From info-iris-request@vmb.brl.mil Fri Jun 14 13:27:35 1991 Date: 14 Jun 91 14:55:43 GMT From: Don Sosoka Organization: NASA/Lewis Research Center, Cleveland Subject: lighted, multi-colored polys To: info-iris@BRL.MIL Status: R I know this should be an easy one and the answer must be docummented some- where but I can't find it. Please Help! I want to draw smooth (GOURAUD) shaded lighted polygons starting with different colors at each vertex. Assuming the lighting model is setup correct (which it seems to be), if I do something like call SHADEM (GOURAU) call BGNPOL do 10 i = 1,N vn(1) = XN(i) vn(2) = YN(i) vn(3) = ZN(i) call N3F (vn) icv(1) = IRED(i) icv(2) = IGREEN(i) icv(3) = IBLUE(i) call C3I (icv) v(1) = X(i) v(2) = Y(i) v(3) = Z(i) call V3F (v) 10 continue call ENDPOL I get smooth shaded colored polygons but no lighting effects. If I reverse the order: call SHADEM (GOURAU) call BGNPOL do 10 i = 1,N icv(1) = IRED(i) icv(2) = IGREEN(i) icv(3) = IBLUE(i) call C3I (icv) vn(1) = XN(i) vn(2) = YN(i) vn(3) = ZN(i) call N3F (vn) v(1) = X(i) v(2) = Y(i) v(3) = Z(i) call V3F (v) 10 continue call ENDPOL I get a nicely lit surface but all gray shaded. What's the trick? (or am I way off base). Thank's. From chemistry-request@ccl.net Fri Jun 14 14:05:19 1991 Date: Fri, 14 Jun 1991 13:35 EST From: "Richard C. Elder, Chemistry, U of Cincinnati" Subject: Staff crystallographer position open at UC To: CHEMISTRY@ccl.net Status: R STAFF X-RAY CRYSTALLOGRAPHER The Chemistry Department of the University of Cincinnati is searching for an expert in X-Ray crystallography to supervise its structure determination service. Hardware includes a Nicolet/Siemens R3 diffractometer and a microVAX II computer networked to the University computing system. Significant experience in X-Ray crystallography and a PhD is required. Postdoctoral experience and/or experience directing such a facility are desirable. Preference will be given to candidates with experience as system manager of a multiuser computer and/or in the field of molecular modeling. This is a permanent staff position and carries full fringe benefits. Applicants should send a resume and request that three letters of recommendation be sent to Professor Estel D. Sprague, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172. The University of Cincinnati is an Equal Opportunity/Affirmative Action employer. From chemistry-request@ccl.net Fri Jun 14 16:13:02 1991 Date: Fri, 14 Jun 91 14:12:14 EST From: Shaun Black Subject: Poly Ala vs Poly Gly To: Scott Le Grand Status: R Scott- I'm not absolutely certain of the answer, but perhaps my thoughts will help you get closer. Poly-L-Ala is a model polymer (as is Poly-L-Glu) of peptides that readily assume an alpha helical conformation. The methyl side chain ("R" group) of Ala is both hydrophobic enough and bulky enough to exclude water, yet not so bulky as to cause unfavorable van der Waal's contacts between adjacent residues; thus, a helical structure is favored. Gly is commonly assumed to be a "helix breaker" because it has an "R" group of Hydrogen which lacks the hydrophobicity and steric bulk needed to exclude water from the helix. If water has access to the helix, the carbonyl...HN- hydrogen bonds can be broken by exchange and the helix would "fall apart" (revert to another conformation). This should be the case for poly-Gly. Thus, if you do energy minimization/dynamics for poly-Gly in vacuuo, I would assume that helical structure would result (left of right handed pitch), because the hydrogen bonds could form and the side chain (hydrogen) would offer no steric repulsion. However, it would be essentially impossible for helical structure to exist in the presence of water. So, my answere is *both* helical and non-helical, depending on the experimental or computational conditions (vacuum/organic solvent vs water). Hope this helps! =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Shaun D. Black | Bitnet: black@ohstphrm.bitnet Ohio State University | Internet: black@ohstphrm.pharmacy.ohio-state.edu College of Pharmacy | Phone: (614) 292-3925 500 West 12th Avenue | FAX: (614) 292-2435 Columbus, OH 43210-1291 | :-) =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Fri Jun 14 17:04:33 1991 Date: Fri, 14 Jun 91 16:11:46 EDT From: shenkin@avogadro.barnard.columbia.edu (Peter S. Shenkin) To: Shaun Black , Subject: Re: Poly Ala vs Poly Gly Status: R Excuse me... It is my recolletion that Poly-Ala is almost completely insoluble in water, though it does form helix in the non-polar solvents that it dissolves in. Can someone verify or correct me? I'm not sure about poly-gly in this regard, but the reason it's felt to be a helix- breaker in proteins is, I think, because so much more of the Ramachandran map is accessible to it, since it has no C-beta; thus there is more of an entropy loss in being frozen into a helix. Now that I think about it, though, this makes little sense, since I know of no data that says that gly is in fact less ordered (eg, higher T factor) than other residues in proteins, though this would be interesteing to look at. But in any case, it has more intrinsic flexibility than the other amino acids, and any interactions present which stress the helix would be likely to break it at its "weak link." -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************* Peter S. Shenkin, Department of Chemistry, Barnard College, New York, NY 10027 (212)854-1418 shenkin@avogadro.barnard.columbia.edu shenkin@cunixc.BITNET ***"In scenic New York... where the third world is only a subway ride away."** From chemistry-request@ccl.net Fri Jun 14 19:14:42 1991 Date: Fri, 14 Jun 91 18:34:31 EST From: Shaun Black Subject: Poly-Ala To: "Peter Shenkin, et al." Status: R It is my recollection that poly-Ala is only sparingly soluble in water, but enough can be gotten into solution to do a CD spectrum and see that it is alpha helical. Poly-Gly will probably be more soluble in water, but only because it likely unfolds and hydrogen bonds with the solvent. My bet is for "random coil" in water. It's not clear to me what the entropic considerations would be, net. More discussion on this would be interesting. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Shaun D. Black | Bitnet: black@ohstphrm.bitnet Ohio State University | Internet: black@ohstphrm.pharmacy.ohio-state.edu College of Pharmacy | Phone: (614) 292-3925 500 West 12th Avenue | FAX: (614) 292-2435 Columbus, OH 43210-1291 | :-) =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Fri Jun 14 20:57:08 1991 Date: Fri, 14 Jun 91 20:09:31 EDT From: shenkin@avogadro.barnard.columbia.edu (Peter S. Shenkin) To: Shaun Black , Subject: Re: Poly-Ala Status: R Gee, a real SCIENCE discussion on this list! I love it! Shaun D. Black | Bitnet: black@ohstphrm.bitnet writes: > It is my recollection that poly-Ala is only sparingly soluble in water, > but enough can be gotten into solution to do a CD spectrum and see that it > is alpha helical. Poly-Gly will probably be more soluble in water, but > only because it likely unfolds and hydrogen bonds with the solvent. My > bet is for "random coil" in water. It's not clear to me what the entropic > considerations would be, net.... In aqueous solution entropic changes in the solvent are important. I'm almost sure poly-ALA is helical in CCl4. If poly-GLY is a random coil in that solvent, my guess is that its greater chain entropy (greater allowed region in the Ramachandran plot is responsible). I admit that this is a supposition on top of a supposition, so maybe someone out there who knows can comment. > ....More discussion on this would be interesting. Always glad to add my $.02 :-) -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************* Peter S. Shenkin, Department of Chemistry, Barnard College, New York, NY 10027 (212)854-1418 shenkin@avogadro.barnard.columbia.edu shenkin@cunixc.BITNET ***"In scenic New York... where the third world is only a subway ride away."** From chemistry-request@ccl.net Fri Jun 14 23:11:35 1991 Date: Fri, 14 Jun 91 20:08:00 PDT From: milik@scripps.edu (Mariusz Milik) To: SML108@PSUVM.PSU.EDU, chemistry@ccl.net Subject: helix-breakers Status: R Scott, some information about role of glycine in turns forming you can find eg. in "Turns in Peptides and Proteins" by G.D.Rose, L.M.Gierasch and J.A.Smith (Advances in Protein Chemistry vol 37 p.1). I'm not specialist in the subject, but it looks, that GLY is really helix-breaker. For example substitution of GLY to the helix sequence: 3K(1) - Ac-AAAKAAAKAAAK-ANH2, breaks helix (Sternberg 1987 (?)), there is many additional examples. Steric and entropic effect may be important in the case of GLY, but it is something like correlation between turn propensity and hydrophobicity profile. May be for break the helix GLY need some help from the neighborhood ? So, may be the conformation of poly-GLY in CCl4 is weak connected with role of GLY in real protein sequence and your calculations are valid? I will appreciate if you can send me more information about your calculation. I try to make simple lattice model of an (alpha-alpha) hairpin, last time and I am looking for information in this subject. From chemistry-request@ccl.net Fri Jun 14 23:42:41 1991 Date: Fri, 14 Jun 91 23:08:30 EST From: Shaun Black Subject: Poly-Ala II To: Peter Shenkin et al II Status: R I would still estimate that poly-Ala and poly-Gly will be helical in CCl4, and that only the latter will unfold in water. But, that brings up an interesting (ignorant?) question. Can the chlorine atoms of CCl4 serve as hydrogen bond acceptors? Certainly, there is no net charge on carbon tet, but significant partial negative charges must be present on the chlorines. Any thoughts? =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Shaun D. Black | Bitnet: black@ohstphrm.bitnet Ohio State University | Internet: black@ohstphrm.pharmacy.ohio-state.edu College of Pharmacy | Phone: (614) 292-3925 500 West 12th Avenue | FAX: (614) 292-2435 Columbus, OH 43210-1291 | :-) =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=