From: FyD <fy...@q4...> - 2008-10-30 08:20:27
|
Dear All, At http://q4md-forcefieldtools.org/RED/index-test.php, one can see the DMSO molecule (Tripos mol2 file format loaded). I am surprised by the color of the carbons/hydrogens is pink while the oxygen/sulfur colors are correct. I guess it is because the name of the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23 Does it mean that only the chemical symbols are recognized as atom names ? So what about atom names in amino-acids such as CA, CB etc... Thanks, regards, Francois |
From: Angel H. <ang...@ua...> - 2008-10-30 10:02:02
|
FyD wrote: > At http://q4md-forcefieldtools.org/RED/index-test.php, one can see the > DMSO molecule (Tripos mol2 file format loaded). > > I am surprised by the color of the carbons/hydrogens is pink That's Jmol color for non-identified elements. > I guess it is because the name of > the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23 It's usually an issue with misaligned atom names (at least in pdb format, I'm not used to mol2). Check the mol2 format specification. > Does it mean that only the chemical symbols are recognized as atom names ? > So what about atom names in amino-acids such as CA, CB etc... Absolutely not. CA are read as "carbon, type CA i.e. alpha carbon of proteins". But in PDB, there is a space before the C; if you shift it one character to the left, it would be read as calcium. In addition, pdb has a field specific for the element symbol (close to column 79) which will be used in preference to that dedcue form the atom name. mol2 may have one too. 1. Check your mol2 format and whatever program is generating it. 2. Open the file in another viewer and see how it reads it, or even export it again to mol2 3. Edit the mol2 file and insert/delete a blank column where appropriate |
From: Angel H. <ang...@ua...> - 2008-10-30 10:14:05
|
OK, I've got it Jmol is not using the atom name for element identification; mol2 has an "atom type" field which seems to be both the cause and the cure. http://www.tripos.com/data/support/mol2.pdf In your DMSO file, the atom type for the offending atoms is CT and H1. This is not supported by mol2 spec. See http://www.tripos.com/mol2/atom_types.html http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html If you cahnge that to just C and H, Jmol behaves. You should maybe use the proper types, which seem to be C.3, H, S.o, O.2 They also work in Jmol. > > I guess it is because the name of > > the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23 As I said, not that name, but the type at column 50. |
From: FyD <fy...@q4...> - 2008-10-30 12:16:15
|
Dear Angel, > In your DMSO file, the atom type for the offending atoms is CT and H1. Yes, I agree. > This is not supported by mol2 spec. See > http://www.tripos.com/mol2/atom_types.html > http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html Yes > If you cahnge that to just C and H, Jmol behaves. You should maybe > use the proper types, which seem to be C.3, H, S.o, O.2 > They also work in Jmol. OK, but you consider here only the force field atom types from the Tripos force field. This means Jmol is not compatible with other force fields such as CHARMM, AMBER, etc... I think it would be more suitable that Jmol understand many force fields and not only this Tripos force field. The Tripos file format can be used by many programs different from Tripos Inc. For instance Amber force fields use CT, H1 force field atom types. This is why I provided CT, H1 in the force field atom type column of the DMSO.mol2 file... regards, Francois |
From: Robert H. <ha...@st...> - 2008-10-30 13:38:23
|
Francois, please try the JAR files in http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip These have a new mol2 reader that recognizes AMBER and GAFF atom types. Needs checking. Bob On Thu, Oct 30, 2008 at 6:44 AM, FyD <fy...@q4...> wrote: > Dear Angel, > > > In your DMSO file, the atom type for the offending atoms is CT and H1. > > Yes, I agree. > > > This is not supported by mol2 spec. See > > http://www.tripos.com/mol2/atom_types.html > > http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html > > Yes > > > If you cahnge that to just C and H, Jmol behaves. You should maybe > > use the proper types, which seem to be C.3, H, S.o, O.2 > > They also work in Jmol. > > OK, but you consider here only the force field atom types from the > Tripos force field. This means Jmol is not compatible with other force > fields such as CHARMM, AMBER, etc... I think it would be more suitable > that Jmol understand many force fields and not only this Tripos force > field. The Tripos file format can be used by many programs different > from Tripos Inc. > > For instance Amber force fields use CT, H1 force field atom types. > This is why I provided CT, H1 in the force field atom type column of > the DMSO.mol2 file... > > regards, Francois > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Robert H. <ha...@st...> - 2008-10-30 12:24:20
|
Francois, The bad news: Looks like we have a file format issue here. Angel has it right, that the mol2 format as specified uses SYBYL atom types. The AMBER team has co-opted that file format for their own purposes, still calling it "mol2" but using non-SYBYL atom types. Jmol expects a mol2 file to have mol2 format. The good news: Jmol is very flexible, and we have a rapid development cycle. So we should be able to get it to do just about anything anyone wants it to do. I'd particularly like to see the AMBER community embrace Jmol as an alternative visualization tool. So let's get this working for you. The solution: For example, the AMBER, GAFF atom type list is small. Perhaps we could have the mol2 reader map that list to element symbols. All this would be easier if there were some identifying characteristic within the mol2 file that clearly identified it as not being "true" mol2 format. But we can work with just about anything. Bob On Thu, Oct 30, 2008 at 5:15 AM, Angel Herraez <ang...@ua...> wrote: > OK, I've got it > > Jmol is not using the atom name for element identification; mol2 has > an "atom type" field which seems to be both the cause and the cure. > http://www.tripos.com/data/support/mol2.pdf > > In your DMSO file, the atom type for the offending atoms is CT and > H1. > > This is not supported by mol2 spec. See > http://www.tripos.com/mol2/atom_types.html > http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html > > If you cahnge that to just C and H, Jmol behaves. You should maybe > use the proper types, which seem to be C.3, H, S.o, O.2 > They also work in Jmol. > > > > I guess it is because the name of > > > the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23 > > As I said, not that name, but the type at column 50. > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: FyD <fy...@q4...> - 2008-10-30 12:46:21
|
Dear Bob, > The bad news: Looks like we have a file format issue here. Angel has it > right, that the mol2 format as specified uses SYBYL atom types. The AMBER > team has co-opted that file format for their own purposes, still calling it > "mol2" but using non-SYBYL atom types. Jmol expects a mol2 file to have mol2 > format. Openbabel does the same ;-) > The good news: Jmol is very flexible, and we have a rapid development cycle. > So we should be able to get it to do just about anything anyone wants it to > do. I'd particularly like to see the AMBER community embrace Jmol as an > alternative visualization tool. So let's get this working for you. > > The solution: For example, the AMBER, GAFF atom type list is small. Perhaps > we could have the mol2 reader map that list to element symbols. All this > would be easier if there were some identifying characteristic within the > mol2 file that clearly identified it as not being "true" mol2 format. But we > can work with just about anything. AMBER force fields (not only one force field but parm94, parm96, parm98, parm99, ff03 etc...) for proteins/nucleic acids use capital letters such CT, H1, H2, H3 etc... GLYCAM force field uses the same force field atom type definition as AMBER FF. GAFF force field uses small letters suc as c3, h1, h2 etc.. CHARMM force fields use other rules Why not simply taking the column of the FF atom types available in the Tripos mol2 file format & display it "as it is" ? -> If there are Sybyl force field atom types ( C.3, H, S.o, O.2, etc...), let's display them. -> If there are only chemical symbols, just display chemical symbols. -> If there are CHARMM, GLYCAM or GAFF force field atom types just display them as they are. best regards, Francois > On Thu, Oct 30, 2008 at 5:15 AM, Angel Herraez <ang...@ua...> wrote: > >> OK, I've got it >> >> Jmol is not using the atom name for element identification; mol2 has >> an "atom type" field which seems to be both the cause and the cure. >> http://www.tripos.com/data/support/mol2.pdf >> >> In your DMSO file, the atom type for the offending atoms is CT and >> H1. >> >> This is not supported by mol2 spec. See >> http://www.tripos.com/mol2/atom_types.html >> http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html >> >> If you cahnge that to just C and H, Jmol behaves. You should maybe >> use the proper types, which seem to be C.3, H, S.o, O.2 >> They also work in Jmol. >> >> > > I guess it is because the name of >> > > the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23 >> >> As I said, not that name, but the type at column 50. |
From: Angel H. <ang...@ua...> - 2008-10-30 13:15:56
|
El 30 Oct 2008 a las 13:44, FyD escribió: > Why not simply taking the column of the FF atom types available in the > Tripos mol2 file format & display it "as it is" ? I think it's not a question of just "displaying" them, because they must be converted (mapped) to element names, or you'll get the pink color problem. |
From: Robert H. <ha...@st...> - 2008-10-30 15:42:11
|
This is done. Jmol 11.7.6 will display all mol2 atom types as found in the file and map correctly (so I claim!) atom types to element symbols for the following force fields: AMBER, GAFF, ESFF, CFF91, CHARMM, COMPASS, CVFF, CVFF_aug, PCFF as described in http://www.chem.cmu.edu/courses/09-560/docs/msi/ffbsim/B_AtomTypes.html Any more you want, just let me know. Bob On Thu, Oct 30, 2008 at 8:17 AM, Angel Herraez <ang...@ua...> wrote: > El 30 Oct 2008 a las 13:44, FyD escribió: > > Why not simply taking the column of the FF atom types available in the > > Tripos mol2 file format & display it "as it is" ? > > I think it's not a question of just "displaying" them, because they > must be converted (mapped) to element names, or you'll get the pink > color problem. > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: FyD <fy...@q4...> - 2008-10-30 19:44:11
|
Dear Bob, > This is done. Jmol 11.7.6 will display all mol2 atom types as found in the > file and map correctly (so I claim!) atom types to element symbols for the > following force fields: > AMBER, GAFF, ESFF, CFF91, CHARMM, COMPASS, CVFF, CVFF_aug, PCFF This is great... Thanks a lot ! > as described in > http://www.chem.cmu.edu/courses/09-560/docs/msi/ffbsim/B_AtomTypes.html As you saw Accelrys Inc. uses the Tripos mol2 file format for their own FFs: CVFF, CFF etc... as people from AMBER. I started to use the version you provide @ http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip A test is available @ http://q4md-forcefieldtools.org/RED/index-test.php It looks like the hydrogens are pink: 1 C1 1.352237 -0.856933 0.225852 CT 1 DMSO -0.2897 2 H11 1.336243 -1.843530 -0.221408 H1 1 DMSO 0.1284 3 H12 1.276947 -0.923392 1.304085 H1 1 DMSO 0.1284 4 H13 2.275139 -0.356278 -0.035153 H1 1 DMSO 0.1284 5 S2 -0.000004 0.136959 -0.414455 S 1 DMSO 0.3177 6 O3 -0.000040 1.405694 0.357557 O 1 DMSO -0.5085 7 C4 -1.352189 -0.857006 0.225851 CT 1 DMSO -0.2897 8 H41 -2.275117 -0.356396 -0.035149 H1 1 DMSO 0.1284 9 H42 -1.336143 -1.843599 -0.221415 H1 1 DMSO 0.1284 10 H43 -1.276895 -0.923466 1.304085 H1 1 DMSO 0.1284 regards, Francois |
From: Robert H. <ha...@st...> - 2008-10-30 21:11:15
|
H1 is not listed as an AMBER atom type in that reference I used. Nor H4 H5 HP OK, so I've added those from the JACS paper. See http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip Those pink H atoms should be gone. Bob On Thu, Oct 30, 2008 at 2:43 PM, FyD <fy...@q4...> wrote: > Dear Bob, > > > This is done. Jmol 11.7.6 will display all mol2 atom types as found in > the > > file and map correctly (so I claim!) atom types to element symbols for > the > > following force fields: > > AMBER, GAFF, ESFF, CFF91, CHARMM, COMPASS, CVFF, CVFF_aug, PCFF > > This is great... Thanks a lot ! > > > as described in > > http://www.chem.cmu.edu/courses/09-560/docs/msi/ffbsim/B_AtomTypes.html > > As you saw Accelrys Inc. uses the Tripos mol2 file format for their > own FFs: CVFF, CFF etc... as people from AMBER. > > I started to use the version you provide @ > http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip > > A test is available @ > http://q4md-forcefieldtools.org/RED/index-test.php > > It looks like the hydrogens are pink: > 1 C1 1.352237 -0.856933 0.225852 CT 1 DMSO -0.2897 > 2 H11 1.336243 -1.843530 -0.221408 H1 1 DMSO 0.1284 > 3 H12 1.276947 -0.923392 1.304085 H1 1 DMSO 0.1284 > 4 H13 2.275139 -0.356278 -0.035153 H1 1 DMSO 0.1284 > 5 S2 -0.000004 0.136959 -0.414455 S 1 DMSO 0.3177 > 6 O3 -0.000040 1.405694 0.357557 O 1 DMSO -0.5085 > 7 C4 -1.352189 -0.857006 0.225851 CT 1 DMSO -0.2897 > 8 H41 -2.275117 -0.356396 -0.035149 H1 1 DMSO 0.1284 > 9 H42 -1.336143 -1.843599 -0.221415 H1 1 DMSO 0.1284 > 10 H43 -1.276895 -0.923466 1.304085 H1 1 DMSO 0.1284 > > regards, Francois > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Robert H. <ha...@st...> - 2008-10-31 19:58:02
|
OK, I will add those. I've also added a new setting in Jmol 11.7.7: set atomTypes "abcd=>C;efgh=>H" this setting allows atom types in MOL2 file formats (5th field) to define the element associated with that atom type. Not necessary in general, but for future changes in the force fields, introduction of new forcefields, or user-defined atom types, this allows complete flexibility in that regard. Bob On Fri, Oct 31, 2008 at 11:39 AM, FyD <fy...@q4...> wrote: > Dear Bob, > > H1 is not listed as an AMBER atom type in that reference I used. Nor H4 H5 >> HP >> >> OK, so I've added those from the JACS paper. >> See http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip >> >> Those pink H atoms should be gone. >> > > Thanks. Few points: > > - Below, you will find the listing of the FF atom types available for AMBER > & GLYCAM FF in the AMBER10 distribution... > > - I think you did not add the "CG" & "CY" FF atom types from Glycam. In > fact, you can consider GLYCAM + AMBER FF as a single "AMBER" FF. > > - I think a problem will show up with Jmol when a user will define its own > FF atom types, i.e. when a users create a new FF atom types: I think Jmol > will color it in pink each time... > > best regards, Francois > > > AMBER FF: > PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP > incl.02/04/99 > C 12.01 0.616 ! sp2 C carbonyl group > CA 12.01 0.360 sp2 C pure aromatic (benzene) > CB 12.01 0.360 sp2 aromatic C, 5&6 membered ring > junction > CC 12.01 0.360 sp2 aromatic C, 5 memb. ring HIS > CD 12.01 0.360 sp2 C atom in the middle of: C=CD-CD=C > CK 12.01 0.360 sp2 C 5 memb.ring in purines > CM 12.01 0.360 sp2 C pyrimidines in pos. 5 & 6 > CN 12.01 0.360 sp2 C aromatic 5&6 memb.ring > junct.(TRP) > CQ 12.01 0.360 sp2 C in 5 mem.ring of purines between > 2 N > CR 12.01 0.360 sp2 arom as CQ but in HIS > CT 12.01 0.878 sp3 aliphatic C > CV 12.01 0.360 sp2 arom. 5 memb.ring w/1 N and 1 H > (HIS) > CW 12.01 0.360 sp2 arom. 5 memb.ring w/1 N-H and 1 H > (HIS) > C* 12.01 0.360 sp2 arom. 5 memb.ring w/1 subst. (TRP) > CY 12.01 0.360 nitrile C (Howard et > al.JCC,16,243,1995) > CZ 12.01 0.360 sp C (Howard et al.JCC,16,243,1995) > C0 40.08 calcium > H 1.008 0.161 H bonded to nitrogen atoms > HC 1.008 0.135 H aliph. bond. to C without > electrwd.group > H1 1.008 0.135 H aliph. bond. to C with 1 electrwd. > group > H2 1.008 0.135 H aliph. bond. to C with 2 > electrwd.groups > H3 1.008 0.135 H aliph. bond. to C with 3 > eletrwd.groups > HA 1.008 0.167 H arom. bond. to C without elctrwd. > groups > H4 1.008 0.167 H arom. bond. to C with 1 electrwd. > group > H5 1.008 0.167 H arom.at C with 2 elctrwd. gr,+HCOO > group > HO 1.008 0.135 hydroxyl group > HS 1.008 0.135 hydrogen bonded to sulphur (pol?) > HW 1.008 0.000 H in TIP3P water > HP 1.008 0.135 H bonded to C next to positively > charged gr > HZ 1.008 0.161 H bond sp C (Howard et > al.JCC,16,243,1995) > F 19.00 0.320 fluorine > Cl 35.45 1.910 chlorine (Applequist) > Br 79.90 2.880 bromine (Applequist) > I 126.9 4.690 iodine (Applequist) > IM 35.45 3.235 assumed to be Cl- (ion minus) > IB 131.0 'big ion w/ waters' for vacuum (Na+, > 6H2O) > MG 24.305 0.120 magnesium > N 14.01 0.530 sp2 nitrogen in amide groups > NA 14.01 0.530 sp2 N in 5 memb.ring w/H atom (HIS) > NB 14.01 0.530 sp2 N in 5 memb.ring w/LP > (HIS,ADE,GUA) > NC 14.01 0.530 sp2 N in 6 memb.ring w/LP (ADE,GUA) > N2 14.01 0.530 sp2 N in amino groups > N3 14.01 0.530 sp3 N for charged amino groups (Lys, > etc) > NT 14.01 0.530 sp3 N for amino groups amino groups > N* 14.01 0.530 sp2 N > NY 14.01 0.530 nitrile N (Howard et > al.JCC,16,243,1995) > O 16.00 0.434 carbonyl group oxygen > O2 16.00 0.434 carboxyl and phosphate group oxygen > OW 16.00 0.000 oxygen in TIP3P water > OH 16.00 0.465 oxygen in hydroxyl group > OS 16.00 0.465 ether and ester oxygen > P 30.97 1.538 > phosphate,pol:JACS,112,8543,90,K.J.Miller > S 32.06 2.900 S in disulfide > linkage,pol:JPC,102,2399,98 > SH 32.06 2.900 S in cystine > CU 63.55 copper > FE 55.00 iron > Li 6.94 0.029 lithium, ions > pol:J.PhysC,11,1541,(1978) > IP 22.99 0.250 assumed to be Na+ (ion plus) > Na 22.99 0.250 Na+, ions pol:J.PhysC,11,1541,(1978) > K 39.10 1.060 potassium > Rb 85.47 rubidium > Cs 132.91 cesium > Zn 65.4 Zn2+ > LP 3.00 0.000 lone pair > > GLYCAM FF: > GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004 > CG 12.01 ! sp3 C aliphatic > CT 12.01 sp3 C aliphatic > CY 12.01 sp3 C aliphatic > C 12.01 sp2 C carbonyl group > H 1.008 H Bonded to nitrogen atoms > H1 1.008 H aliph. bond. to C with 1 electrwd. > groups > H2 1.008 H aliph. bond. to C with 2 electrwd. > groups > HC 1.008 H aliph. bond. to C without electrwd. > groups > HO 1.008 H hydroxyl group > HW 1.008 H TIP3P water > N 14.01 sp2 N amide group > O 16.00 O carbonyl group > O2 16.00 O carboxyl group > OH 16.00 O hydroxyl group > OS 16.00 O ether > OW 16.00 O TIP3P water > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: FyD <fy...@q4...> - 2008-10-31 22:09:35
|
Dear All, I use Jmol 11.6.1. under fedora linux 32-bits with Opera 9.61. If I use the following script, the corresponding loop works fine: jmolApplet(200, "load ./DMSO1.cml; set echo top left;color echo black;font echo 10 serif bold;echo Atomic charges;select all;label %-8.3P;font label 10 serif bold;zoom 120; spin on; delay 5; load ./DMSO2.cml; set echo top left;color echo black;font echo 10 serif bold;echo Force field atom types;select all;label %B;font label 10 serif bold;zoom 120; spin on; delay 5; load ./DMSO3.cml; set echo top left;color echo black;font echo 10 serif bold;echo Atom names;select all;label %a;font label 10 serif bold;zoom 120; spin on; delay 5; loop 1") If I add 3 times the "axis 0.01" command in the loop, the loop does not start/work: jmolApplet(200, "load ./DMSO1.cml; axis 0.01; set echo top left;color echo black;font echo 10 serif bold;echo Atomic charges;select all;label %-8.3P;font label 10 serif bold;zoom 120; spin on; delay 5; load ./DMSO2.cml; axis 0.01; set echo top left;color echo black;font echo 10 serif bold;echo Force field atom types;select all;label %B;font label 10 serif bold;zoom 120; spin on; delay 5; load ./DMSO3.cml; axis 0.01; set echo top left;color echo black;font echo 10 serif bold;echo Atom names;select all;label %a;font label 10 serif bold;zoom 120; spin on; delay 5; loop 1") Same problem with adding 3 times "isosurface molecular map MEP; color isosurface translucent;" On the contrary, with "boundbox", the loop works fine. Any idea why ? Thanks, regards, Francois |
From: Robert H. <ha...@st...> - 2008-11-01 12:24:24
|
It's just that the command is "axes" not "axis" Francois, I'm starting to see where having atom types in more than mol2 files is of interest. You posted something about that. Where are these cml files coming from? Peter can tell us what the story is on adding something like atom type to the cml specification. Can you send us one of these CML files to look at? Bob On Fri, Oct 31, 2008 at 4:33 PM, FyD <fy...@q4...> wrote: > Dear All, > > I use Jmol 11.6.1. under fedora linux 32-bits with Opera 9.61. > > If I use the following script, the corresponding loop works fine: > > jmolApplet(200, "load ./DMSO1.cml; set echo top left;color echo > black;font echo 10 serif bold;echo Atomic charges;select all;label > %-8.3P;font label 10 serif bold;zoom 120; spin on; delay 5; load > ./DMSO2.cml; set echo top left;color echo black;font echo 10 serif > bold;echo Force field atom types;select all;label %B;font label 10 > serif bold;zoom 120; spin on; delay 5; load ./DMSO3.cml; set echo top > left;color echo black;font echo 10 serif bold;echo Atom names;select > all;label %a;font label 10 serif bold;zoom 120; spin on; delay 5; loop > 1") > Interesting loop -- this is perhaps a bit cleaner: load caffeine.xyz message _loop set echo top left color echo black font echo 10 serif bold echo Atomic charges select all label %-8.3P font label 10 serif bold zoom 120 spin on delay 5 set echo top left color echo black font echo 10 serif bold echo Force field atom types select all label %B font label 10 serif bold zoom 120 spin on delay 5 set echo top left color echo black font echo 10 serif bold echo Atom names select all label %a font label 10 serif bold zoom 120 spin on delay 5 goto _loop > > If I add 3 times the "axis 0.01" command in the loop, the loop does > not start/work: > > jmolApplet(200, "load ./DMSO1.cml; axis 0.01; set echo top left;color > echo black;font echo 10 serif bold;echo Atomic charges;select > all;label %-8.3P;font label 10 serif bold;zoom 120; spin on; delay 5; > load ./DMSO2.cml; axis 0.01; set echo top left;color echo black;font > echo 10 serif bold;echo Force field atom types;select all;label > %B;font label 10 serif bold;zoom 120; spin on; delay 5; load > ./DMSO3.cml; axis 0.01; set echo top left;color echo black;font echo > 10 serif bold;echo Atom names;select all;label %a;font label 10 serif > bold;zoom 120; spin on; delay 5; loop 1") > > Same problem with adding 3 times "isosurface molecular map MEP; color > isosurface translucent;" > > On the contrary, with "boundbox", the loop works fine. > > Any idea why ? > > Thanks, regards, Francois > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: FyD <fy...@q4...> - 2008-11-01 13:31:33
|
Dear Bob, > It's just that the command is "axes" not "axis" Thanks a lot for your loop examples & sorry for "axes" vs "axis"... @ http://q4md-forcefieldtools.org/RED/index-test.php, using a Tripos mol2 file format, you have a working example with: FF atom types + atomic charges + atom names + MEP using Jmol 11.7.6 All is perfect ! I will now make this more general on our web sites... > Francois, I'm starting to see where having atom types in more than mol2 > files is of interest. You posted something about that. Yes, in the CML file format (besides the Tripos mol2 file format). Angel wrote: >>> That would depend on the official specification of the CML format. >>> Jmol can be adapted to read anything the file contains, but it must >>> be defined as an official format spec. >> Yes, this is my understanding: so how to define a specific card for >> force field atom type in the CML file format recognized by Jmol: >> >> For charges, Jmol recognizes: >> <scalar dictRef="jmol:charge">-0.287</scalar> >> Could we imagine, something similar for force field atom types such as: >> <scalar dictRef="jmol:forcefield">CT</scalar> ? > Where are these cml files coming from? Tripos mol2 files from R.E.D. http://q4md-forcefieldtools.org/RED/ --> CML files for R.E.DD.B. http://q4md-forcefieldtools.org/REDDB/ using a perl script, I wrote: See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#15 & http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#17 http://q4md-forcefieldtools.org/Tutorial/0-Script/mol2tocml.pl > Peter can tell us what the story is > on adding something like atom type to the cml specification. Can you send us > one of these CML files to look at? You have many examples of CML files in R.E.DD.B. See for instance complex projects in R.E.DD.B.: http://q4md-forcefieldtools.org/REDDB/up/W-46/ or http://q4md-forcefieldtools.org/REDDB/up/F-60/ regards, Francois > On Fri, Oct 31, 2008 at 4:33 PM, FyD <fy...@q4...> wrote: > >> Dear All, >> >> I use Jmol 11.6.1. under fedora linux 32-bits with Opera 9.61. >> >> If I use the following script, the corresponding loop works fine: >> >> jmolApplet(200, "load ./DMSO1.cml; set echo top left;color echo >> black;font echo 10 serif bold;echo Atomic charges;select all;label >> %-8.3P;font label 10 serif bold;zoom 120; spin on; delay 5; load >> ./DMSO2.cml; set echo top left;color echo black;font echo 10 serif >> bold;echo Force field atom types;select all;label %B;font label 10 >> serif bold;zoom 120; spin on; delay 5; load ./DMSO3.cml; set echo top >> left;color echo black;font echo 10 serif bold;echo Atom names;select >> all;label %a;font label 10 serif bold;zoom 120; spin on; delay 5; loop >> 1") >> > > Interesting loop -- this is perhaps a bit cleaner: > > load caffeine.xyz > > message _loop > set echo top left > color echo black > font echo 10 serif bold > echo Atomic charges > select all > label %-8.3P > font label 10 serif bold > zoom 120 > spin on > delay 5 > > set echo top left > color echo black > font echo 10 serif bold > echo Force field atom types > select all > label %B > font label 10 serif bold > zoom 120 > spin on > delay 5 > > set echo top left > color echo black > font echo 10 serif bold > echo Atom names > select all > label %a > font label 10 serif bold > zoom 120 > spin on > delay 5 > goto _loop > > >> If I add 3 times the "axis 0.01" command in the loop, the loop does >> not start/work: >> >> jmolApplet(200, "load ./DMSO1.cml; axis 0.01; set echo top left;color >> echo black;font echo 10 serif bold;echo Atomic charges;select >> all;label %-8.3P;font label 10 serif bold;zoom 120; spin on; delay 5; >> load ./DMSO2.cml; axis 0.01; set echo top left;color echo black;font >> echo 10 serif bold;echo Force field atom types;select all;label >> %B;font label 10 serif bold;zoom 120; spin on; delay 5; load >> ./DMSO3.cml; axis 0.01; set echo top left;color echo black;font echo >> 10 serif bold;echo Atom names;select all;label %a;font label 10 serif >> bold;zoom 120; spin on; delay 5; loop 1") >> >> Same problem with adding 3 times "isosurface molecular map MEP; color >> isosurface translucent;" >> >> On the contrary, with "boundbox", the loop works fine. >> >> Any idea why ? >> >> Thanks, regards, Francois |
From: Robert H. <ha...@st...> - 2008-11-01 22:29:20
|
On Sat, Nov 1, 2008 at 8:31 AM, FyD <fy...@q4...> wrote: > > > You have many examples of CML files in R.E.DD.B. > See for instance complex projects in R.E.DD.B.: > http://q4md-forcefieldtools.org/REDDB/up/W-46/ > or > http://q4md-forcefieldtools.org/REDDB/up/F-60/ > I don't see anything about atomType there. -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: FyD <fy...@q4...> - 2008-11-02 06:20:01
|
Dear Bob, >> You have many examples of CML files in R.E.DD.B. >> See for instance complex projects in R.E.DD.B.: >> http://q4md-forcefieldtools.org/REDDB/up/W-46/ >> or >> http://q4md-forcefieldtools.org/REDDB/up/F-60/ > > I don't see anything about atomType there. Yes, this is not implemented yet: those CML files are regular CML files without force field atom types. I just wait for this new feature to be implemented in the CML file format. It will take 5 minutes to update the mol2cml.pl script. However, before to implement this in R.E.DD.B., I need to know the official keyword to define the force field atom types in the CML file format: <scalar dictRef="jmol:forcefield">CT</scalar> ? or <scalar dictRef="jmol:ffatomtype">CT</scalar> ? If you decide to add this new feature in the CML file format, we could go one step further and we could also imagine to add other features in the CML file i.e. allowing the CML file format to handle a real force field library! regards, Francois |