Re: [ccp4bb] chiral volumes--2nd try
Berhard, Then you have to define what you mean by smallest. SHELXL uses the (ASCII) alphabetical order of the three atom names for this purpose (SHELX manual page 7-23) so that it is unambiguous (since the names are not allowed to be the same), but presumably other programs use other conventions (e.g. the Cahn-Ingold-Prelog rules). George 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 Mon, 19 Apr 2010, Bernhard Rupp wrote: The problem of discrete values in restraints can be circumvented by computing a corresponding continuous value such as a chiral volume Vc, which is given by a scalar triple vector product A (B x C) originating at the central atom. With the smallest ligand pointed toward the observer and clockwise assignment of the vectors, the sign of the chiral volume is positive, and computes to about 2.5 Å3. An alternative method of restraining chirality is by restraining the improper torsion (or improper dihedral or zeta-value) between CaNCCb to +34 deg. p 630 ;-) BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Patrick Loll Sent: Monday, April 19, 2010 2:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] chiral volumes--2nd try Sorry, the original post looks garbled (mirroring my internal state, no doubt). I'm trying again, sending as plain text: Friends, A question about the definition of chiral volumes: I'm looking for the definition of the SIGN of a chiral volume. The only ccp4 reference I can find (readily) is this: http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html This page gives an algorithm for determining the sign, which I paraphrase here: * Call the central (chiral) carbon a, and its three non-hydrogen substituents b, c, and d. * Arrange things so that as you look from b to c to d, your eye is moving clockwise. * If atom a is below the plane formed by b, c, d, then the chiral volume is positive (otherwise negative) Clear enough. However, when I start to apply this rule to basically every library I have ever used, I get the opposite result. Try it, for example, with the ALA.cif file distributed with ccp4: _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign ALA chir_01 CA N CB C negativ Assigning a as the centre atom and atoms b-d as numbers 1-3, when I apply the rule from the refmac page I get a positive chiral volume, not the negative one found in the cif file. Ditto for every other example that I have tried. Am I mis-reading what is meant by above and below? I'm assuming that if atoms b, c, and d all lie in a vertical plane, and you are facing that plane, then below means on the far side of that plane and above means between you and the plane. When I use the definition V1 * (V2 x V3), where V1 is vector FROM chiral atom to 1st substituent (e.g., CA to N in alanine example above), V2 = vector from chiral atom to 2nd substituent, etc., then I get the expected sign for the chiral volume. So is the refmac page wrong, or am I falling prey to some roaringly obvious stupidity? Having a rough Monday--starting to question my sanity. Thanks, Pat ps It appears that the term _chem_comp_chir.volume_sign is not defined in either the core or mmCIF dictionaries. Can this be right? --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] how to make cholesterol solution
Jerry, Steroids have a certain solubility also in ethylene glycol and PEG. You might be able to work out a crystallization strategy around this. The ethanol/PEG combination was used in: http://www.nature.com/nature/journal/v437/n7055/full/nature03923.html Enrico. Dear ALL: Sorry for this kind of off-topic question. I am going to co-crystallize one protein with cholesterol. I read some papers saying that their protein can be pre-incubated with 1mM cholesterol in the presence of 5% (v/v) ethanol. TO do so, I first dissolved cholesterol in 100% ethanol at a concentration of 10mM. However, it is very difficult to make the dilution into 5% ethanol either just in water or some buffers. Does anyone have such experience to make cholesterol solution in normal buffers plus some ethanol? Thanks a lot, -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] how to make cholesterol solution
if you are crystallizing membrane protein here is a useful protocol from JCIPMT website follow the link http://jcimpt.scripps.edu/protocols/JCIMPT_PreparationofCHSStock.pdf in my experience even after extensive sonication i filter the buffers otherwise we found that cholestrol comes out of solution when concentrating the protein at a later stage. padayatti On Mon, Apr 19, 2010 at 10:39 PM, Jerry McCully for-crystallizai...@hotmail.com wrote: Dear ALL: Sorry for this kind of off-topic question. I am going to co-crystallize one protein with cholesterol. I read some papers saying that their protein can be pre-incubated with 1mM cholesterol in the presence of 5% (v/v) ethanol. TO do so, I first dissolved cholesterol in 100% ethanol at a concentration of 10mM. However, it is very difficult to make the dilution into 5% ethanol either just in water or some buffers. Does anyone have such experience to make cholesterol solution in normal buffers plus some ethanol? Thanks a lot, Jerry McCully The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. Get busy. -- Pius S Padayatti Scientist, Polgenix, Inc. 11000 Cedar Ave, Suite 260 Cleveland, OH 44106 Phone: 216-658-4528 Fax: 216-658-4529
Re: [ccp4bb] Mysterious Crystals?
could try reverse matrix seed On Sun, Apr 18, 2010 at 10:46 PM, tat cheung cheng theif...@yahoo.com.hk wrote: Hi all, I have got some crystals, the purified protein was in Tris buffer with 300mM NaCl for crystallization. they grew in light weight PEG, PEG400 or monomethyl ethyl PEG500, they were needle shaped, could be long (~0.2mm) but very thin all the time and sometimes grew into sea-urchin like needle cluster. What interesting is, when i gridded crystallization conditions against pH or PEG amount, the crystals sizes and shapes varied, and the crystals were fragile so i believed they were protein crystals in nature. But upon X-ray diffraction, they gave no reflection at all, not even a faint spot. I wonder, beside silly mistakes like misalignment of the crystal to the beam, not enough exposure time, what could be the reason for this mysterious crystals? Are they protein or PEG or what? Thanks very much. Tc -- Pius S Padayatti Scientist, Polgenix, Inc. 11000 Cedar Ave, Suite 260 Cleveland, OH 44106 Phone: 216-658-4528 Fax: 216-658-4529
Re: [ccp4bb] chiral volumes--2nd try
Then you have to define what you mean by smallest. Correct. A little manual reading often goes along way :-) br
[ccp4bb] The effect of the absence of various diffraction data to the electronic density
I've seen a website where there are some dynamic pictures to show the effects of the absence of various diffraction data to the electronic density, such as the changing process of the electron density as the deletion of low-resolution data. But I can't find this website now, could anyone here also know this website? I first found that website from a CCP4BB email last winter. Thanks in advance, Yuan SHANG
[ccp4bb] Position Available
Hello all, I would appreciate it if you could distribute this flier to potential applicants. Thank you, Mark Walter Post-doctoral position: Structural Biology of Cytokine-Receptor Signaling A Post-doctoral position is available immediately to study the structure and function of cytokine receptor complexes that play essential roles in the development and control of the adaptive immune response. The inter-cellular communication provided by these molecules is controlled by a dazzling array of protein-protein interactions that our lab is unraveling. We also study the structure and function of virally encoded proteins produced by herpes and poxviruses that target the IL-10 family and allow the viruses to escape elimination by the immune system. Understanding the competing molecular strategies used by the host and virus to activate or deactivate the immune system may to lead novel ways of controlling chronic inflammation and/or improving the detection and elimination of persistent viral infections. The lab performs the techniques required to answer mechanistic questions about molecular recognition, viral immune evasion, and cell signaling including protein biochemistry, X-ray crystallography, surface plasmon resonance, isothermal titration calorimetry, computational and bioinformatic approaches, and structure-based functional assays in cells. Applicants are expected to be proficient in molecular biology, protein expression (multiple systems is a benefit), and protein purification methodologies. Experience in X-ray crystallography, or other structural or biophysical science (e.g. NMR, SAXS, etc), is a plus. Interested applicants should send a CV, statement of research interests, and list of references to: Dr. Mark R. Walter Department of Microbiology University of Alabama at Birmingham (UAB) RM 144 CBSE 1025 18th Street South Birmingham, AL 35243 wal...@uab.edu
Re: [ccp4bb] chiral volumes--2nd try
Dear Bernhard, You indeed have plenty of space to extend the margin notes on page 631! In the REFMAC monomer library that is also used by PHENIX, the sign of the chiral volume is explicitely defined for each chiral atom by _chem_comp_chir.volume_sign. For the L-aminoacids it is always defined by the order N CB C and the word negative. When I wrote SHELXL (long before REFMAC and PHENIX) I decided not to use any dictionaries; they often contain typos and I prefer to write stand-alone executables. I did not want the order of the atoms in the input file to influence the sign. So I used the ASCII (alphabetical) order of the atoms, and I defined the sign so that the L-amino-acids would all have positive C-alpha chiral volumes. Note that the Cahn-Ingold-Prelog rules make L-Cysteine R and the other 18 standard L-amino-acids S, which would be confusing. I suspect that the sequence rules described in the REFMAC documentation were not actually always used in determining the order of atoms specified in the monomer library. At least for the standard L-amino-acids (including CB of Thr and Ile) the sign is always opposite to that used by SHELXL. Note that the RTAB instuction in SHELXL can be used to print out chiral volumes without specifying the three bonded atoms, they are taken from the connectivity table. Best wishes, George 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 Tue, 20 Apr 2010, Bernhard Rupp wrote: Actually, I have some space left under the figure caption this section refers to and will add the way SHELXL does it as another example. The CIPs are in a sidebar. Thx, BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of George M. Sheldrick Sent: Tuesday, April 20, 2010 12:17 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] chiral volumes--2nd try Berhard, Then you have to define what you mean by smallest. SHELXL uses the (ASCII) alphabetical order of the three atom names for this purpose (SHELX manual page 7-23) so that it is unambiguous (since the names are not allowed to be the same), but presumably other programs use other conventions (e.g. the Cahn-Ingold-Prelog rules). George 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 Mon, 19 Apr 2010, Bernhard Rupp wrote: The problem of discrete values in restraints can be circumvented by computing a corresponding continuous value such as a chiral volume Vc, which is given by a scalar triple vector product A ? (B x C) originating at the central atom. With the smallest ligand pointed toward the observer and clockwise assignment of the vectors, the sign of the chiral volume is positive, and computes to about 2.5 �3. An alternative method of restraining chirality is by restraining the improper torsion (or improper dihedral or zeta-value) between Ca?N?C?Cb to +34 deg. p 630 ;-) BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Patrick Loll Sent: Monday, April 19, 2010 2:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] chiral volumes--2nd try Sorry, the original post looks garbled (mirroring my internal state, no doubt). I'm trying again, sending as plain text: Friends, A question about the definition of chiral volumes: I'm looking for the definition of the SIGN of a chiral volume. The only ccp4 reference I can find (readily) is this: http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html This page gives an algorithm for determining the sign, which I paraphrase here: * Call the central (chiral) carbon a, and its three non-hydrogen substituents b, c, and d. * Arrange things so that as you look from b to c to d, your eye is moving clockwise. * If atom a is below the plane formed by b, c, d, then the chiral volume is positive (otherwise negative) Clear enough. However, when I start to apply this rule to basically every library I have ever used, I get the opposite result. Try it, for example, with the ALA.cif file distributed with ccp4: _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign ALA chir_01 CA N CB C negativ Assigning a as the centre atom and atoms b-d as numbers 1-3, when I apply the rule from the refmac page I get a positive chiral volume, not the negative one found in the cif file. Ditto for every other example that I have tried. Am I mis-reading what is meant by above and below? I'm
[ccp4bb] Faculty Job Posting
Applications are being accepted for a tenure track position at the Assistant or Associate Professor level in the Department of Biology, Faculty of Science, University of Waterloo. Applicants should have a PhD and postdoctoral experience with a research record in Macromolecular X-ray Crystallography. Duties of the position include establishment of an independent research program, teaching and supervision at the undergraduate and graduate levels, and participation in the running of the Department and University. The University has instrumentation for macromolecular crystallography, including a Rigaku Micromax/R-Axis 4++ diffractometer system. Inquiries and applications, consisting of a full curriculum vitae with publication record, statement of research interest and teaching experience, and names of three references, should be sent electronically to David R. Rose, Chair, Department of Biology, University of Waterloo, c/o Gini Kennings, gi...@uwaterloo.ca. The closing date for applications will be September 1, 2010, with a starting date on or after January 1, 2011. All qualified candidates are encouraged to apply; however Canadians and permanent residents will be given priority. The University of Waterloo encourages applications from all qualified individuals, including women, members of visible minorities, native peoples, and persons with disabilities.
Re: [ccp4bb] The effect of the absence of various diffraction data to the electronic density
On Tue, Apr 20, 2010 at 7:35 AM, 商元 shangyuan5...@gmail.com wrote: I've seen a website where there are some dynamic pictures to show the effects of the absence of various diffraction data to the electronic density, such as the changing process of the electron density as the deletion of low-resolution data. But I can't find this website now, could anyone here also know this website? I first found that website from a CCP4BB email last winter. You're probably thinking of James Holton's site: http://ucxray.berkeley.edu/~jamesh/movies/ or: http://bl831.als.lbl.gov/~jamesh/movies/ -Nat
[ccp4bb] Research Associate in X-ray Protein Crystallography of Light Induced Reactions at Imperial College London
Job Title Research Associate in X-ray Protein Crystallography of Light Induced Reactions Department/Division/Faculty Division of Molecular Biosciences, Faculty of Natural Sciences South Kensington Campus, London SW7 2AZ Closing Date 1 June 2010 (midnight GMT/BST) Fixed term for 24 months Applications are invited for a Research Associate position in the Division of Molecular Biosciences in the field of time resolved Laue X-ray crystallography of light sensitive proteins in the group of Dr. Jasper van Thor. The successful candidate will develop and employ experiments for time resolved X-ray diffraction using the pink-Laue technique at specialised beam line stations that combine pulsed broadband hard X-rays with pulsed optical excitation, at the SLS, APS and ESRF. The post will be based at Imperial College London, South Kensington campus The work will be conducted in a multidisciplinary environment which includes facilities for ultrafast electronic and vibrational spectroscopies to support the optical control of photolysis and reaction initiation in macromolecular crystals. The research deals with the light induced reactions in photoreceptors and fluorescent proteins and will focus on crystallisation of existing and new targets, analysis and optimisation of Laue diffraction, data processing and structure calculation of sub-ns intermediates. The van Thor group also provides support for ultrafast spectroscopic investigation of light induced reactions in targets. You will be required to work with members of the team on spectroscopic characterisation and photolysis control. You will have a PhD in Biochemistry, Chemistry, or Physics or the equivalent professional qualifications and experience with a track record in Structural Biology. Extensive experience in X-ray protein crystallography using synchrotron sources as well as experience with data processing and structure calculation of macromolecules are essential. You will also have experience in crystallographic data processing and structure calculation. Experience in biomolecular spectroscopy would be an advantage. Experience with molecular biology, protein purification and crystallisation will be desirable. Our preferred method of application is online via this website. Please download the following application form and save to your computer. Once completed, please upload your application form prior to submitting your application. Please enter job ID NS2010070AB into the College recruiting webpages http://www3.imperial.ac.uk/employment or directly https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?akRegionCode=IRC_VIS_VAC_DISPLAY_PAGEakRegionApplicationId=800transactionid=1751883119retainAM=YaddBreadCrumb=Sp_svid=17014p_spid=862010oapc=7oas=gMemD704ZdjaWC14QWLTmA.. Should you have any queries please contact: Dr Jasper van Thor – j.vant...@imperial.ac.uk -- Jasper van Thor Royal Society University Research Fellow Division of Molecular Biosciences South Kensington Campus Imperial College London London SW7 2AZ, UK Email j.vant...@imperial.ac.uk Phone +44-(0)20-75945071 http://www3.imperial.ac.uk/people/j.vanthor SOON: One Day Symposium on Ultrafast Vibrational Dynamics of Biomolecules, Thursday 29 April 2010 at Imperial College http://www3.imperial.ac.uk/molecularbiosciences/seminars/ultrafast-vibrational-dynamics-of-biomolecules
Re: [ccp4bb] chiral volumes--2nd try
For CB_ILE, the chiral volume sign in the REFMAC monomer library is the same as used by SHELXL, not the opposite as stated in my last posting. Apologies! George 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
[ccp4bb] A postdoc position at OpenEye Scientific Software, Inc, Santa Fe, NM USA
Postdoctoral Position in Structural Biology at OpenEye Scientific Software, Inc. Applications are invited for a postdoctoral position at OpenEye Scientific Software, Inc. to work on structural assessment and re-refinement of a large number of protein-ligand complex structures from a number of pharmaceutical companies to be deposited with the Community Structure-Activity Resource (CSAR) and the PDB. We seek a highly motivated Ph.D. with extensive experience in protein structure determination by X-ray crystallography to work in our Santa Fe, NM office. Experience with structure determination and interpretation are essential. Familiarity with protein-small molecule complex structures, refmac, phenix.refine and python are beneficial. Applicants must have a Ph.D. and fewer than 2 years of postdoctoral experience. This is s full time position of fixed term for two (2) years. A 401k plan, medical dental benefits, and profit sharing are all part of our standard compensation package. OpenEye Scientific Software Inc. is an Equal Opportunity Employer. Qualified individuals should submit a resume and cover letter along with the contact information for three references via e-mail to h...@eyesopen.commailto:h...@eyesopen.com. Please reference job code Structural Biology Position. HR: Structural Biology Position OpenEye Scientific Software, Inc. 9 Bisbee Court, Suite D Santa Fe, NM 87508
Re: [ccp4bb] The effect of the absence of various diffraction data to the electronic density
Sounds like you could be referring to my movies page: http://bl831.als.lbl.gov/~jamesh/movies/ -James Holton MAD Scientist 商元 wrote: I've seen a website where there are some dynamic pictures to show the effects of the absence of various diffraction data to the electronic density, such as the changing process of the electron density as the deletion of low-resolution data. But I can't find this website now, could anyone here also know this website? I first found that website from a CCP4BB email last winter. Thanks in advance, Yuan SHANG
Re: [ccp4bb] Proportion of MR in PDB
For once, I actually agree with Ian! I too refer to the process as molecular replacement, even if you don't run a molecular replacement program. For those who are interested in more than one opinion, other popular method used to determine the structure in the PDB that I still call MR are: 2639 fourier synthesis 447 difference fourier 96 rigid body refinement 39 rigid body 37 difference fourier plus refinement 31 isomorphous 31 difference fourier methods 25 refinement 21 rigid-body refinement 17 direct replacement 15 refmac 15 molecular substitution 15 molecular replacemen 15 difference map 14 native model phases 14 molrep 13 isomorphous molecular replacement 11 direct refinement 10 isomorphous with pdb entry 10 fourier difference 9 known phases 8 refined directly 8 isostructural to 8 difference fourier method 7 phaser 7 isomorphous to native 7 difference fourier from previously determined, related structure 6 rigid body refinement into new data 5 used previously- determined structure 5 direct based on known model 5 difference fourier maps 4 starting model was used without molecular replacement 4 protein structure is known in this cell -James Holton MAD Scientist Ian Tickle wrote: I would say it should still be classed as MR: the distinguishing feature of MR is surely that it uses an known structure as a starting model, not that it does a rotation/translation search. In any case the distinction between a rigid-body search and RB refinement is moot. At Astex our automated scripts routinely do a limited MR search for all our protein-ligand structures, even though it may not be necessary in all cases. This is because we have found from experience that RB refinement alone is often not sufficient: presumably the degree of non-isomorphism induced by soaking and/or freezing the crystals (e.g. we often see 5-10% changes in cell parameters) takes it beyond the radius of convergence of the refinement. We use a limited search MR to avoid issues of finding symmetry-related or origin-shifted solutions. Cheers -- Ian On Mon, Apr 19, 2010 at 3:06 PM, Edward A. Berry ber...@upstate.edu wrote: Quite a lot of structures in the PDB involve minor variations on structures that have already been solved (different ligands, mutants, high res), so the solution involves refining the previous structure against the new data, perhaps starting with rigid body refinement to correct minor variations in cell parameters. Would you include this in molecular replacement? Ed Nicholas Keep wrote: Thanks to several people for helpful comments to my question on the Proportion of MR in the PDB. I got two very detailed responses one from the OCA team at the Weizmann which went to the Bulletin Board This is what OCA has: From un total of 64,623 PDB structure files, 30,784 have 'MOLECULAR REPLACEMENT' as Method for Structure Determination. However, you must remember that we have a large number of false negatives Several reasons: - Only 47,557 structure files from the total of 64,623 report which method was used for structure determination. For example, 1CRY whose title reports using the MR method does not include the info in the proper REMARK. - Users are allowed to write almost anything as the METHOD USED TO DETERMINE THE STRUCTURE, making it difficult an accurate report. OCA found PDB italian speaking structure files reporting 'MOLECULARE REPLACEMENT' ... This and other problems are being reported to RCSB. and one from U of Virginia Based on information from Remark200 lines, 31761 structures were solved using MR, what comprise for 56.8% of all X-RAY structures (55843). Considering structures which were determined using 'primitive MR' the number grows to 34949 (62.6%). There are also some structures determined using combination of MR with SAD, MAD, SIR and MIR. If we would add them, the number will increase to 35258 (63.1%). Thanks again Nick
[ccp4bb] geometry problems with sugars
Hi All, My question is concerning geometry of NAGs in a glycoprotein structure. I recently solved the structure of a glycoprotein to 3 Å and modeled NAGs linked to Asn at 3 different places. NAGs and Asn-NAG links are refined in Phenix.refine as per the Phenix dictionary. However, when submitting the structure to the PDB, internal validation of PDB found that NAGs at 2 places have geometry problems (atoms surrounding the C1 of NAG are in the same plane). What I learned from Phenix bulletin board is that the refinement program is probably fixing the NAG into a local minimal structure to fit to the density the best (I have OK density for sugars) and that's causing the problem. So, I tried to fix the geometry of NAG while refining, so that the refinement does not change the geometry of the sugar. But, still the internal validation of PDB found the same problem with the sugars. Then, I tried replacing the NAGs with ideal monomers from Coot. Still, the problem persisted. PDB annotator's suggestion is to get the NAG coordinates from HIC-Up and try refinement in another program. I am wondering if any one else noticed (or had ) a similar problem with NAG geometry using either Phenix.refine or Coot. What baffles me is that the ideal NAG from coot dictionary did not pass the internal validation of the PDB. I would appreciate if any one has any suggestion (other than trying a different refinement program) to get around this problem. Is there a way to compare the NAGs in your structure to the ideal and get to know what to fix ? Thanks in advance Tirumal
Re: [ccp4bb] chiral volumes--2nd try
Joel, Agh. I can honestly say that this explanation never occurred to me, even though it is consistent with the data (But come on, any introductory organic chem text explains the R/S rules by moving from atom 2 to 3 to 4, and not by jumping from 2 to 4...surely you would follow the same convention in the refmac documentation, right?) What amazes me is my inability to find ANY documentation that actually explains the meaning of terms in the CIF used to define chiral volumes. OK, some of the terms ARE found in the mmCIF dictionary, but others seem made-up, like _chem_comp_chir.atom_id_1. Given that both refmac and phenix rely upon upon these libraries for determining geometries, you'd think that somewhere the terms would be defined explicitly. As several posters have pointed out, the triple scalar product is of course the correct way to define the chiral volume; but my point is that if you don't know which atoms the program is assigning to which vector, you're still in a pickle... Pat On 20 Apr 2010, at 3:51 PM, Bard, Joel wrote: Hi Patrick- I feel your pain having gone through exactly the same problem. It all has to do with the definition of When the eye goes from atom 2 to atom 4. I think we both assumed that this meant from 2 to 4 via 3 but I guess it doesn't. The ful text of my 2004 post: I think that two of the numbers are reversed in Figure 3 of the chiral center documentation for refmac5: http://www.ccp4.ac.uk/dist/html/refmac5/theory/chiral.html If one follows the Procedure to find the sign of a chiral centre with reference to the figure the eye would move from atom 2 through atom 3 to atom 4 as it traveled clockwise. This would generate a left handed coordinate system if atom 1 was behind the plane of the web browser so the sign of the chiral volume would be negative rather than positive as the text says. Switching the labels of atoms 2 and 3 (or 2 and 4 or 3 and 4 but 2 and 3 make it easier to visualize the right-hand-rule) would make it work. It seems like a very little thing but I'm feeble-minded enough to have spent more time than I'd like to admit trying to figure out why a little program I'd written was coming up with the wrong sign for the chiral volume when it had been correct the whole time. Of course I should have realized that it would be absurd for the statement: When the eye goes from atom2 to atom4 it should travel clockwise, to mean When the eye goes from atom2 to atom4 by passing through atom3 it should travel clockwise. It might be worth fixing, though, since I know for a fact that there are other people out there who are almost as easily confused as I am. Cheers, Joel --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] geometry problems with sugars
tirumal wrote: Hi All, My question is concerning geometry of NAGs in a glycoprotein structure. Fire away... I recently solved the structure of a glycoprotein to 3 Å and modeled NAGs linked to Asn at 3 different places. NAGs and Asn-NAG links are refined in Phenix.refine as per the Phenix dictionary. Errr.. that'll be the Refmac dictionary. However, when submitting the structure to the PDB, internal validation of PDB found that NAGs at 2 places have geometry problems (atoms surrounding the C1 of NAG are in the same plane). The surrounding atoms being the ND2, O5 and C2, I presume. The C1 should not (of course) be in the plane of those 3 atoms. What I learned from Phenix bulletin board is that the refinement program is probably fixing the NAG into a local minimal structure to fit to the density the best (I have OK density for sugars) and that's causing the problem. It seems unlikely to me that you density would be sufficiently strong to put C1, ND2, O5 and C2 into a plane. So, I tried to fix the geometry of NAG while refining, so that the refinement does not change the geometry of the sugar. But, still the internal validation of PDB found the same problem with the sugars. I don't follow this. How can you fix the atoms of the NAG and then refine it (and expect things to move)? Then, I tried replacing the NAGs with ideal monomers from Coot. Get Monomer in Coot use LIBCHECK to generate coordinates and restraints. I can use Get Monomer to import a NAG and create and refine a N-link quite happily (after deleting the O1 and HO1 of course - Coot won't do that for you yet). Still, the problem persisted. PDB annotator's suggestion is to get the NAG coordinates from HIC-Up and try refinement in another program. A very worthy path to pursue... I am wondering if any one else noticed (or had ) a similar problem with NAG geometry using either Phenix.refine or Coot. I don't see a problem. What baffles me is that the ideal NAG from coot dictionary did not pass the internal validation of the PDB. I'd find that surprising too (and to be accurate, it's from LIBCHECK and just imported into Coot). I would appreciate if any one has any suggestion (other than trying a different refinement program) to get around this problem. Perish the thought of suggesting a CCP4 refinement program on this list... :) Is there a way to compare the NAGs in your structure to the ideal and get to know what to fix ? I must admit that I'm curious to know what the PDB has against CCP4's NAG. HTH, Paul.
