Re: [Jmol-users] Coordination Compound Questions

On Thu, Nov 11, 2010 at 7:37 PM, Otis Rothenberger wrote: > Bob is the master of Jmol SMILES, so I'll direct the second question to > him. > > The SMILES on these compounds present another problem in Jmol. By way of > example, if we construct an unconnected ferrocene in SPARTAN and then > edit th

[Jmol-users] Coordination Compound Questions

All- I'm looking for some advice from inorganic chemists (or others) on the subject of appropriate molfiles for coordination compounds. To put the question in perspective, we are assembling a database of organic compounds found in standard organic text. This list will, of course, include some

Re: [Jmol-users] colouring isosurface of specific residues?

Hi Steve and Bob, One perhaps simpler way is to define the surface for each residue or chain separately? Such as (analogous to Bob's example): define proteinchain1 :a; isoSurface proteinchain1surf select(proteinchain1) sasurface opaque red; define proteinchain2 :b; isoSurface proteinchain2surf se

Re: [Jmol-users] FW: add new atoms via Cartesian coordinates

This assumes you want cartesians -- If you want fractional coordinates, you will need to use a CIF format, I think, and use the LOAD DATA version of the command, perhaps. I have to think about that. I guess you could actually write a DATA command using a Jmol script, converting fractionals to carte

Re: [Jmol-users] FW: add new atoms via Cartesian coordinates

Can you give me more details about (simple XYZ file format) so the command will be set appendNew false DATA "model" (Fe fx fy fz, O fx fy fz, etc. ) end "model" On Thu, Nov 11, 2010 at 6:40 PM, P.Canepa wrote: > > --- > From: Robert Hanson[SMTP:hans...@

Re: [Jmol-users] FW: FW: change cell parameters

On Thu, Nov 11, 2010 at 9:30 AM, pieremanuele canepa wrote: > Yes you leave the atoms in their positions rebuilding the cell around. Of > course the symmetry is lost. This is the price the user has to pay. > > So, you mean, just giving them different fractional coordinates. They are stored as Car

Re: [Jmol-users] add new atoms via Cartesian coordinates

the simplest way to do it if you have several atoms to add is: set appendNew false and then DATA "model" (simple XYZ file format) end "model" We also have a new (undocumented) command ASSIGN that we use for the model kit. On Thu, Nov 11, 2010 at 10:45 AM, pieremanuele canepa wrote: > Dear All

Re: [Jmol-users] partial bonds in cobalt chelate

Oh, I thought that Jmol completely ignored the CONECT records. Quite exotic situation, anyway. No more fuss. There's always place for new discoveries. Thanks -- Centralized Desktop Delivery: Dell and VMware Reference

[Jmol-users] add new atoms via Cartesian coordinates

Dear All, Can you show me the Jmol command to add a new atom knowing its fractional or Cartesian coordinates? Thanks a lot, Piero -- *Please consider the environment before printing this e-mail.* ** Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Bui

[Jmol-users] (no subject)

Dear All, Can you show me the Jmol command to add a new atom knowing its fractional or Cartesian coordinates? Thanks a lot, Piero -- *Please consider the environment before printing this e-mail.* ** Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Bui

Re: [Jmol-users] FW: FW: change cell parameters

Yes you leave the atoms in their positions rebuilding the cell around. Of course the symmetry is lost. This is the price the user has to pay. It would be interesting especially if you want to to run cluster type systems within PWs codes. Or if you want to extract a cluster from a periodic system.

Re: [Jmol-users] FW: change cell parameters

The big question would be: What do you want to do about the atom coordinates? Move them based on the new unit cell parameters, or leave them where they are? Give me some more idea of what you are talking about. Bob On Thu, Nov 11, 2010 at 7:11 AM, pieremanuele canepa wrote: > Yes. Imagine if we

Re: [Jmol-users] Jmol & P2N file format

progress! On Thu, Nov 11, 2010 at 9:05 AM, Robert Hanson wrote: > OK, great to hear you are flexible on this, and that the file format might > be adjustable. > > REMARKs -- I would strongly recommend following the PDB spec for that, with > a suitable numeric code in columns 8-10. > > Maybe: > >

Re: [Jmol-users] Jmol & P2N file format

OK, great to hear you are flexible on this, and that the file format might be adjustable. REMARKs -- I would strongly recommend following the PDB spec for that, with a suitable numeric code in columns 8-10. Maybe: REMARK1 P2N format created by version:... date: > --add ele

Re: [Jmol-users] Jmol and PDB file format

questions answered in line below... On Thu, Nov 11, 2010 at 7:57 AM, FyD wrote: > Dear Bob, dear Angel, > > > As you can see > http://cluster.q4md-forcefieldtools.org/~ucpublic1/javaappletpdb-1.html > is ok, while > http

Re: [Jmol-users] Jmol & P2N file format

Bob, Angel, > Well, at this point you have announced your P2N format, so I'm not sure you > have the flexibility to modify it. adding "REMARK P2N FILE FORMAT JMOL COMPATIBLE" or whatever message you think (1st line of the file) is quite simple... moreover, if this line is absent the P2N file c

Re: [Jmol-users] partial bonds in cobalt chelate

Those are hydrogen bonds. PDB specs read: * If more than four fields are required for non-hydrogen and nonsalt-bridge bonds, a second CONECT record with the same atom serial number in columns 7 - 11 will be used. There is a vague reference thre to hydrogen bonds and salt bridges. They are not spe

[Jmol-users] Jmol and PDB file format

Dear Bob, dear Angel, In relation with the P2N file format (previous messages), I also have a question regarding the PDB file format & Jmol. I wrote two Jmol applets @ http://cluster.q4md-forcefieldtools.org/~ucpublic1/javaappletpdb-1.html which loads http://cluster.q4md-forcefieldtools.org/

[Jmol-users] partial bonds in cobalt chelate

I just tested this file (mentioned in a different thread) http://q4md-forcefieldtools.org/Tutorial/P2N/Metal- complex/Mol_red1.p2n in Jmol 12.1.15, which reads it as pdb format. I'm curious: how is it that Jmol draws from the central cobalt 4 regular single bonds and 2 dashed, partial bonds? Wh

Re: [Jmol-users] FW: change cell parameters

Yes. Imagine if we want to enter space into cell for certain reasons. It would be interesting having this option. I would like to introduce myself such option in Jmol if you teach me something about how vectors and matrices works in Jmol. I'm willing to have a thorough knowledge of Jmol, now I know

Re: [Jmol-users] colouring isosurface of specific residues?

Don't know that I'd call that SIMPLE. But it should work. On Thu, Nov 11, 2010 at 5:42 AM, Steven Platt wrote: > Many thanks Bob. I knew I had to be missing something simple somewhere > > > > Steve > > > -- > > *From:* Robert Hanson [mailto:hans...@stolaf.edu] >

Re: [Jmol-users] change cell parameters

Wow, do you mean totally redefining the underlying fractional coordinate system for the model? On Wed, Nov 10, 2010 at 5:21 PM, pieremanuele canepa wrote: > Dear all, > > can anyone of you suggest me how I can modify cell parameters once loaded a > structure? > > Thanks, Piero > > -- > *Please c

Re: [Jmol-users] Jmol & P2N file format

Francois and Piotr, Well, at this point you have announced your P2N format, so I'm not sure you have the flexibility to modify it. I agree with Angel, though. The PQR format works because they are replacing numerical data with numerical data. Your format could easily break all sorts of programs th

Re: [Jmol-users] colouring isosurface of specific residues?

Many thanks Bob. I knew I had to be missing something simple somewhere Steve From: Robert Hanson [mailto:hans...@stolaf.edu] Sent: 11 November 2010 11:30 To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] colouring isosurface of specific residu

Re: [Jmol-users] colouring isosurface of specific residues?

Steve, What you would do is set a property of the atom to a given number, and then color the isosurface using the user custom scheme {*:A}.property_color = 1 {*:B}.property_color = 2 set usercolorscheme red yellow isosurface sasurface map property_color colorScheme "user" Bob On Wed, Nov 10, 2

Re: [Jmol-users] Jmol & P2N file format

Sorry to meddle, but I thougth I would give my opinion in case it is interesting for you. > - What if you check for this second column of atom names only for > files with the .p2n or .P2N extension. Jmol does not rely on file extensions for reading any format. > - or we can add a header in