and some other people may be too -:) Why don't we rename you Mr. Refmac -:) ? Pavel. On 8/25/10 2:25 PM, Garib Murshudov wrote: Are you suggesting ccp4 is collapsing and people are coming back to the original source? Garib On 25 Aug 2010, at 22:17, Pavel Afonine wrote: On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) All the best! Pavel. -- 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] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
But equation given in slide #4 is exactly least-square equation with
some modified maps. Just use Pareval's theorem, then for case of 2mFo-
Dfc you will have
sum_{reflection used) (2mFo-DF_{c current) -k F_{model})^2
F_model is equal to F_{c current} at the point of calculation. All
gradients can be calculated analytically.
That is an interesting observation.
regard
Garib
On 25 Aug 2010, at 23:33, Pavel Afonine wrote:
Ethan,
I still don't understand. Real space refinement will minimize a fit
of model to density in whatever map you give it. It's up to you
which coefficients are used to calculate the map you are refining
against.
This is true.
However, I guess, the way it is implemented in Coot is a bit
different (Paul, please correct me if I'm wrong).
Compare slides #4 and #5:
http://cci.lbl.gov/~afonine/rsr.pdf
Pavel.
Re: [ccp4bb] (non-crystallographic content ALERT)
While I have as keen an interest in Russian history as the next person, I personally feel that this thread has travelled far enough from CCP4 and crystallography to warrant moving any further discussion in this vein to another forum. On Aug 25, 2010, at 3:57 PM, Ed Pozharski wrote: I don't see what George's attempt to point out that pure-phenix questions should be asked in phenix bb (and the point itself may be subject to different opinions) has to do with renaming Moscow streets and subway stations (unless you thought that the proposition to rename ccp4bb is serious). You do realize that most of the renamed streets existed prior to 1917 and were renamed by Bolsheviks at some point to honor the ideology and group of people who committed the most massive atrocity in the history of humankind? The comprehensive list of renamed streets can be found here http://onlinelibrary.wiley.com/doi/10./j.1467-9434.2005.00371.x/abstract and except for occasional writer with anti-monarchy leanings or anarchist we are talking about representatives of the first class mass murder machine. I sincerely hope you are not allergic to changing Dzerzhinsky square back to Lubyanka (which name people used anyway). Cheers, Ed. On Wed, 2010-08-25 at 14:38 -0700, Pavel Afonine wrote: Hey Garib, LOL... no of course, I was just saying that I'm a bit allergic to re-naming well established things, and some other people may be too -:) Why don't we rename you Mr. Refmac -:) ? Pavel. On 8/25/10 2:25 PM, Garib Murshudov wrote: Are you suggesting ccp4 is collapsing and people are coming back to the original source? Garib On 25 Aug 2010, at 22:17, Pavel Afonine wrote: On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) All the best! Pavel. -- 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 / -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Marian Harris [ mshar...@lbl.gov ] [ 1-510-486-6886 ] --
Re: [ccp4bb] Local real-space refinement by phenix
The fault is entirely with those who respond to phenix questions. You can't blame the askers for guessing that CCP4BB will get a better response. I call this The Republican Fallacy. This fallacy is predicated on the assumption that it is easier to modify behavior than it is to modify the environment. James On Aug 25, 2010, at 2:07 PM, Pavel Afonine wrote: P.S.: Second reminder: there is PHENIX mailing list to use for PHENIX related questions.
