Re: [PyMOL] nucleic acid (one or two letter) residue names
that's true, residue names should be right-justified. http://www.wwpdb.org/documentation/format32/sect1.html Residue nameOne of the standard amino acid or nucleic acids, as listed below, or the non-standard group designation as defined in the HET dictionary. Field is right-justified. Cheers, Thomas On 05/17/2011 07:44 PM, Pascal Auffinger wrote: Hi Jason, A more difficult one (at least for me) Pymol seems to write (through save command) nucleic acid residue names not as suggested by PDB convention. Here is an extract of a PDB file (any PDB file containing nucleic acid residues shows the same – try 100D for example) ATOM 1 O5' C A 1 -4.549 5.095 4.262 1.00 28.71O ATOM 2 C5' C A 1 -4.176 6.323 3.646 1.00 27.35C ATOM 3 C4' C A 1 -3.853 7.410 4.672 1.00 24.41C When I save this file (save command in pymol) i get this Output from pymol X (this is added by me) ATOM 1 O5' C A 1 -4.549 5.095 4.262 1.00 28.71O ATOM 2 C5' C A 1 -4.176 6.323 3.646 1.00 27.35C ATOM 3 C4' C A 1 -3.853 7.410 4.672 1.00 24.41C In one instance, the C residue name is left justified and right justified in the other. Of course, this cannot happen for the three letter residue names. Any clue ? I tried the following : *pdb_truncate_residue_name* (boolean, default: off) controls whether or not PDB residue names are truncated to three letters only. with no effect Thanks for help Pascal -- Thomas Holder MPI for Developmental Biology -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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
Re: [PyMOL] nucleic acid (one or two letter) residue names
Hi, On Wed, May 18, 2011 at 6:00 AM, Thomas Holder spel...@users.sourceforge.net wrote: that's true, residue names should be right-justified. This is a bug. Please file it on our open-source bug tracker http://sourceforge.net/tracker/?group_id=4546atid=104546. I will fix it when I get the chance. Cheers, -- Jason http://www.wwpdb.org/documentation/format32/sect1.html Residue name One of the standard amino acid or nucleic acids, as listed below, or the non-standard group designation as defined in the HET dictionary. Field is right-justified. Cheers, Thomas On 05/17/2011 07:44 PM, Pascal Auffinger wrote: Hi Jason, A more difficult one (at least for me) Pymol seems to write (through save command) nucleic acid residue names not as suggested by PDB convention. Here is an extract of a PDB file (any PDB file containing nucleic acid residues shows the same – try 100D for example) ATOM 1 O5' C A 1 -4.549 5.095 4.262 1.00 28.71O ATOM 2 C5' C A 1 -4.176 6.323 3.646 1.00 27.35C ATOM 3 C4' C A 1 -3.853 7.410 4.672 1.00 24.41C When I save this file (save command in pymol) i get this Output from pymol X (this is added by me) ATOM 1 O5' C A 1 -4.549 5.095 4.262 1.00 28.71O ATOM 2 C5' C A 1 -4.176 6.323 3.646 1.00 27.35C ATOM 3 C4' C A 1 -3.853 7.410 4.672 1.00 24.41C In one instance, the C residue name is left justified and right justified in the other. Of course, this cannot happen for the three letter residue names. Any clue ? I tried the following : *pdb_truncate_residue_name* (boolean, default: off) controls whether or not PDB residue names are truncated to three letters only. with no effect Thanks for help Pascal -- Thomas Holder MPI for Developmental Biology -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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 Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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
Re: [PyMOL] nucleic acid (one or two letter) residue names
Hi Pascal,
On 05/18/2011 04:46 PM, Pascal Auffinger wrote:
Thanks, could you do that and provide a binary ?
I can't provide a binary, sorry.
Or alternatively, could
you post precisely which line to change to what ? Or change it in the
source code so that we could download an updated version.
see attached patch (untested, since my build seems to be broken at the
moment).
This an
important bug (at least for me). I and many others on the list don't
master C languages (oups ... Am i the only one ?)
for sure you're not the only one ;-)
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Index: layer2/CoordSet.c
===
--- layer2/CoordSet.c (revision 3948)
+++ layer2/CoordSet.c (working copy)
@@ -678,6 +678,13 @@
strcpy(resn, ai-resn);
if(SettingGetGlobal_b(G, cSetting_pdb_truncate_residue_name)) {
resn[3] = 0;/* enforce 3-letter residue name in PDB files */
+/* right-justify */
+int i = strlen(resn);
+if (i 3) {
+ int j = 3;
+ while(i 0) resn[--j] = resn[--i];
+ while(j 0) resn[--j] = ' ';
+}
}
if(SettingGetGlobal_b(G, cSetting_pdb_formal_charges)) {
--
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Re: [PyMOL] nucleic acid (one or two letter) residue names
On 05/18/2011 05:01 PM, Jason Vertrees wrote: This is a bug. Please file it on our open-source bug tracker http://sourceforge.net/tracker/?group_id=4546atid=104546. I will fix it when I get the chance. Bugs item #3304003 https://sourceforge.net/tracker/?func=detailaid=3304003group_id=4546atid=104546 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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
Re: [PyMOL] PyMOL-users Digest, Vol 60, Issue 7
Hi PyMOL Community, I have a trajectory file loaded into PyMOL but I would like to play the movie in reverse order. Is there a way to achieve this within PyMOL? I know that I could do this by outputting the states as PNG files and then reversing them in an external program but I would like to be able to easily do this within PyMOL's visualization environment. The reason why I want to reverse the trajectory is because it was generated from Principal Component Analysis and then the original trajectory was projected onto one of the eigenvectors in order to see the motions involved in a transition. Unfortunately, the direction that was produced is opposite of what I actually observe. Thanks Sean -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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
Re: [PyMOL] PyMOL-users Digest, Vol 60, Issue 7
On 05/18/2011 06:50 PM, Sean Law wrote: Hi PyMOL Community, I have a trajectory file loaded into PyMOL but I would like to play the movie in reverse order. Is there a way to achieve this within PyMOL? If you have 100 states, type: mset 100-1 See also: http://www.pymolwiki.org/index.php/Mset Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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
[PyMOL] change transparency for only a selection
Hello list, I would like to change the stick_transparency for a selection but it doesn't seem to work. I am using the xyz file from the wiki: http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_commented_example and the attached script. What am I doing wrong? Thanks already, nick example.xyz Description: Xmol XYZ data example.pml Description: application/vnd.ctc-posml signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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
Re: [PyMOL] change transparency for only a selection
Hi Nick, Sticks are bonds. For that we use set_bond not set. Try: set_bond stick_transparency, 0.8, rest set_bond stick_transparency, 0.0, sel_01 Cheers, -- Jason On Wed, May 18, 2011 at 1:39 PM, Nicolas Bock nicolasb...@gmail.com wrote: Hello list, I would like to change the stick_transparency for a selection but it doesn't seem to work. I am using the xyz file from the wiki: http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_commented_example and the attached script. What am I doing wrong? Thanks already, nick -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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 Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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
Re: [PyMOL] change transparency for only a selection
Hi Nick, On Wed, 2011-05-18 11:39 EDT, Nicolas Bock nicolasb...@gmail.com wrote: Hello list, I would like to change the stick_transparency for a selection but it doesn't seem to work. I am using the xyz file from the wiki: http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_commented_example and the attached script. What am I doing wrong? Thanks already, nick Your commands are: load example.xyz hide all show sticks select sel_01, ID 38 ID 39 ID 42 ID 43 ID 44 ID 45 select rest, all and not sel_01 disable rest set stick_transparency, 0.8, rest set stick_transparency, 0.0, sel_01 I think you'll find that the transparency settings only work with whole objects and not with selections that are subsets of objects. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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
Re: [PyMOL] change transparency for only a selection
Hi Jason, thanks, that works! nick On 05/18/11 12:08, Jason Vertrees wrote: Hi Nick, Sticks are bonds. For that we use set_bond not set. Try: set_bond stick_transparency, 0.8, rest set_bond stick_transparency, 0.0, sel_01 Cheers, -- Jason On Wed, May 18, 2011 at 1:39 PM, Nicolas Bock nicolasb...@gmail.com wrote: Hello list, I would like to change the stick_transparency for a selection but it doesn't seem to work. I am using the xyz file from the wiki: http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_commented_example and the attached script. What am I doing wrong? Thanks already, nick -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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 signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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
[PyMOL] movie: interpolate between different states
Hi, can pymol interpolate between states in a movie? Suppose I have coordinates of a docking process with several states, and I would like to animate that process, but smoothly. I would madd 1 x15 madd 2 x15 . . . but would like pymol to interpolate in those 15 frames between state 1 and 2, then 2 and 3, and so on. Thanks, nick signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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
Re: [PyMOL] nucleic acid (one or two letter) residue names
Hi Thomas, Thanks for submitting the bug. I've modified and applied the patch and pushed the code. It's fixed. Cheers, -- Jason On Wed, May 18, 2011 at 11:43 AM, Thomas Holder spel...@users.sourceforge.net wrote: On 05/18/2011 05:01 PM, Jason Vertrees wrote: This is a bug. Please file it on our open-source bug tracker http://sourceforge.net/tracker/?group_id=4546atid=104546. I will fix it when I get the chance. Bugs item #3304003 https://sourceforge.net/tracker/?func=detailaid=3304003group_id=4546atid=104546 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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
Re: [PyMOL] movie: interpolate between different states
Hi Nick, You can use the smooth command (http://www.pymolwiki.org/index.php/Smooth) on the structure of choice. Incentive PyMOL comes with a molecular morpher called rigimol that morphs a starting structure into an ending structure. I suggest trying the smooth command first if you already have the states. Cheers, -- Jason On Wed, May 18, 2011 at 3:39 PM, Nicolas Bock nicolasb...@gmail.com wrote: Hi, can pymol interpolate between states in a movie? Suppose I have coordinates of a docking process with several states, and I would like to animate that process, but smoothly. I would madd 1 x15 madd 2 x15 . . . but would like pymol to interpolate in those 15 frames between state 1 and 2, then 2 and 3, and so on. Thanks, nick -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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 Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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
Re: [PyMOL] movie: interpolate between different states
Hi Jason, I have the incentive version, but how do I use rigimol? I can't find documentation for it on the documentation webpage. The link from http://pymol.org/dsc/dokuwiki/doku.php?id=ips=rigimol seems to be dead. Thanks, nick On 05/18/11 15:20, Jason Vertrees wrote: Hi Nick, You can use the smooth command (http://www.pymolwiki.org/index.php/Smooth) on the structure of choice. Incentive PyMOL comes with a molecular morpher called rigimol that morphs a starting structure into an ending structure. I suggest trying the smooth command first if you already have the states. Cheers, -- Jason On Wed, May 18, 2011 at 3:39 PM, Nicolas Bock nicolasb...@gmail.com wrote: Hi, can pymol interpolate between states in a movie? Suppose I have coordinates of a docking process with several states, and I would like to animate that process, but smoothly. I would madd 1 x15 madd 2 x15 . . . but would like pymol to interpolate in those 15 frames between state 1 and 2, then 2 and 3, and so on. Thanks, nick -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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 signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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
[PyMOL] change atom coordiates?
Hello, can I selectively change coordinates of particular atoms in a state? It seems that alter_state is not able to do that, since the expression (at least according to the help text) seems to apply to the x-coordinate of all atoms in the state for instance. The result of cmd.get_model() might be useful here, but I can't figure out how to access individual coordinates and then store them back into the state. Any hints are greatly appreciated. Thanks, nick signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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
Re: [PyMOL] change atom coordiates?
Hi Nicolas, can I selectively change coordinates of particular atoms in a state? Yes, you just need to properly select that atom. It seems that alter_state is not able to do that, since the expression (at least according to the help text) seems to apply to the x-coordinate of all atoms in the state for instance. alter_state applies to more than just the x-coordinate. Take the following for example: # make an alanine frag ala # add another state frag ala # alter the C-alpha position in state 2 alter_state 2, ala and n. CA, (x,y,z)=(1,1,1) # go to state 2 set state, 2 Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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
