From: Rolf S. A. <rs...@gm...> - 2012-04-19 03:54:22
|
I am using pymol to display the surface of inorganic crystals, and have used it successfully in the past for relatively small molecules. I am not trying to display larger surfaces (>1e6 atoms), and now notice a discrepancy between the number of atoms present in and loaded from the source file, and that reported by pymol. I have included an example using a file with 1398146 atoms. VMD loads and displays the same file and reports the correct number of atom entries. However, pymol oddly reports 139814 atoms, not 1398146. However, as far as I can tell, the atoms do *appear* in the graphical display. I've posted some screen captures at http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png to illustrate this. Can anyone guess at the cause of this? I am using version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1 kernel, 12012MB RAM). Many thanks //Rolf |
From: Jason V. <jas...@sc...> - 2012-04-19 07:40:40
|
Hi Rolf, That's pretty strange. Any chance you can share the file? It looks like PyMOL's somehow missing the last number in the result. I've easily loaded millions of atoms before and got the correct atom count. Cheers, -- Jason On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson <rs...@gm...> wrote: > I am using pymol to display the surface of inorganic crystals, and > have used it successfully in the past for relatively small molecules. > I am not trying to display larger surfaces (>1e6 atoms), and now > notice a discrepancy between the number of atoms present in and loaded > from the source file, and that reported by pymol. I have included an > example using a file with 1398146 atoms. VMD loads and displays the > same file and reports the correct number of atom entries. However, > pymol oddly reports 139814 atoms, not 1398146. However, as far as I > can tell, the atoms do *appear* in the graphical display. I've posted > some screen captures at > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png > > to illustrate this. Can anyone guess at the cause of this? I am using > version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1 > kernel, 12012MB RAM). > Many thanks //Rolf > > ------------------------------------------------------------------------------ > For Developers, A Lot Can Happen In A Second. > Boundary is the first to Know...and Tell You. > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! > http://p.sf.net/sfu/Boundary-d2dvs2 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Rolf S. A. <rs...@gm...> - 2012-04-19 12:59:10
|
Hi Jason, Thanks for the speedy reply. I've posted the ASCII .xyz data file, compressed equivalent, and screen caps at http://www.ruf.rice.edu/~rsa4046/_private/pymol/ I have had some recent problems with pymol apparently hanging on this machine (possibly due to an opengl + nouveau-nvidia driver issue), that has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't know if my problem with atom count was related. You're right, it does indeed seem as if the last digit is just truncated. To test if this was just a display issue, I also tried loading the same data file within pymol (without the LIBGL statement) on a remote machine (although same version, OS, and libraries) via ssh X-forwarding, and derived the same result in terms of reported number of atoms from count_atoms, although I don't know if such a test is really definitive. Thanks very much for any insight you can provide. Cheers //Rolf On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote: > Hi Rolf, > > That's pretty strange. Any chance you can share the file? It looks > like PyMOL's somehow missing the last number in the result. I've > easily loaded millions of atoms before and got the correct atom count. > > Cheers, > > -- Jason > > On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson <rs...@gm...> wrote: > > I am using pymol to display the surface of inorganic crystals, and > > have used it successfully in the past for relatively small molecules. > > I am not trying to display larger surfaces (>1e6 atoms), and now > > notice a discrepancy between the number of atoms present in and loaded > > from the source file, and that reported by pymol. I have included an > > example using a file with 1398146 atoms. VMD loads and displays the > > same file and reports the correct number of atom entries. However, > > pymol oddly reports 139814 atoms, not 1398146. However, as far as I > > can tell, the atoms do *appear* in the graphical display. I've posted > > some screen captures at > > > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png > > > > to illustrate this. Can anyone guess at the cause of this? I am using > > version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1 > > kernel, 12012MB RAM). > > Many thanks //Rolf > > > > ------------------------------------------------------------------------------ > > For Developers, A Lot Can Happen In A Second. > > Boundary is the first to Know...and Tell You. > > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! > > http://p.sf.net/sfu/Boundary-d2dvs2 > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrödinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 |
From: Jason V. <jas...@sc...> - 2012-04-19 16:56:34
|
Rolf, Thanks for posting the file. I will look at it later tonight and get back to you. Cheers , Sent from my Android. On Apr 19, 2012 5:58 AM, "Rolf S. Arvidson" <rs...@gm...> wrote: > Hi Jason, > > Thanks for the speedy reply. I've posted the ASCII .xyz data file, > compressed equivalent, and screen caps at > > http://www.ruf.rice.edu/~rsa4046/_private/pymol/ > > I have had some recent problems with pymol apparently hanging on this > machine (possibly due to an opengl + nouveau-nvidia driver issue), that > has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't > know if my problem with atom count was related. You're right, it does > indeed seem as if the last digit is just truncated. To test if this was > just a display issue, I also tried loading the same data file within > pymol (without the LIBGL statement) on a remote machine (although same > version, OS, and libraries) via ssh X-forwarding, and derived the same > result in terms of reported number of atoms from count_atoms, although I > don't know if such a test is really definitive. Thanks very much for any > insight you can provide. > > Cheers //Rolf > > On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote: > > Hi Rolf, > > > > That's pretty strange. Any chance you can share the file? It looks > > like PyMOL's somehow missing the last number in the result. I've > > easily loaded millions of atoms before and got the correct atom count. > > > > Cheers, > > > > -- Jason > > > > On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson <rs...@gm...> > wrote: > > > I am using pymol to display the surface of inorganic crystals, and > > > have used it successfully in the past for relatively small molecules. > > > I am not trying to display larger surfaces (>1e6 atoms), and now > > > notice a discrepancy between the number of atoms present in and loaded > > > from the source file, and that reported by pymol. I have included an > > > example using a file with 1398146 atoms. VMD loads and displays the > > > same file and reports the correct number of atom entries. However, > > > pymol oddly reports 139814 atoms, not 1398146. However, as far as I > > > can tell, the atoms do *appear* in the graphical display. I've posted > > > some screen captures at > > > > > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png > > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png > > > > > > to illustrate this. Can anyone guess at the cause of this? I am using > > > version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1 > > > kernel, 12012MB RAM). > > > Many thanks //Rolf > > > > > > > ------------------------------------------------------------------------------ > > > For Developers, A Lot Can Happen In A Second. > > > Boundary is the first to Know...and Tell You. > > > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! > > > http://p.sf.net/sfu/Boundary-d2dvs2 > > > _______________________________________________ > > > PyMOL-users mailing list (PyM...@li...) > > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > > Archives: > http://www.mail-archive.com/pym...@li... > > > > > > > > -- > > Jason Vertrees, PhD > > PyMOL Product Manager > > Schrödinger, LLC > > > > (e) Jas...@sc... > > (o) +1 (603) 374-7120 > |
From: Rolf S. A. <rs...@gm...> - 2012-04-19 14:00:19
|
Hi Jason, I've also posted a screen cap of VMD with the same file loaded http://www.ruf.rice.edu/~rsa4046/_private/pymol/cap4.png in which the correct atom count is reported. In addition, I tried this with my licensed copy of PyMOL on my laptop (win7), also with same (truncated) result as Linux session. Thanks again for any help you can provide. Cheers //Rolf On Thu, Apr 19, 2012 at 07:58:56AM -0500, Rolf S. Arvidson wrote: > Hi Jason, > > Thanks for the speedy reply. I've posted the ASCII .xyz data file, > compressed equivalent, and screen caps at > > http://www.ruf.rice.edu/~rsa4046/_private/pymol/ > > I have had some recent problems with pymol apparently hanging on this > machine (possibly due to an opengl + nouveau-nvidia driver issue), that > has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't > know if my problem with atom count was related. You're right, it does > indeed seem as if the last digit is just truncated. To test if this was > just a display issue, I also tried loading the same data file within > pymol (without the LIBGL statement) on a remote machine (although same > version, OS, and libraries) via ssh X-forwarding, and derived the same > result in terms of reported number of atoms from count_atoms, although I > don't know if such a test is really definitive. Thanks very much for any > insight you can provide. > > Cheers //Rolf > > On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote: > > Hi Rolf, > > > > That's pretty strange. Any chance you can share the file? It looks > > like PyMOL's somehow missing the last number in the result. I've > > easily loaded millions of atoms before and got the correct atom count. > > > > Cheers, > > > > -- Jason > > > > On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson <rs...@gm...> wrote: > > > I am using pymol to display the surface of inorganic crystals, and > > > have used it successfully in the past for relatively small molecules. > > > I am not trying to display larger surfaces (>1e6 atoms), and now > > > notice a discrepancy between the number of atoms present in and loaded > > > from the source file, and that reported by pymol. I have included an > > > example using a file with 1398146 atoms. VMD loads and displays the > > > same file and reports the correct number of atom entries. However, > > > pymol oddly reports 139814 atoms, not 1398146. However, as far as I > > > can tell, the atoms do *appear* in the graphical display. I've posted > > > some screen captures at > > > > > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png > > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png > > > > > > to illustrate this. Can anyone guess at the cause of this? I am using > > > version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1 > > > kernel, 12012MB RAM). > > > Many thanks //Rolf > > > > > > ------------------------------------------------------------------------------ > > > For Developers, A Lot Can Happen In A Second. > > > Boundary is the first to Know...and Tell You. > > > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! > > > http://p.sf.net/sfu/Boundary-d2dvs2 > > > _______________________________________________ > > > PyMOL-users mailing list (PyM...@li...) > > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > > Archives: http://www.mail-archive.com/pym...@li... > > > > > > > > -- > > Jason Vertrees, PhD > > PyMOL Product Manager > > Schrödinger, LLC > > > > (e) Jas...@sc... > > (o) +1 (603) 374-7120 |
From: Thomas H. <sp...@us...> - 2012-04-19 16:47:01
|
Hi Rolf, the count_atoms command is fine. PyMOL truncates the first line of the xyz file to 6 characters, so it actually stopped reading the file after 139814 atoms. The fix is easy: --- layer2/ObjectMolecule.c (revision 3996) +++ layer2/ObjectMolecule.c (working copy) @@ -3481,7 +3481,7 @@ atInfo = *atInfoPtr; p_store = p; - p = ncopy(cc, p, 6); + p = ncopy(cc, p, 9); if(sscanf(cc, "%d", &nAtom) != 1) { nAtom = 0; tinker_xyz = false; Cheers, Thomas On 04/19/2012 04:00 PM, Rolf S. Arvidson wrote: > Hi Jason, > > I've also posted a screen cap of VMD with the same file loaded > > http://www.ruf.rice.edu/~rsa4046/_private/pymol/cap4.png > > in which the correct atom count is reported. In addition, I tried this > with my licensed copy of PyMOL on my laptop (win7), also with same > (truncated) result as Linux session. Thanks again for any help you can > provide. > > Cheers //Rolf > > On Thu, Apr 19, 2012 at 07:58:56AM -0500, Rolf S. Arvidson wrote: >> Hi Jason, >> >> Thanks for the speedy reply. I've posted the ASCII .xyz data file, >> compressed equivalent, and screen caps at >> >> http://www.ruf.rice.edu/~rsa4046/_private/pymol/ >> >> I have had some recent problems with pymol apparently hanging on this >> machine (possibly due to an opengl + nouveau-nvidia driver issue), that >> has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't >> know if my problem with atom count was related. You're right, it does >> indeed seem as if the last digit is just truncated. To test if this was >> just a display issue, I also tried loading the same data file within >> pymol (without the LIBGL statement) on a remote machine (although same >> version, OS, and libraries) via ssh X-forwarding, and derived the same >> result in terms of reported number of atoms from count_atoms, although I >> don't know if such a test is really definitive. Thanks very much for any >> insight you can provide. >> >> Cheers //Rolf >> >> On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote: >>> Hi Rolf, >>> >>> That's pretty strange. Any chance you can share the file? It looks >>> like PyMOL's somehow missing the last number in the result. I've >>> easily loaded millions of atoms before and got the correct atom count. >>> >>> Cheers, >>> >>> -- Jason >>> >>> On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson<rs...@gm...> wrote: >>>> I am using pymol to display the surface of inorganic crystals, and >>>> have used it successfully in the past for relatively small molecules. >>>> I am not trying to display larger surfaces (>1e6 atoms), and now >>>> notice a discrepancy between the number of atoms present in and loaded >>>> from the source file, and that reported by pymol. I have included an >>>> example using a file with 1398146 atoms. VMD loads and displays the >>>> same file and reports the correct number of atom entries. However, >>>> pymol oddly reports 139814 atoms, not 1398146. However, as far as I >>>> can tell, the atoms do *appear* in the graphical display. I've posted >>>> some screen captures at >>>> >>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png >>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png >>>> >>>> to illustrate this. Can anyone guess at the cause of this? I am using >>>> version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1 >>>> kernel, 12012MB RAM). >>>> Many thanks //Rolf >>> >>> -- >>> Jason Vertrees, PhD >>> PyMOL Product Manager >>> Schrödinger, LLC >>> >>> (e) Jas...@sc... >>> (o) +1 (603) 374-7120 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Jason V. <jas...@sc...> - 2012-04-19 22:37:30
|
Thomas, Thanks--we'll add the fix ASAP. Cheers, -- J On Thu, Apr 19, 2012 at 9:46 AM, Thomas Holder <sp...@us...> wrote: > Hi Rolf, > > the count_atoms command is fine. PyMOL truncates the first line of the > xyz file to 6 characters, so it actually stopped reading the file after > 139814 atoms. The fix is easy: > > --- layer2/ObjectMolecule.c (revision 3996) > +++ layer2/ObjectMolecule.c (working copy) > @@ -3481,7 +3481,7 @@ > atInfo = *atInfoPtr; > > p_store = p; > - p = ncopy(cc, p, 6); > + p = ncopy(cc, p, 9); > if(sscanf(cc, "%d", &nAtom) != 1) { > nAtom = 0; > tinker_xyz = false; > > Cheers, > Thomas > > On 04/19/2012 04:00 PM, Rolf S. Arvidson wrote: >> Hi Jason, >> >> I've also posted a screen cap of VMD with the same file loaded >> >> http://www.ruf.rice.edu/~rsa4046/_private/pymol/cap4.png >> >> in which the correct atom count is reported. In addition, I tried this >> with my licensed copy of PyMOL on my laptop (win7), also with same >> (truncated) result as Linux session. Thanks again for any help you can >> provide. >> >> Cheers //Rolf >> >> On Thu, Apr 19, 2012 at 07:58:56AM -0500, Rolf S. Arvidson wrote: >>> Hi Jason, >>> >>> Thanks for the speedy reply. I've posted the ASCII .xyz data file, >>> compressed equivalent, and screen caps at >>> >>> http://www.ruf.rice.edu/~rsa4046/_private/pymol/ >>> >>> I have had some recent problems with pymol apparently hanging on this >>> machine (possibly due to an opengl + nouveau-nvidia driver issue), that >>> has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't >>> know if my problem with atom count was related. You're right, it does >>> indeed seem as if the last digit is just truncated. To test if this was >>> just a display issue, I also tried loading the same data file within >>> pymol (without the LIBGL statement) on a remote machine (although same >>> version, OS, and libraries) via ssh X-forwarding, and derived the same >>> result in terms of reported number of atoms from count_atoms, although I >>> don't know if such a test is really definitive. Thanks very much for any >>> insight you can provide. >>> >>> Cheers //Rolf >>> >>> On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote: >>>> Hi Rolf, >>>> >>>> That's pretty strange. Any chance you can share the file? It looks >>>> like PyMOL's somehow missing the last number in the result. I've >>>> easily loaded millions of atoms before and got the correct atom count. >>>> >>>> Cheers, >>>> >>>> -- Jason >>>> >>>> On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson<rs...@gm...> wrote: >>>>> I am using pymol to display the surface of inorganic crystals, and >>>>> have used it successfully in the past for relatively small molecules. >>>>> I am not trying to display larger surfaces (>1e6 atoms), and now >>>>> notice a discrepancy between the number of atoms present in and loaded >>>>> from the source file, and that reported by pymol. I have included an >>>>> example using a file with 1398146 atoms. VMD loads and displays the >>>>> same file and reports the correct number of atom entries. However, >>>>> pymol oddly reports 139814 atoms, not 1398146. However, as far as I >>>>> can tell, the atoms do *appear* in the graphical display. I've posted >>>>> some screen captures at >>>>> >>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png >>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png >>>>> >>>>> to illustrate this. Can anyone guess at the cause of this? I am using >>>>> version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1 >>>>> kernel, 12012MB RAM). >>>>> Many thanks //Rolf >>>> >>>> -- >>>> Jason Vertrees, PhD >>>> PyMOL Product Manager >>>> Schrödinger, LLC >>>> >>>> (e) Jas...@sc... >>>> (o) +1 (603) 374-7120 > > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > > ------------------------------------------------------------------------------ > For Developers, A Lot Can Happen In A Second. > Boundary is the first to Know...and Tell You. > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! > http://p.sf.net/sfu/Boundary-d2dvs2 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Rolf S. A. <rs...@gm...> - 2012-04-19 17:12:06
|
Hi Thomas, Thanks very much for this patch, I will apply and post back results. Cheers! // Rolf On Thu, Apr 19, 2012 at 11:46 AM, Thomas Holder <sp...@us...> wrote: > Hi Rolf, > > the count_atoms command is fine. PyMOL truncates the first line of the > xyz file to 6 characters, so it actually stopped reading the file after > 139814 atoms. The fix is easy: > > --- layer2/ObjectMolecule.c (revision 3996) > +++ layer2/ObjectMolecule.c (working copy) > @@ -3481,7 +3481,7 @@ > atInfo = *atInfoPtr; > > p_store = p; > - p = ncopy(cc, p, 6); > + p = ncopy(cc, p, 9); > if(sscanf(cc, "%d", &nAtom) != 1) { > nAtom = 0; > tinker_xyz = false; > > Cheers, > Thomas > > On 04/19/2012 04:00 PM, Rolf S. Arvidson wrote: >> Hi Jason, >> >> I've also posted a screen cap of VMD with the same file loaded >> >> http://www.ruf.rice.edu/~rsa4046/_private/pymol/cap4.png >> >> in which the correct atom count is reported. In addition, I tried this >> with my licensed copy of PyMOL on my laptop (win7), also with same >> (truncated) result as Linux session. Thanks again for any help you can >> provide. >> >> Cheers //Rolf >> >> On Thu, Apr 19, 2012 at 07:58:56AM -0500, Rolf S. Arvidson wrote: >>> Hi Jason, >>> >>> Thanks for the speedy reply. I've posted the ASCII .xyz data file, >>> compressed equivalent, and screen caps at >>> >>> http://www.ruf.rice.edu/~rsa4046/_private/pymol/ >>> >>> I have had some recent problems with pymol apparently hanging on this >>> machine (possibly due to an opengl + nouveau-nvidia driver issue), that >>> has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't >>> know if my problem with atom count was related. You're right, it does >>> indeed seem as if the last digit is just truncated. To test if this was >>> just a display issue, I also tried loading the same data file within >>> pymol (without the LIBGL statement) on a remote machine (although same >>> version, OS, and libraries) via ssh X-forwarding, and derived the same >>> result in terms of reported number of atoms from count_atoms, although I >>> don't know if such a test is really definitive. Thanks very much for any >>> insight you can provide. >>> >>> Cheers //Rolf >>> >>> On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote: >>>> Hi Rolf, >>>> >>>> That's pretty strange. Any chance you can share the file? It looks >>>> like PyMOL's somehow missing the last number in the result. I've >>>> easily loaded millions of atoms before and got the correct atom count. >>>> >>>> Cheers, >>>> >>>> -- Jason >>>> >>>> On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson<rs...@gm...> wrote: >>>>> I am using pymol to display the surface of inorganic crystals, and >>>>> have used it successfully in the past for relatively small molecules. >>>>> I am not trying to display larger surfaces (>1e6 atoms), and now >>>>> notice a discrepancy between the number of atoms present in and loaded >>>>> from the source file, and that reported by pymol. I have included an >>>>> example using a file with 1398146 atoms. VMD loads and displays the >>>>> same file and reports the correct number of atom entries. However, >>>>> pymol oddly reports 139814 atoms, not 1398146. However, as far as I >>>>> can tell, the atoms do *appear* in the graphical display. I've posted >>>>> some screen captures at >>>>> >>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png >>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png >>>>> >>>>> to illustrate this. Can anyone guess at the cause of this? I am using >>>>> version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1 >>>>> kernel, 12012MB RAM). >>>>> Many thanks //Rolf >>>> >>>> -- >>>> Jason Vertrees, PhD >>>> PyMOL Product Manager >>>> Schrödinger, LLC >>>> >>>> (e) Jas...@sc... >>>> (o) +1 (603) 374-7120 > > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > > ------------------------------------------------------------------------------ > For Developers, A Lot Can Happen In A Second. > Boundary is the first to Know...and Tell You. > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! > http://p.sf.net/sfu/Boundary-d2dvs2 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Rolf S. A. <rs...@gm...> - 2012-04-19 18:11:26
|
Hi Thomas, Your patch got the file loaded in its entirety, thanks! $ pymol $SIM -c -d "@./png.pml" ExecutiveLoad: "output/flicker-1811000.xyz" loaded as "flicker-1811000", through state 1. PyMOL>@./png.pml Selector: selection "cube" defined with 1398146 atoms. PyMOL>count_atoms cube Selector: selection "cube" defined with 1398146 atoms. count_atoms: 1398146 atoms ... I posted the result at http://www.ruf.rice.edu/~rsa4046/_private/pymol/flicker-1811000.png Thanks again- Cheers //Rolf On Thu, Apr 19, 2012 at 12:11:56PM -0500, Rolf S. Arvidson wrote: > Hi Thomas, > Thanks very much for this patch, I will apply and post back results. Cheers! > // Rolf > > On Thu, Apr 19, 2012 at 11:46 AM, Thomas Holder > <sp...@us...> wrote: > > Hi Rolf, > > > > the count_atoms command is fine. PyMOL truncates the first line of the > > xyz file to 6 characters, so it actually stopped reading the file after > > 139814 atoms. The fix is easy: > > > > --- layer2/ObjectMolecule.c (revision 3996) > > +++ layer2/ObjectMolecule.c (working copy) > > @@ -3481,7 +3481,7 @@ > > atInfo = *atInfoPtr; > > > > p_store = p; > > - p = ncopy(cc, p, 6); > > + p = ncopy(cc, p, 9); > > if(sscanf(cc, "%d", &nAtom) != 1) { > > nAtom = 0; > > tinker_xyz = false; > > > > Cheers, > > Thomas > > > > On 04/19/2012 04:00 PM, Rolf S. Arvidson wrote: > >> Hi Jason, > >> > >> I've also posted a screen cap of VMD with the same file loaded > >> > >> http://www.ruf.rice.edu/~rsa4046/_private/pymol/cap4.png > >> > >> in which the correct atom count is reported. In addition, I tried this > >> with my licensed copy of PyMOL on my laptop (win7), also with same > >> (truncated) result as Linux session. Thanks again for any help you can > >> provide. > >> > >> Cheers //Rolf > >> > >> On Thu, Apr 19, 2012 at 07:58:56AM -0500, Rolf S. Arvidson wrote: > >>> Hi Jason, > >>> > >>> Thanks for the speedy reply. I've posted the ASCII .xyz data file, > >>> compressed equivalent, and screen caps at > >>> > >>> http://www.ruf.rice.edu/~rsa4046/_private/pymol/ > >>> > >>> I have had some recent problems with pymol apparently hanging on this > >>> machine (possibly due to an opengl + nouveau-nvidia driver issue), that > >>> has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't > >>> know if my problem with atom count was related. You're right, it does > >>> indeed seem as if the last digit is just truncated. To test if this was > >>> just a display issue, I also tried loading the same data file within > >>> pymol (without the LIBGL statement) on a remote machine (although same > >>> version, OS, and libraries) via ssh X-forwarding, and derived the same > >>> result in terms of reported number of atoms from count_atoms, although I > >>> don't know if such a test is really definitive. Thanks very much for any > >>> insight you can provide. > >>> > >>> Cheers //Rolf > >>> > >>> On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote: > >>>> Hi Rolf, > >>>> > >>>> That's pretty strange. Any chance you can share the file? It looks > >>>> like PyMOL's somehow missing the last number in the result. I've > >>>> easily loaded millions of atoms before and got the correct atom count. > >>>> > >>>> Cheers, > >>>> > >>>> -- Jason > >>>> > >>>> On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson<rs...@gm...> wrote: > >>>>> I am using pymol to display the surface of inorganic crystals, and > >>>>> have used it successfully in the past for relatively small molecules. > >>>>> I am not trying to display larger surfaces (>1e6 atoms), and now > >>>>> notice a discrepancy between the number of atoms present in and loaded > >>>>> from the source file, and that reported by pymol. I have included an > >>>>> example using a file with 1398146 atoms. VMD loads and displays the > >>>>> same file and reports the correct number of atom entries. However, > >>>>> pymol oddly reports 139814 atoms, not 1398146. However, as far as I > >>>>> can tell, the atoms do *appear* in the graphical display. I've posted > >>>>> some screen captures at > >>>>> > >>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png > >>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png > >>>>> > >>>>> to illustrate this. Can anyone guess at the cause of this? I am using > >>>>> version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1 > >>>>> kernel, 12012MB RAM). > >>>>> Many thanks //Rolf > >>>> > >>>> -- > >>>> Jason Vertrees, PhD > >>>> PyMOL Product Manager > >>>> Schrödinger, LLC > >>>> > >>>> (e) Jas...@sc... > >>>> (o) +1 (603) 374-7120 > > > > > > -- > > Thomas Holder > > MPI for Developmental Biology > > Spemannstr. 35 > > D-72076 Tübingen > > > > ------------------------------------------------------------------------------ > > For Developers, A Lot Can Happen In A Second. > > Boundary is the first to Know...and Tell You. > > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! > > http://p.sf.net/sfu/Boundary-d2dvs2 > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... |