From flicker@colloid.engin.umich.edu Thu Jan 7 06:50:07 1993 Date: Thu, 7 Jan 93 11:50:07 -0500 From: Scott Gregory Flicker Message-Id: <9301071650.AA04096@colloid.engin.umich.edu> To: chemistry@ccl.net Subject: \email address I am looking for the email address of Max L. Berkowitz Department of Chemistry University of North Carolina, Chapel Hill Thanks Scott Flicker From rdh@iris36.biosym.com Thu Jan 7 00:33:49 1993 Date: Thu, 7 Jan 93 08:33:49 -0800 From: rdh@iris36.biosym.com (Russ Helfand) Message-Id: <9301071633.AA24774@iris36.biosym.com> To: CHEMISTRY@ccl.net Subject: Solid rendition of solvent access. surf. with Insight II Several days ago, a query was put out over this network asking for a way to visualize a solvent accessible surface as a solid contour. If you have Insight II and DELPHI, the following method will make this visualization possible. * Invoke Insight II. * Build your molecule. * Fix the potentials and charges of all atoms. * Select the DELPHI module. * In the SETUP pulldown select the GRID command. Set the border space to 5.0 and select EXECUTE. * Select the FILES command in the SETUP pulldown. Toggle DIELECTRIC_MAP to ON and select EXECUTE. * Select the ITERATIONS command in the SETUP pulldown. Toggle AUTO_ITERATIONS to OFF. Set the LINEAR ITERATIONS to 0. Toggle the CONVERGE_CRITERIA to ON. Set both the RMS DIFF and the MAX DIFF to 10. * Select the RUN command from the RUN_DELPHI pulldown. Set EXECUTE MODE to COM. Set the ASSEMBLY/MOLECULE to be the molecule whose surface you wish to examine. Select EXECUTE. * Pop the textport forward and place the cursor in it. From the keyboard enter ^Z (hold down the control key and hit the z key). * Edit (with vi or any other editor) the new file created with the prm extention. Look for a line that describes how many Linear PB iterations there will be. Even though you set it to 0 with the ITERATIONS command the prm file may show that it is 200. (This is a bug that we are going to try to fix.) In the editor set this value to 0. * Get out of the editor and enter fg. This should return you to Insight II. * In the SETUP pulldown choose the INITIALIZE command. Set the PARAMETER OPTION to USER_PARAM_FILE and select the prm file that you just edited as the PARAMETER FILE NAME and select EXECUTE. * Again select the RUN command from the RUN_DELPHI pulldown. This time set the EXECUTION MODE to BACKGROUND and select EXECUTE. * The job should take about 20-30 seconds (maybe a bit longer for large proteins). It should result in an eps file being created. * When the job completes, enter the Insight II command: unix "epstogrd " where is the name of the eps file created. It will be named based on the JOB NAME given in the RUN command but will terminate with a 0 and an extension of eps. If you are unsure of what the file is, execute the command: unix "ls -t *.eps" before you do the epstogrd (above). * Select the GET command from the GRID pulldown. Choose the grd file listed in the value-aid. It should be named _eps.grd. It was created by epstogrd. * Select the CONTOUR command from the GRID pulldown. Set the GRID NAME to be the grid that you created with the GET command. Select any name you like for the CONTOUR_NAME_ROOT. Set the CONTOUR LEVEL to 3. This is the interfacial level between the solvent and the protein. It will show you the solvent accessible surface!!! Select SOLID as your DISPLAY STYLE. Pick any color. * If you like, you can later recolor the solid surface that you created to be coded by electrostatic potential. Use the COLOR command from the CONTOUR pulldown. If you have problems or questions with this method, please feel free to contact me. --------------------------------------------------------------------------- Russ Helfand "Eat beans, not beings ... Eat sushi, not ushi or mushi" From J_BROWN@uvmvax.uvm.edu Thu Jan 7 10:06:00 1993 Date: Thu, 7 Jan 1993 15:06 EST From: J_BROWN@uvmvax.uvm.edu Subject: Conformational analysis book references provided To: chemistry@ccl.net Message-Id: <01GT8PF80GWG0008I8@uvmvax.uvm.edu> Don: Try these books: Acyclic Organonitrogen Stereodynamics Joseph B. Lambert and Yoshito Takeuchi VCH 1991 ISBN 1-56081-555-8 Cyclic Organonitrogen Stereodynamics Joseph B. Lambert and Yoshito Takeuchi VCH 1991 ISBN 0-89573-773-6 The Conformational Analysis of Cyclohexenes, Cyclohexadienes, and Related Hydroaromatic Compounds Peter W. Rabideau VCH 1989 ISBN 0-89573-702-7 -Jay From adit@Kodak.COM Thu Jan 7 11:04:06 1993 Date: Thu, 7 Jan 93 16:04:06 EST From: adit@Kodak.COM (Adi Treasurywala) Message-Id: <9301072104.AA18944@bcc9.kodak.com> To: chemistry@ccl.net Subject: Structures of cyclic hexapeptides Folks, I am looking for any and all hard data that I can lay myhands on for the following: Solution structure (NOE data etc) on cyclic hexapeptides which are made up of all L amino acids and which **DO NOT CONTAIN A PROLINE**. I already have the four crystal structures from the Cambridge Database. I will be happy to send out a summary of the answers if there is sufficient interest. Thanks Adi