From grzesb@asp.biogeo.uw.edu.pl Sat Jun 8 10:52:30 1996 Received: from asp.biogeo.uw.edu.pl for grzesb@asp.biogeo.uw.edu.pl by www.ccl.net (8.7.5/950822.1) id KAA02868; Sat, 8 Jun 1996 10:48:50 -0400 (EDT) Received: by asp.biogeo.uw.edu.pl (5.61/1.34) id AA11312; Sat, 8 Jun 96 16:52:56 +0200 Date: Sat, 8 Jun 96 16:52:56 +0200 From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Message-Id: <9606081452.AA11312@asp.biogeo.uw.edu.pl> To: chemistry@www.ccl.net Subject: Summary: Rainbow spectrum in InsightII Daear Netter Few days ago I asked a question about rainbow spectrum in InsightII (MSI/[BIOSYM]). Below there is summary of responses I've got. Following these responses I've created macros for making such spectrums. First one - SIMPLE_RAINBOW can be used under InsightII ver3.00. It is from -0.1 (BLUE) to 0.1 (RED) divided into four subranges. Second one: FULL_RAINBOW can be used under InsightII ver 95.0.3. It is from -0.1 (VIOLET) to (0.1) DARK_RED divided into ten subranges. In both cases underrange values are colored using minimal color (blue or violet repectively) and overrange values are fully transparent - it is useful to color potential surfaces with molecules inside a map. It is worth to note that one can modify subranges (number of, values, color) and this way create his own spectrum. It can be useful to show some particular properties of electrostatic potential. Thanks all who responded and see you again, CCL. Yours sincerely - Grzegorz Bakalarski P.S. Does anybody know why insightII v.3.00 does NOT read spectrums created with insightII v.3.00 ? ******************************************************************************* MACROS ****************************************************************************** *********************MACRO: simple_rainbow ; insightII v.3.00 ************** Create Spectrum simple_rainbow Continuous -0.1 blue 0.1 red blue 255,0,0,0 Subrange Spectrum New_Subrange simple_rainbow Continuous -0.1 blue -0.03000001 0,255,255,255 Subrange Spectrum New_Subrange simple_rainbow Continuous -0.03 0,255,255,255 -0.00000001 green Subrange Spectrum New_Subrange simple_rainbow Continuous 0.00000001 green 0.03 yellow Subrange Spectrum New_Subrange simple_rainbow Continuous 0.03000001 yellow 0.1 red Orient Spectrum simple_rainbow North Right/Under *********************MACRO: full_rainbow ; insightII v. 95.0.3 *************** #m:Edit Spectrum new_spectrum_dlg spectrum FULL_RAINBOW -0.100000 0.100000 127,0,255,255 127,0,0,255 10 edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 1 -d_discrete 0 -d_split -d_delete -0.100000 -0.080000 127,0,255,255 blue edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 2 -d_discrete 0 -d_split -d_delete -0.080000 -0.060000 blue 0,127,255,255 edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 3 -d_discrete 0 -d_split -d_delete -0.060000 -0.040000 0,127,255,255 cyan edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 4 -d_discrete 0 -d_split -d_delete -0.040000 -0.020000 cyan 0,255,127,255 edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 5 -d_discrete 0 -d_split -d_delete -0.020000 0.000000 0,255,127,255 green edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 6 -d_discrete 0 -d_split -d_delete 0.000000 0.020000 green 127,255,0,255 edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 7 -d_discrete 0 -d_split -d_delete 0.020000 0.040000 127,255,0,255 yellow edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 6 -d_discrete 0 -d_split -d_delete 0.000000 0.020000 green 127,255,0,255 edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 8 -d_discrete 0 -d_split -d_delete 0.040000 0.060000 yellow orange edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 9 -d_discrete 0 -d_split -d_delete 0.060000 0.080000 orange red edit_spectrum_dlg spectrum FULL_RAINBOW left_e_d_pos 127,0,255,255 0,0,0,0 10 -d_discrete 0 -d_split -d_delete 0.080000 0.100000 red 127,0,0,255 edit_spectrum_dlg spectrum FULL_RAINBOW above_e_d_pos 127,0,255,255 0,0,0,0 1 -d_discrete 0 -d_split -d_delete -0.100000 -0.080000 127,0,255,255 blue ************************END of MACROS ************************************************** SUMMARY ************************ Original Querry ********************************** Dear NeT, I'd like to ask if anyone knows how could I create rainbow color spectrum in InsightII program (from MSI (Biosym)). I'd like to color my slice trough electrostatic potential using rainbow spectrum ( violet, bue , green, yellow, orange, red). Thanks for any suggestions. Best regards. Grzegorz Bakalarski Warsaw University Poland **************************** Responses ************************************** ################################################# From: "Adrian Roitberg" Combinations of these should do... Create Spectrum zfin_hc_sp Continuous -0.301 blue 0.283 red blue red Subrange Spectrum New_Subrange zfin_hc_sp Continuous -0.301 blue -0.009 green Subrange Spectrum New_Subrange zfin_hc_sp Continuous -0.008 green 0.283 red Orient Spectrum zfin_hc_sp North Right/Under Best regards adrian -- Adrian E. Roitberg ======================================================================== National Institute for | Phone: (301) 975-4469. Fax (301) 330-3447 Standards and Technology | E-mail : adrian@nist.gov Bioprocess Engineering Group | Building 222, A-353 | URL : http://www.chem.nwu.edu/~adrian Gaithersburg, MD 20899 | ======================================================================== ############################################################################ From: chatt@tniri.go.jp (Abhijit Chatterjee) In INSIGHTII of biosym there is a colour menu in contour, you can change the colour of the potential map using that. regards Abhijit ############################################################################# From: katagiri@nightmare.qub.ac.uk (katagiri) Dear Dr. Grzegorz, As for the rainbow color, if you have tbl file, I know how to creat. Please send me your tbl file. Sincerly Yours, -Masa Katagiri ----------------------------------------------------------------------- Masa Katagiri Queen's University of Belfast Atomistic Simulation Group http://titus.phy.qub.ac.uk School of Mathematics and Physics Tel:+44 1232 245133 ext.3528 Belfast BT7 1NN Fax:+44 1232 241958 Northern Ireland E-mail:katagiri@nightmare.qub.ac.uk ----------------------------------------------------------------------- ############################################################################## From: "Ryan Koehler" Subject: Time: 9:57 AM OFFICE MEMO rainbow in insightII Date: 5/30/96 By using the 'spectrum' command you can create / modify color spectrums that may be used to map to grid values (i.e. what you wish to slice) producing a rainbow color effect...... Of course (given that its insightII) this is not as straight forward as it might be: The 5.3 version only allows you to create spectrums as linear transverses of RGB space. Since no such RGB transverse lets you sample all the hues of the rainbow, you cannot get a rainbow in a single step. Instead, you have to create an initial (non-rainbow) spectrum then sequentially divide it into smaller color ranges using the 'subrange' command under spectrum. For example, if you want to map the rainbow (violet, blue, green, yellow, orange, red -V,B,G,Y,O,R) to the value range -2 to 3, you would perform the following (not sure of exact syntex, but if you play with the interface you should be able to figure it out): Make an initial spectrum from -2 (V) to 3 (R). Make a subrange from -2 (V) to -1 (B) Make a subrange from -1 (B) to 0 (G) Make a subrange from 0 (G) to 1 (Y) Make a subrange from 1 (Y) to 2 (O) Make a subrange from 2 (O) to 2.99 (R) -the 2.99 is important for some obscure reason, as if you try 3, insight won't allow you to make the final subrange. Once you have this, save the spectrum. Also save the log file so that you can do this again (with different colors or values) without doing all of this >from the menu. -Hope this helps, Ryan ******************** End of Responses ********************************************** From chpajt@bath.ac.uk Sat Jun 8 17:52:35 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.7.5/950822.1) id RAA03737; Sat, 8 Jun 1996 17:26:27 -0400 (EDT) Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Sat, 8 Jun 1996 22:26:17 +0100 Date: Sat, 8 Jun 1996 22:26:13 +0100 (BST) From: A J Turner To: chemistry@www.ccl.net Subject: Glycosidic enzymes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I am performing QM/MM modeling using a local development of the CHARMM program. At present I wish to compare the ability of this program to model glycoside hydrolysis with COSMO and similar methods (in solution). However, the aim is to move on to enzyme work a.s.a.p. So - does anyone know of an enzyme involved with glycoside hydrolisys (or similar reactions) for which a structure is known and some kinetic isotope effects are known? Thanks in advance Alex P.S. Thanks for the help on ESP/MOPAC. The best resonces have been on CCL anyway, but if anyone is especially interested I will forward all responces. +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+