[Jmol-users] Another Molecular Editor Question
Hello- I'm using a data statement to add a detached ethane to a model so that I can edit the ethane and add the subsequent substructure to the original model. This all works well within the context of the editors click callback routines. Subsequent clean-up or the new structure by minimize makes it clear that it would be nice to rotate the original model relative to the substructure prior to the substructure attachment. The minimize works best if the two fragments are in a chemically logical position prior to attachment. Is there any way to click/rotate the original structure independent of the substructure? Alternatively, can Jmol's left, right, back, front, top, bottom be applied to the original model independent of the new substructure? This latter approach could be used to put almost any atom in the original molecule close to a chemically logical attaching position of the substructure. -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Molecular Editor Questions
On Wed, Feb 24, 2010 at 3:24 PM, Otis Rothenberger o...@chemagic.comwrote:
I included point and click atom and bond deletion into a Jmol molecular
editor. This works just fine, but there are some deletion followup issues:
1) minimize addHydrogens is not functional on a multivalent atom that has
atoms deleted or bonds broken.
Hmm. Thought I fixed that. You sure? I do this:
load caffeine.xyz
set picking deleteatom
[click on the NH hydrogen, and it disappears]
minimize addHydrogens
[two H atoms appear on that N, which is correct, since I don't have multiple
bonding in this model, and the model minimizes]
I do this:
load caffeine.xyz
connect {N21} {c20} double
set picking deleteatom
minimize addHydrogens
[one H appears on that hydrogen, and the minimization looks good.]
So what am I missing?
3) The exception: If the multivalent atom is not connected to any other
multivalent or non-hydrogen atoms, then the atom replacement step above
simply creates a single atom with no hydrogen atoms attached.
That I believe. An atom by itself with no connections will not generate a
full set of H atoms. We could program Jmol to do that, just haven't.
Bob
By way of example, if I break a C-C bond in cyclohexane, then the terminal
CH2 groups will be rectified by the following swap - i.e. both end C's are
swapped with new C's:
evalRasmol({atomIndex = _atomPicked}.element = ' + buildAtom +
';);
evalRasmol(select hydrogen and connected({atomIndex =
_atomPicked});delete selected;);
evalRasmol(minimize addHydrogens;);
evalRasmol(select *;wireframe 0.15; spacefill 23%;boundbox
{*};centerat boundbox;echo Calculating UFF Minimum...;);
evalRasmol(minimize steps 100;);
I really need to see the Jmol script, not this. Perhaps displaying the
command history. Also, I'm wondering why you want to do all those individual
scripts. Why not just one:
jmolScript({atomIndex = _atomPicked}.element = ' + buildAtom
+ ';select hydrogen and connected({atomIndex =
_atomPicked});delete selected;
+ minimize addHydrogens;select *;wireframe 0.15; spacefill
23%;boundbox {*};centerat boundbox;echo Calculating UFF Minimum...;minimize
steps 100;);
Hmm, now looking at that -- Why two minimize commands?
When I do this, I'm really using jmol.js and the jmolScript() function. By
running this script text through a function of my own before jmolScript(), I
have the ability to define some jmol script commnads of my own from
jmolScript combinations. I'm not suing any of my defined commands above.
sure - wish you wouldn't call it evalRasmol though. Not much Rasmol in
it! :)
Continuing with my example, if I break a methly group off of hexane with
the intent of reconnecting the pieces to form 2-methylpentane, then all is
well. But if I try to rectify the fragments by the swap described above to
create a molecule of methane and a molecule of pentane, then pentane forms,
but the CH3 fragment is reduced to a single carbon atom that cannot be H
rectified.
right -- haven't implemented adding a full set of H atoms to a C.
As a point of information, if I break hexane into two CH3CH2CH2 fragments,
I can reconnect the two fragments any way I want. I can also make two
separate molecules of ethane. It appears that breaking off the following
groups from a larger molecule creates the problem described above:
CH3
OH
NH2
SH
Any suggestions?
Once the C is reconnected, it sprouts 3 H atoms, right?
Bob
Otis
--
Otis Rothenberger
http://chemagic.org
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
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
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Molecular Editor Questions
On Fri, Feb 26, 2010 at 1:05 PM, Robert Hanson hans...@stolaf.edu wrote: Hmm, now looking at that -- Why two minimize commands? instead, for example, why not: calculate hydrogens select * minimize steps 100 That second select might be important, since there are new atoms there. Bob -- 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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Animating non-consecutive frames?
On Sat, Feb 20, 2010 at 12:53 PM, Eric Martz martze...@yahoo.com wrote: Is it possible to animate non-consecutive frames? For example, in http://proteopedia.org/wiki/index.php/Sandbox_5_Eric_Martz I would like to animate just 2 frames, 1.1 and 1.10. I didn't guess any syntax to display two non-consecutive frames concurrently. Along the same lines, it is occasionally useful to play models in different arbitrary orders. Thus, I'd like these commands (or something similar) frame 1.9 1.7 1.3 1.5 frame play No, sorry, we just have frame range x y inclusive. to animate just the 4 frames specified, and in the ORDER specified. However, that would be rarely used. I don't think we could do it with order specified. They need to go in order. On the other hand, the ability to animate just 2 frames (in order) would be immediately useful. True, I could construct different PDB files for each animation, but I'm hoping it would not be too much work for Jmol to have that capability added. Two frames -- well, there's no order issue there, right, because you can always either play it backward or forward. What if we made it such that if there are no atoms DISPLAYED in a frame, it skips the frame? It seems to me then you could at least construct a linear sequence of selected frames. Another suggestion: when the command 'anim on' is run, it would be very helpful if this message were generated: frame range reset to all frames. use 'frame play' to prevent reset. I find the resetting by 'anim on' very unexpected and confusing and on several occasions (many months apart) I've had to spend the better part of an hour to figure out why 'frame 1.1-1.10' was being ignored by 'anim on'. a good suggestion. Bob -- Eric Martz, Ph.D. Professor Emeritus, Microbiology, University of Massachusetts, Amherst http://martz.molviz.org -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Molecular Editor Questions
Bob- Using your approach, picking deletes an H on propane. But minimize addHydrogens does not add it back. I'm thinking maybe I have the wrong Jmol version. I'm using 11.9.30_dev 2010-02-12 12:26. Is this the wong version? The two minimization steps simply reflect the fact that I forgot calculate hydrogens was an option. I also need to clean the multi-step calls to jmoScript(). That goes back to when I thought I had timing problems. I was playing with delays in various parts of the script, and breaking things apart was just a convenience. evalRasol is history! How about sortOutOtisConvolutedWayOfDoingThings() for the replacement. :) I guess I'll just use processJmol(). Actually, the function processes Jmol and JavaScipt entered in the page's text field. Otis -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Re : Re: Problem w/ electron dens. maps
Ha! Yeah, I don't think Google was a consideration when this program was named back in the 70's... O was written and is still maintained by T. Alwyn Jones of Uppsala University in Sweden. His central clearing house can be found at: http://xray.bmc.uu.se/alwyn/ I have already written to him and inquired about where to locate the format of the DSN6 maps... I'll let you know what I find out. -Tom On Fri, Feb 26, 2010 at 11:33 AM, Robert Hanson hans...@stolaf.edu wrote: Thanks, Tom. Sounds fine to me. I'd like to know more about the O format. We have other binary readers, and if this would be of interest, why not? It's easy enough to set up a new reader. I couldn't find anything about it myself, because it's basically unGooglable. Bob On Wed, Feb 24, 2010 at 10:48 AM, Thomas Stout thomasjst...@gmail.comwrote: Regarding EDS CNS format I wrote to Gerard Klegveyt, one of the principal authors of EDS, and asked about the CNS map format issue. Here is his response, which I think further nullifies CNS as a viable streaming format: Hi Tom, No, it seems that Jmol and you made the same mistake that I made a long time ago in assuming that the last line contains the average and sigma - it does not! There was a bug in MAPMAN for many years because of this which wasn't fixed until 2006: 061124 -7.8.2- fixed bug in writing ASCII CNS maps (last line should contain 0 and 1 instead of the actual average and st. dev. of the density, since the maps are not scaled) The reason why nobody picked up on this previously was probably that most programs simply ignore the last line. So: the two numbers are a scale and an offset in case you have scaled the values in the map, and they should be applied to the density values upon reading the map if you want to do things properly. Hope this helps, --Gerard We could certainly ask for RMS and other map stats to be added to the header, but then it would no longer be CNS/XPLOR format EDS would undoubtedly not be willing to risk breaking other people's use of the CNS format maps served by EDS. If CCP4 format is working, then I don't see much need to pursue the CNS format. The root format that EDS is using is DSN6 (O format), but since that is a binary file format I'm guessing that's not preferred for on demand slice reading either. -Tom On Wed, Feb 24, 2010 at 5:06 AM, Robert Hanson hans...@stolaf.eduwrote: resending -- message was too long for list. snip for length and OK, progress! Good job, Thomas. Well, it wouldn't be the first time that we have found errors in other systems while working on Jmol. Still proud of finding the bug in ORTEP! Right, so here is where we are: a) Then I have Jmol working correctly now for MRC/CCP4 files, and Eric should be telling us soon that all is to his liking, even with the default of not specifying sigma, since that will go in as sigma=1.0, which is what he wants, I think. b) If you can look into the Uppsala problem, that would be great. Unless I'm way off base there, that needs to be fixed. I just can't see how it can have essentially the same min, max, and mean as the MRC data from the same server and not have those reported in the file. Should be pretty easy for them to check out. c) That said, the CNS/Xplor format very disappointingly is not designed with streaming in mind. One of Jmol's newer features is that it never has to actually load all the volumetric data (the way PyMOL does). It just streams the data in slice by slice and creates the surface on the fly. This is far faster and far more memory efficient and allows Jmol now to display huge surfaces that it never could before. Well, for that to work, you clearly have to have the cutoff initially set. But if it comes at the end of a file -- that's fine for reading a file off the hard drive, but over the web -- where you don't have the equivalent of file.seek() to jump to the end first, get the info, and then come back -- that's just not possible. That's too bad. So the point is that while I think it's important that that gets fixed, if it really is in error, fixing that is not going to allow Jmol to read those files efficiently. I hate to think that we would have to read them twice just to do the job. I suppose we could do that In any case, the MRC/CCP4 files should be scaling properly now. d) Thomas, if you could look into the electron microscopy business, that would be great as well. and Great. Thanks, Tom. Sigma -- This all makes good sense. It explains why 2sigma was a better match to the EM data, which was the original reason I implemented the MRC format. But it also seems to me to be quite reasonable to just set sigma=1 to be the default and let people who want to display EM data set the sigma explicitly. EDS CNS -- Perhaps we could lobby for also including an indication of RMSD in the header comment. -- Robert M. Hanson Professor of Chemistry St.
Re: [Jmol-users] Animating non-consecutive frames?
An idea just popped up for Eric:
As a roundabout solution:
Maybe you could load just the selected frames, in the desired order, using
load models
and then animate them?
So,
http://proteopedia.org/wiki/index.php/Sandbox_5_Eric_Martz I would like to
animate just 2 frames, 1.1 and 1.10.
load models ({0 9}) filename
I'd like these commands (or something similar)
frame 1.9 1.7 1.3 1.5
frame play
load models ({8}) filename
load append models ({6}) filename
load append models ({2 4}) filename
It seems to work!
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Animating non-consecutive frames?
Note that you have two options there with loading a specific model:
load models ({0:3 6 8 10}) filename.pdb
will load models 0, 1, 2, 3, 6, 8, and 10, where 0 is the first model.
These aren't model numbers as found on the PDB MODEL line. These are counted
from the beginning starting with 0.
load filename.pdb 5
This is a model number, as indicated on the MODEL line of the PDB file.
Slightly different.
[Also, note, there is a bug there. The list of models is not preserved in
the state with the ({a b c d}) notation. Fixing now]
Bob
2010/2/26 Angel Herráez angel.herr...@uah.es
An idea just popped up for Eric:
As a roundabout solution:
Maybe you could load just the selected frames, in the desired order, using
load models
and then animate them?
So,
http://proteopedia.org/wiki/index.php/Sandbox_5_Eric_Martz I would like
to
animate just 2 frames, 1.1 and 1.10.
load models ({0 9}) filename
I'd like these commands (or something similar)
frame 1.9 1.7 1.3 1.5
frame play
load models ({8}) filename
load append models ({6}) filename
load append models ({2 4}) filename
It seems to work!
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
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
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Re : Re: Problem w/ electron dens. maps
Looks like it is here: http://www.uoxray.uoregon.edu/tnt/manual/node104.html Alas, sadly, a binary file that does not identify itself. Too bad not everyone thinks of adding a magic number at the beginning. Still, we might be able to do something with this. Bob On Fri, Feb 26, 2010 at 1:55 PM, Thomas Stout thomasjst...@gmail.comwrote: Ha! Yeah, I don't think Google was a consideration when this program was named back in the 70's... O was written and is still maintained by T. Alwyn Jones of Uppsala University in Sweden. His central clearing house can be found at: http://xray.bmc.uu.se/alwyn/ I have already written to him and inquired about where to locate the format of the DSN6 maps... I'll let you know what I find out. -Tom On Fri, Feb 26, 2010 at 11:33 AM, Robert Hanson hans...@stolaf.eduwrote: Thanks, Tom. Sounds fine to me. I'd like to know more about the O format. We have other binary readers, and if this would be of interest, why not? It's easy enough to set up a new reader. I couldn't find anything about it myself, because it's basically unGooglable. Bob On Wed, Feb 24, 2010 at 10:48 AM, Thomas Stout thomasjst...@gmail.comwrote: Regarding EDS CNS format I wrote to Gerard Klegveyt, one of the principal authors of EDS, and asked about the CNS map format issue. Here is his response, which I think further nullifies CNS as a viable streaming format: Hi Tom, No, it seems that Jmol and you made the same mistake that I made a long time ago in assuming that the last line contains the average and sigma - it does not! There was a bug in MAPMAN for many years because of this which wasn't fixed until 2006: 061124 -7.8.2- fixed bug in writing ASCII CNS maps (last line should contain 0 and 1 instead of the actual average and st. dev. of the density, since the maps are not scaled) The reason why nobody picked up on this previously was probably that most programs simply ignore the last line. So: the two numbers are a scale and an offset in case you have scaled the values in the map, and they should be applied to the density values upon reading the map if you want to do things properly. Hope this helps, --Gerard We could certainly ask for RMS and other map stats to be added to the header, but then it would no longer be CNS/XPLOR format EDS would undoubtedly not be willing to risk breaking other people's use of the CNS format maps served by EDS. If CCP4 format is working, then I don't see much need to pursue the CNS format. The root format that EDS is using is DSN6 (O format), but since that is a binary file format I'm guessing that's not preferred for on demand slice reading either. -Tom On Wed, Feb 24, 2010 at 5:06 AM, Robert Hanson hans...@stolaf.eduwrote: resending -- message was too long for list. snip for length and OK, progress! Good job, Thomas. Well, it wouldn't be the first time that we have found errors in other systems while working on Jmol. Still proud of finding the bug in ORTEP! Right, so here is where we are: a) Then I have Jmol working correctly now for MRC/CCP4 files, and Eric should be telling us soon that all is to his liking, even with the default of not specifying sigma, since that will go in as sigma=1.0, which is what he wants, I think. b) If you can look into the Uppsala problem, that would be great. Unless I'm way off base there, that needs to be fixed. I just can't see how it can have essentially the same min, max, and mean as the MRC data from the same server and not have those reported in the file. Should be pretty easy for them to check out. c) That said, the CNS/Xplor format very disappointingly is not designed with streaming in mind. One of Jmol's newer features is that it never has to actually load all the volumetric data (the way PyMOL does). It just streams the data in slice by slice and creates the surface on the fly. This is far faster and far more memory efficient and allows Jmol now to display huge surfaces that it never could before. Well, for that to work, you clearly have to have the cutoff initially set. But if it comes at the end of a file -- that's fine for reading a file off the hard drive, but over the web -- where you don't have the equivalent of file.seek() to jump to the end first, get the info, and then come back -- that's just not possible. That's too bad. So the point is that while I think it's important that that gets fixed, if it really is in error, fixing that is not going to allow Jmol to read those files efficiently. I hate to think that we would have to read them twice just to do the job. I suppose we could do that In any case, the MRC/CCP4 files should be scaling properly now. d) Thomas, if you could look into the electron microscopy business, that would be great as well. and Great. Thanks, Tom. Sigma -- This all makes good sense. It explains why 2sigma was a better match to the EM data, which was the
Re: [Jmol-users] Re : Re: Problem w/ electron dens. maps
Ah - Good find! And yes, that's the modern version of the format - the DSN2 or Frodo-style map has been relegated to the dustbins of history. There are no other useful map formats listed on that web site. My opinion would be that the triad of CCP4/MRC, CNS/XPLOR and DSN6 (O-style) covers 99+% of the electron density maps in general use in macromolecular X-ray crystallography. -Tom On Fri, Feb 26, 2010 at 2:47 PM, Robert Hanson hans...@stolaf.edu wrote: Looks like it is here: http://www.uoxray.uoregon.edu/tnt/manual/node104.html Alas, sadly, a binary file that does not identify itself. Too bad not everyone thinks of adding a magic number at the beginning. Still, we might be able to do something with this. Bob On Fri, Feb 26, 2010 at 1:55 PM, Thomas Stout thomasjst...@gmail.comwrote: Ha! Yeah, I don't think Google was a consideration when this program was named back in the 70's... O was written and is still maintained by T. Alwyn Jones of Uppsala University in Sweden. His central clearing house can be found at: http://xray.bmc.uu.se/alwyn/ I have already written to him and inquired about where to locate the format of the DSN6 maps... I'll let you know what I find out. -Tom On Fri, Feb 26, 2010 at 11:33 AM, Robert Hanson hans...@stolaf.eduwrote: Thanks, Tom. Sounds fine to me. I'd like to know more about the O format. We have other binary readers, and if this would be of interest, why not? It's easy enough to set up a new reader. I couldn't find anything about it myself, because it's basically unGooglable. Bob On Wed, Feb 24, 2010 at 10:48 AM, Thomas Stout thomasjst...@gmail.comwrote: Regarding EDS CNS format I wrote to Gerard Klegveyt, one of the principal authors of EDS, and asked about the CNS map format issue. Here is his response, which I think further nullifies CNS as a viable streaming format: Hi Tom, No, it seems that Jmol and you made the same mistake that I made a long time ago in assuming that the last line contains the average and sigma - it does not! There was a bug in MAPMAN for many years because of this which wasn't fixed until 2006: 061124 -7.8.2- fixed bug in writing ASCII CNS maps (last line should contain 0 and 1 instead of the actual average and st. dev. of the density, since the maps are not scaled) The reason why nobody picked up on this previously was probably that most programs simply ignore the last line. So: the two numbers are a scale and an offset in case you have scaled the values in the map, and they should be applied to the density values upon reading the map if you want to do things properly. Hope this helps, --Gerard We could certainly ask for RMS and other map stats to be added to the header, but then it would no longer be CNS/XPLOR format EDS would undoubtedly not be willing to risk breaking other people's use of the CNS format maps served by EDS. If CCP4 format is working, then I don't see much need to pursue the CNS format. The root format that EDS is using is DSN6 (O format), but since that is a binary file format I'm guessing that's not preferred for on demand slice reading either. -Tom On Wed, Feb 24, 2010 at 5:06 AM, Robert Hanson hans...@stolaf.eduwrote: resending -- message was too long for list. snip for length and OK, progress! Good job, Thomas. Well, it wouldn't be the first time that we have found errors in other systems while working on Jmol. Still proud of finding the bug in ORTEP! Right, so here is where we are: a) Then I have Jmol working correctly now for MRC/CCP4 files, and Eric should be telling us soon that all is to his liking, even with the default of not specifying sigma, since that will go in as sigma=1.0, which is what he wants, I think. b) If you can look into the Uppsala problem, that would be great. Unless I'm way off base there, that needs to be fixed. I just can't see how it can have essentially the same min, max, and mean as the MRC data from the same server and not have those reported in the file. Should be pretty easy for them to check out. c) That said, the CNS/Xplor format very disappointingly is not designed with streaming in mind. One of Jmol's newer features is that it never has to actually load all the volumetric data (the way PyMOL does). It just streams the data in slice by slice and creates the surface on the fly. This is far faster and far more memory efficient and allows Jmol now to display huge surfaces that it never could before. Well, for that to work, you clearly have to have the cutoff initially set. But if it comes at the end of a file -- that's fine for reading a file off the hard drive, but over the web -- where you don't have the equivalent of file.seek() to jump to the end first, get the info, and then come back -- that's just not possible. That's too bad. So the point is that while I think it's important that that gets fixed, if it really is in error,
Re: [Jmol-users] Molecular Editor Questions
Bob- OK, I think I see something consistent in the delete problem now: Delete followed by minimize addHydrogens works if the deleted hydrogen is the only hydrogen on the multivalent atom. In every other case I look at, I see it failing: I'll use methanol to exemplify this, but I think it's pretty general: 1) Delete the alcohol H, and you can put it back on. 2) Delete 1 methyl H, and you cannot put it back on. 3) Delete 2nd methyl H, and you cannot put it (or the first deleted) back on. 4) Delete final methyl H, and you can put them all back on. Otis On Fri, Feb 26, 2010 at 2:50 PM, Otis Rothenberger o...@chemagic.comwrote: Bob- Using your approach, picking deletes an H on propane. But minimize addHydrogens does not add it back. I'm thinking maybe I have the wrong Jmol version. I'm using 11.9.30_dev 2010-02-12 12:26. Is this the wong version? The two minimization steps simply reflect the fact that I forgot calculate hydrogens was an option. I also need to clean the multi-step calls to jmoScript(). That goes back to when I thought I had timing problems. I was playing with delays in various parts of the script, and breaking things apart was just a convenience. evalRasol is history! How about sortOutOtisConvolutedWayOfDoingThings() for the replacement. :) I guess I'll just use processJmol(). Actually, the function processes Jmol and JavaScipt entered in the page's text field. Otis -- Otis Rothenberger http://chemagic.org -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Multiple clipping planes (using slab/depth HKL)
Jmol Users, Here's something I've always wanted to do with Jmol -- use clipping planes to show students the *fractions* of atoms in a unit cell (similar to attached image of NaCl generated using POV-Ray). I know I can use slab HKL and depth HKL, but those don't slice through the atoms like the normal slab and depth commands. I think there was a thread a while back on something like this, but I couldn't track it down. I've also thought about generating isosurfaces to represent the fractions of atoms, but that seemed tedious. Dean attachment: nacl.gif-- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Another Molecular Editor Question
Oops, I missed that the original molecule is pretty easy to select after the append of ethane. RotateSelected then gets the job done. I'm still interested in finding out if a mouse click/drag rotation is possible on selected atoms, however. Otis On Fri, Feb 26, 2010 at 1:54 PM, Otis Rothenberger o...@chemagic.comwrote: Hello- I'm using a data statement to add a detached ethane to a model so that I can edit the ethane and add the subsequent substructure to the original model. This all works well within the context of the editors click callback routines. Subsequent clean-up or the new structure by minimize makes it clear that it would be nice to rotate the original model relative to the substructure prior to the substructure attachment. The minimize works best if the two fragments are in a chemically logical position prior to attachment. Is there any way to click/rotate the original structure independent of the substructure? Alternatively, can Jmol's left, right, back, front, top, bottom be applied to the original model independent of the new substructure? This latter approach could be used to put almost any atom in the original molecule close to a chemically logical attaching position of the substructure. -- Otis Rothenberger http://chemagic.org -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
