Hello, What I want to do seems so simple, I just can't find the documentation. Would anyone know how to just change the colors of only certain states when they are appended to the same object?
For instance I have a simulation that shows atoms moving all over the place for states 1-300 and a nice even smoothing step for steps 300-N. I wanted sticks to be visible in states 1-300 but not visible in states 300-N. Is this possible, Thanks On Mar 20, 2012, at 9:12 AM, pymol-users-requ...@lists.sourceforge.net wrote: > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. Re: Editing of the pdb structure (Thomas Holder) > 2. Re: stereo under OSX Lion with Nvidia Quadro 4000 and Nvidia > Glasses? (Jason Vertrees) > 3. Query of running script of Contact Map Visualizer Plugin > (Suhaila Haji Mohd Hussin) > 4. Re: Editing of the pdb structure (Tsjerk Wassenaar) > 5. Re: PyMOL help (Genedoc) > 6. Re: Editing of the pdb structure (Tsjerk Wassenaar) > 7. Re: Editing of the pdb structure (David Hall) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 20 Mar 2012 13:14:31 +0100 > From: Thomas Holder <spel...@users.sourceforge.net> > Subject: Re: [PyMOL] Editing of the pdb structure > To: Tsjerk Wassenaar <tsje...@gmail.com> > Cc: pymol-users@lists.sourceforge.net > Message-ID: <4f6874a7.6060...@users.sourceforge.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 03/20/2012 11:35 AM, Tsjerk Wassenaar wrote: >> In addition to Thomas' answer... What is _wrong_ about the TER >> statement? Your chain is broken, indicated by the nonconsecutive >> numbers. That means you have two distinct molecules, and they are >> separated by a TER statement. Doesn't seem wrong. Yeah, they might be >> the same chain, but having a broken chain without considering them as >> separate molecules seems more wrong to me. > > depends on circumstances. Many algorithms (like alignment/superposition) > work fine even with gapped chains. There are some applications which > stop reading a PDB file on the first TER record, like TMalign. So when > preparing input for TMalign with PyMOL, you most likely want to skip any > TER records. > > Cheers, > Thomas > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 T?bingen > > > > ------------------------------ > > Message: 2 > Date: Tue, 20 Mar 2012 08:15:05 -0400 > From: Jason Vertrees <jason.vertr...@schrodinger.com> > Subject: Re: [PyMOL] stereo under OSX Lion with Nvidia Quadro 4000 and > Nvidia Glasses? > To: Harry Mark Greenblatt <harry.greenbl...@weizmann.ac.il> > Cc: "pymol-users@lists.sourceforge.net" > <pymol-users@lists.sourceforge.net> > Message-ID: > <CAAx+4zcjB9yHf4ULi5YH=33uxrjf_dspmbz4zwtbbounorr...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Harry, > > I have not seen any evidence of the NVidia 3D NVision system working > on a modern Mac OS X system. For the Mac, you'll have to use something > passive like Zalman (or maybe the new anaglyph). > > Cheers, > > -- Jason > > On Tue, Mar 20, 2012 at 3:59 AM, Harry Mark Greenblatt > <harry.greenbl...@weizmann.ac.il> wrote: >> BS"D >> >> Dear All, >> >> Can anybody confirm that they have a >> >> Mac Pro + Quadro 4000 + OSX 10.7.x + Nvidia 3D Vision glasses + compatible >> (non-Zalman) 120 Hz LCD screen >> >> working with quad buffered stereo? >> >> Thanks >> >> Harry >> >> >> ------------------------------------------------------------------------- >> >> Harry M. Greenblatt >> >> Associate Staff Scientist >> >> Dept of Structural Biology? ? ?? ?? ?harry.greenbl...@weizmann.ac.il >> >> Weizmann Institute of Science? ? ? ??Phone:??972-8-934-3625 >> >> 234 Herzl St.? ? ? ? ? ? ? ? ? ? ? ? Facsimile:???972-8-934-4159 >> >> Rehovot, 76100 >> >> Israel >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> This SF email is sponsosred by: >> Try Windows Azure free for 90 days Click Here >> http://p.sf.net/sfu/sfd2d-msazure >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schr?dinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > > > ------------------------------ > > Message: 3 > Date: Wed, 21 Mar 2012 00:41:20 +1200 > From: Suhaila Haji Mohd Hussin <bell_beaut...@hotmail.com> > Subject: [PyMOL] Query of running script of Contact Map Visualizer > Plugin > To: <pymol-users@lists.sourceforge.net> > Message-ID: <snt139-w56e79cfbfbbd0bf6f283aa8a...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Hello I know the plugin mentioned above (in the Subject) will work if I go to > Plugin > Manage Plugins > Install > contact_map_visualizer I get that. But > nothing happens if I run the plugin if I go to File > Run > > contact_map_visualizer.py I do this because I need it for my project, > preferably running the script via this method. Can anyone please tell me why > it is not working on the second method? I know it's a plugin and it's just a > python script anyway, no? Regards,Suhaila > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 4 > Date: Tue, 20 Mar 2012 13:44:03 +0100 > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [PyMOL] Editing of the pdb structure > To: Thomas Holder <spel...@users.sourceforge.net> > Cc: pymol-users@lists.sourceforge.net > Message-ID: > <CABzE1SiD6AC5FJev8ZaQTWmV1S1pMZ=aww5tozjjazi9vo3...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Thomas, > > 'Wrong', certainly in the context it was given in, is a statement of > judgment. It suggest that there is a failure in the functioning, and > is a criticism to the developer, becoming a wrongdoer. My argument is, > that the answer given (with TER statements) is not wrong, but from a > chemical and biological point of view, and in light of the PDB format, > is actually more correct. It may be inconvenient for post-processing > with some other tools, but that is easily taken care of by changing a > setting (unset use_ter_records), or by post-processing (sed -i /TER/d > file.pdb). > > Cheers, > > Tsjerk > > On Tue, Mar 20, 2012 at 1:14 PM, Thomas Holder > <spel...@users.sourceforge.net> wrote: >> On 03/20/2012 11:35 AM, Tsjerk Wassenaar wrote: >>> >>> In addition to Thomas' answer... What is _wrong_ about the TER >>> statement? Your chain is broken, indicated by the nonconsecutive >>> numbers. That means you have two distinct molecules, and they are >>> separated by a TER statement. Doesn't seem wrong. Yeah, they might be >>> the same chain, but having a broken chain without considering them as >>> separate molecules seems more wrong to me. >> >> >> depends on circumstances. Many algorithms (like alignment/superposition) >> work fine even with gapped chains. There are some applications which stop >> reading a PDB file on the first TER record, like TMalign. So when preparing >> input for TMalign with PyMOL, you most likely want to skip any TER records. >> >> Cheers, >> ?Thomas >> >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 T?bingen > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > > > > ------------------------------ > > Message: 5 > Date: Tue, 20 Mar 2012 14:12:15 +0100 > From: Genedoc <peter.kjel...@genedoc.se> > Subject: Re: [PyMOL] PyMOL help > To: pymol-users@lists.sourceforge.net > Message-ID: <4f68822f.30...@genedoc.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hani, > > You can these GUI commands: > A (Action)---preset---ligand sites or > A---find---polar contacts > > Hope this helps you! > > Peter > > syed.abidi skrev 2012-03-19 12:19: >> Dear All, >> >> I have a small query regarding PyMol and I would appreciate if you can help >> me with it. My query is: >> >> How do I analyze interactions with PyMol after I have docked my files? I >> wanted to know which molecules/amino acids are interacting in the docked >> confirmation. >> >> I would really appreciate your help. >> >> Thanks, >> >> Hani >> >> ________________________________ >> >> This e-mail may contain information that is privileged or confidential. If >> you are not the intended recipient, please delete the e-mail and any >> attachments and notify us immediately. >> >> >> ------------------------------------------------------------------------------ >> This SF email is sponsosred by: >> Try Windows Azure free for 90 days Click Here >> http://p.sf.net/sfu/sfd2d-msazure >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > -- > Peter Kjellen, Dr. Med. Sci. > CEO > Genedoc Pharmaceuticals AB > Kullsbackav?gen 30 > 239 42 Fasterbo > Sweden > Phone:+46 70 5952568 > > > > > ------------------------------ > > Message: 6 > Date: Tue, 20 Mar 2012 15:07:11 +0100 > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [PyMOL] Editing of the pdb structure > To: David Hall <li...@cowsandmilk.net> > Cc: pymol-users@lists.sourceforge.net > Message-ID: > <CABzE1SiKacd4paR3VwWQ6xYNAp0Xmh=uadkoawd6yzt_flz...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Shucks! So much for trying to keep the developer out of the wind. But > he's a wrongdoer by PDB definitions anyway! So it would be best to > modify the behaviour concerning writing of TER records. Feel free to > file it as suggestion. > > Gotta love polemics! -- Next time I'll manage, David. Next time... :p > > Tsjerk > > On Tue, Mar 20, 2012 at 2:48 PM, David Hall <li...@cowsandmilk.net> wrote: >> On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >>> Hi Thomas, >>> >>> 'Wrong', certainly in the context it was given in, is a statement of >>> judgment. It suggest that there is a failure in the functioning, and >>> is a criticism to the developer, becoming a wrongdoer. My argument is, >>> that the answer given (with TER statements) is not wrong, but from a >>> chemical and biological point of view, and in light of the PDB format, >>> is actually more correct. >> >> The PDB format says: >> The TER records occur in the coordinate section of the entry, and >> indicate the last residue presented for each polypeptide and/or >> nucleic acid chain for which there are determined coordinates. For >> proteins, the residue defined on the TER record is the >> carboxy-terminal residue; for nucleic acids it is the 3'-terminal >> residue. >> ( http://www.wwpdb.org/documentation/format33/sect9.html#TER ) >> >> Chain breaks in crystal structures are generally not the >> carboxy-terminal residues. >> >> -David > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > > > > ------------------------------ > > Message: 7 > Date: Tue, 20 Mar 2012 09:48:59 -0400 > From: David Hall <li...@cowsandmilk.net> > Subject: Re: [PyMOL] Editing of the pdb structure > To: Tsjerk Wassenaar <tsje...@gmail.com> > Cc: pymol-users@lists.sourceforge.net > Message-ID: > <CAPUwN__ynjMr9SJG9-e6aFs4ekHdK9PKO2Nh6Xbk5=_4x89...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> Hi Thomas, >> >> 'Wrong', certainly in the context it was given in, is a statement of >> judgment. It suggest that there is a failure in the functioning, and >> is a criticism to the developer, becoming a wrongdoer. My argument is, >> that the answer given (with TER statements) is not wrong, but from a >> chemical and biological point of view, and in light of the PDB format, >> is actually more correct. > > The PDB format says: > The TER records occur in the coordinate section of the entry, and > indicate the last residue presented for each polypeptide and/or > nucleic acid chain for which there are determined coordinates. For > proteins, the residue defined on the TER record is the > carboxy-terminal residue; for nucleic acids it is the 3'-terminal > residue. > ( http://www.wwpdb.org/documentation/format33/sect9.html#TER ) > > Chain breaks in crystal structures are generally not the > carboxy-terminal residues. > > -David > > > > ------------------------------ > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > > ------------------------------ > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest, Vol 70, Issue 18 > ******************************************* ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
