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From: Warren D. <wa...@de...> - 2006-04-15 18:04:57
|
Paulo, Thank you for the simple and helpful suggestion -- this is exactly the = kind of input that can enable us to improve the software with a trivial = amount of effort on everyone's part. PyMOL will now issue a warning if you save a PDB file using an extension = it does not recognize. =20 Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Paulo Martel > Sent: Friday, April 14, 2006 6:45 PM > Cc: pym...@li... > Subject: [PyMOL] saving files in pymol >=20 >=20 > Hello, >=20 > one thing I find a little bit annoying: the "save" command in=20 > Pymol will accept any of <file>.<ext>, and if the <ext> is=20 > unknown, it will simple save a pdb file. While some people=20 > may find this a useful feature, I think it is quite=20 > dangerous. For instance, suppose I'm trying to save=20 > "work.pse" and mistakenly type "work.psf", without noticing=20 > it. If I close Pymol, I will end up with a pdb file called=20 > "work.psf", and all my session work goes down the drain. This=20 > is not an hypothetical situation, it happened a couple of=20 > times, to my great dismay. What do you think, Warren ?... >=20 > Regards, > Paulo >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking=20 > scripting language that extends applications into web and=20 > mobile media. Attend the live webcast and join the prime=20 > developer group breaking into this new coding territory! > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720& dat=3D121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
From: Geng T. <gen...@ho...> - 2006-04-15 05:18:29
|
Sorry, wrong thread. This should be my answer to laura's question about different sphere size. Too excited to be of a little help here. Tiger >From: "Geng Tian" <gen...@ho...> >To: pm...@ua... >CC: pym...@li... >Subject: RE: [PyMOL] saving files in pymol >Date: Sat, 15 Apr 2006 05:08:57 +0000 > >Hi, Paulo: >I hope these entries from my old pml file might help you: > >select c11, resi 11 and chain c >show sphere, c11 >alter c11, vdw=vdw*0.2 > >select c124, resi 124 and chain c >show sphere, c124 >alter c124, vdw=vdw*2 > >Tiger > > > > > > > >>From: Paulo Martel <pm...@ua...> >>CC: pym...@li... >>Subject: [PyMOL] saving files in pymol >>Date: Sat, 15 Apr 2006 02:40:39 +0100 >> >> >>Hello, >> >>one thing I find a little bit annoying: the "save" command in Pymol will >>accept any of <file>.<ext>, and if the <ext> is unknown, >>it will simple save a pdb file. While some people may find this a useful >>feature, I think it is quite dangerous. For instance, suppose >>I'm trying to save "work.pse" and mistakenly type "work.psf", without >>noticing it. If I close Pymol, I will end up with a pdb file >>called "work.psf", and all my session work goes down the drain. This is >>not an hypothetical situation, it happened a couple of times, to >>my great dismay. What do you think, Warren ?... >> >>Regards, >>Paulo >> >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by xPML, a groundbreaking scripting >>language >>that extends applications into web and mobile media. Attend the live >>webcast >>and join the prime developer group breaking into this new coding >>territory! >>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 >>_______________________________________________ >>PyMOL-users mailing list >>PyM...@li... >>https://lists.sourceforge.net/lists/listinfo/pymol-users > >_________________________________________________________________ >Express yourself instantly with MSN Messenger! Download today - it's FREE! >http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > > >------------------------------------------------------- >This SF.Net email is sponsored by xPML, a groundbreaking scripting language >that extends applications into web and mobile media. Attend the live >webcast >and join the prime developer group breaking into this new coding territory! >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 >_______________________________________________ >PyMOL-users mailing list >PyM...@li... >https://lists.sourceforge.net/lists/listinfo/pymol-users _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ |
From: Geng T. <gen...@ho...> - 2006-04-15 05:09:05
|
Hi, Paulo: I hope these entries from my old pml file might help you: select c11, resi 11 and chain c show sphere, c11 alter c11, vdw=vdw*0.2 select c124, resi 124 and chain c show sphere, c124 alter c124, vdw=vdw*2 Tiger >From: Paulo Martel <pm...@ua...> >CC: pym...@li... >Subject: [PyMOL] saving files in pymol >Date: Sat, 15 Apr 2006 02:40:39 +0100 > > >Hello, > >one thing I find a little bit annoying: the "save" command in Pymol will >accept any of <file>.<ext>, and if the <ext> is unknown, >it will simple save a pdb file. While some people may find this a useful >feature, I think it is quite dangerous. For instance, suppose >I'm trying to save "work.pse" and mistakenly type "work.psf", without >noticing it. If I close Pymol, I will end up with a pdb file >called "work.psf", and all my session work goes down the drain. This is not >an hypothetical situation, it happened a couple of times, to >my great dismay. What do you think, Warren ?... > >Regards, >Paulo > > > >------------------------------------------------------- >This SF.Net email is sponsored by xPML, a groundbreaking scripting language >that extends applications into web and mobile media. Attend the live >webcast >and join the prime developer group breaking into this new coding territory! >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 >_______________________________________________ >PyMOL-users mailing list >PyM...@li... >https://lists.sourceforge.net/lists/listinfo/pymol-users _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ |
From: Geng T. <gen...@ho...> - 2006-04-15 04:56:59
|
Hi, there: The problem was temporarily solved by putting each monomer in a separated file and load into pymol. Hiding the two residues doesn't work. The weird linkage will just jump to the next residues. Thank you all. Tiger >From: "Noinaj" <no...@uk...> >To: "Tsjerk Wassenaar" ><ts...@gm...>,<pym...@li...> >Subject: Re: [PyMOL] question about ca trace >Date: Fri, 14 Apr 2006 11:23:52 -0400 > >Tsjerk, > >Nice point, and probably easier to just create new objects in Pymol. > > > >nick > > > ----- Original Message ----- > From: Tsjerk Wassenaar > To: pym...@li... > Sent: Friday, April 14, 2006 4:29 AM > Subject: Re: [PyMOL] question about ca trace > > > Hi Tiger, > > Nick is largely right. The cause for the link to show up is that pymol >just traces through all c-alphas in the object, regardless of chains or >distances. So, selecting the linked residues and hiding the trace should >solve your problem. Also, creating two files will do the trick. >Alternatively, you can create two objects and draw the trace for each of >these. > > Cheers, > > Tsjerk > > > On 4/13/06, Noinaj <no...@uk...> wrote: > Tiger, > > I am no expert by far, but can you select the linkage? If so, just >select > and hide. Also, you might try just hiding the two residues that are >linked, > this might get rid of the link and you probably wouldn't notice the >missing > residues unless it is a small protein. alternatively, and probably >the best > solution is to edit the pdb file to create two individual files, one >for > each dimer (this can be done in any text editor). then open both in >Pymol > and you should then be able to edit independently. > > The problem may be, and again I remind you that I am no expert, that >these > atoms are two close to each other and may be getting mistaken for a >covalent > interaction, can't tell without actually seeing though. > > Hope any or all of this helps. Good Luck! > > > > Cheers, > Nick > > > > > > > ----- Original Message ----- > From: "Geng Tian" <gen...@ho... > > To: <pym...@li...> > Sent: Thursday, April 13, 2006 3:19 PM > Subject: [PyMOL] question about ca trace > > > > Hi, There: > > I have a pdb file for a dimer. only coordinates of alph carbons are >in the > > pdb. In the pymol, I > > set cartoon_trace, 1 > > and > > show cartoon > > each monomer is fine but a weird linkage showed up between the last > > residue of chain a and first residue of chain b. I just can't remove >this > > ugly linkage. Do you have any idea? Thank you. Actually I tried >ribbon > > mode and no this weird linkage but I like the figure qualify of the > > cartoon. > > Tiger > > > > _________________________________________________________________ > > Express yourself instantly with MSN Messenger! Download today - it's >FREE! > > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by xPML, a groundbreaking scripting > > language > > that extends applications into web and mobile media. Attend the live > > webcast > > and join the prime developer group breaking into this new coding > > territory! > > >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting >language > that extends applications into web and mobile media. Attend the live >webcast > and join the prime developer group breaking into this new coding >territory! > >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > -- > > Tsjerk A. Wassenaar, M.Sc. > Groningen Biomolecular Sciences and Biotechnology Institute (GBB) > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh 4 > 9747AG Groningen, The Netherlands > +31 50 363 4336 _________________________________________________________________ Dont just search. Find. Check out the new MSN Search! http://search.msn.click-url.com/go/onm00200636ave/direct/01/ |
From: Paulo M. <pm...@ua...> - 2006-04-15 01:40:51
|
Hello, one thing I find a little bit annoying: the "save" command in Pymol will accept any of <file>.<ext>, and if the <ext> is unknown, it will simple save a pdb file. While some people may find this a useful feature, I think it is quite dangerous. For instance, suppose I'm trying to save "work.pse" and mistakenly type "work.psf", without noticing it. If I close Pymol, I will end up with a pdb file called "work.psf", and all my session work goes down the drain. This is not an hypothetical situation, it happened a couple of times, to my great dismay. What do you think, Warren ?... Regards, Paulo |
From: L. D. <du...@ia...> - 2006-04-14 20:42:10
|
Hello, I need to have spheres or dots of different sizes on a RNA ribbon. We are trying to show that residues modify at a smaller or larger extent. So, I need to have at different places differently sized spheres. Hopefully I was explicetly enough. Thank you, Laura Laura Dutca |
From: Noinaj <no...@uk...> - 2006-04-14 15:24:08
|
Tsjerk, Nice point, and probably easier to just create new objects in Pymol. =20 nick ----- Original Message -----=20 From: Tsjerk Wassenaar=20 To: pym...@li...=20 Sent: Friday, April 14, 2006 4:29 AM Subject: Re: [PyMOL] question about ca trace Hi Tiger, Nick is largely right. The cause for the link to show up is that pymol = just traces through all c-alphas in the object, regardless of chains or = distances. So, selecting the linked residues and hiding the trace should = solve your problem. Also, creating two files will do the trick. = Alternatively, you can create two objects and draw the trace for each of = these. Cheers, Tsjerk On 4/13/06, Noinaj <no...@uk...> wrote: Tiger, I am no expert by far, but can you select the linkage? If so, just = select and hide. Also, you might try just hiding the two residues that are = linked, this might get rid of the link and you probably wouldn't notice the = missing=20 residues unless it is a small protein. alternatively, and probably = the best solution is to edit the pdb file to create two individual files, one = for each dimer (this can be done in any text editor). then open both in = Pymol=20 and you should then be able to edit independently. The problem may be, and again I remind you that I am no expert, that = these atoms are two close to each other and may be getting mistaken for a = covalent interaction, can't tell without actually seeing though.=20 Hope any or all of this helps. Good Luck! Cheers, Nick ----- Original Message ----- From: "Geng Tian" <gen...@ho... > To: <pym...@li...> Sent: Thursday, April 13, 2006 3:19 PM Subject: [PyMOL] question about ca trace > Hi, There:=20 > I have a pdb file for a dimer. only coordinates of alph carbons = are in the > pdb. In the pymol, I > set cartoon_trace, 1 > and > show cartoon > each monomer is fine but a weird linkage showed up between the = last=20 > residue of chain a and first residue of chain b. I just can't = remove this > ugly linkage. Do you have any idea? Thank you. Actually I tried = ribbon > mode and no this weird linkage but I like the figure qualify of = the=20 > cartoon. > Tiger > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today - = it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting = > language > that extends applications into web and mobile media. Attend the = live > webcast > and join the prime developer group breaking into this new coding > territory! > = http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D= 121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -------------------------------------------------------=20 This SF.Net email is sponsored by xPML, a groundbreaking scripting = language that extends applications into web and mobile media. Attend the live = webcast and join the prime developer group breaking into this new coding = territory!=20 = http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D= 121642 _______________________________________________=20 PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users=20 --=20 Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 |
From: Warren D. <wa...@de...> - 2006-04-14 15:10:24
|
FYI: all. =20 This is a bug that has been fixed in the source and will not occur with = future releases. Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Tsjerk Wassenaar > Sent: Friday, April 14, 2006 5:04 AM > To: pym...@li... > Subject: Re: [PyMOL] question about ca trace >=20 > Hi Tiger, >=20 > Nick is largely right. The cause for the link to show up is=20 > that pymol just traces through all c-alphas in the object,=20 > regardless of chains or distances. So, selecting the linked=20 > residues and hiding the trace should solve your problem.=20 > Also, creating two files will do the trick. Alternatively,=20 > you can create two objects and draw the trace for each of these. >=20 > Cheers, >=20 > Tsjerk >=20 >=20 > On 4/13/06, Noinaj <no...@uk...> wrote: >=20 > Tiger, > =09 > I am no expert by far, but can you select the linkage? =20 > If so, just select > and hide. Also, you might try just hiding the two=20 > residues that are linked, > this might get rid of the link and you probably=20 > wouldn't notice the missing=20 > residues unless it is a small protein. alternatively,=20 > and probably the best > solution is to edit the pdb file to create two=20 > individual files, one for > each dimer (this can be done in any text editor). then=20 > open both in Pymol=20 > and you should then be able to edit independently. > =09 > The problem may be, and again I remind you that I am no=20 > expert, that these > atoms are two close to each other and may be getting=20 > mistaken for a covalent > interaction, can't tell without actually seeing though.=20 > =09 > Hope any or all of this helps. Good Luck! > =09 > =09 > =09 > Cheers, > Nick > =09 > =09 > =09 > =09 > =09 > =09 > ----- Original Message ----- > From: "Geng Tian" <gen...@ho... > > To: <pym...@li...> > Sent: Thursday, April 13, 2006 3:19 PM > Subject: [PyMOL] question about ca trace > =09 > =09 > > Hi, There:=20 > > I have a pdb file for a dimer. only coordinates of=20 > alph carbons are in the > > pdb. In the pymol, I > > set cartoon_trace, 1 > > and > > show cartoon > > each monomer is fine but a weird linkage showed up=20 > between the last=20 > > residue of chain a and first residue of chain b. I=20 > just can't remove this > > ugly linkage. Do you have any idea? Thank you.=20 > Actually I tried ribbon > > mode and no this weird linkage but I like the figure=20 > qualify of the=20 > > cartoon. > > Tiger > > > >=20 > _________________________________________________________________ > > Express yourself instantly with MSN Messenger!=20 > Download today - it's FREE! > >=20 > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01 > / <http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/>=20 > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by xPML, a=20 > groundbreaking scripting=20 > > language > > that extends applications into web and mobile media.=20 > Attend the live > > webcast > > and join the prime developer group breaking into this=20 > new coding > > territory! > >=20 > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720& dat=3D121642 <http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944> = &bid=3D241720&dat=3D121642>=20 > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li...=20 > <mailto:PyM...@li...>=20 > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > =09 > =09 > =09 > -------------------------------------------------------=20 > This SF.Net email is sponsored by xPML, a=20 > groundbreaking scripting language > that extends applications into web and mobile media.=20 > Attend the live webcast > and join the prime developer group breaking into this=20 > new coding territory!=20 > =09 > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720& dat=3D121642 > _______________________________________________=20 > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users=20 > =09 >=20 >=20 >=20 >=20 > --=20 >=20 > Tsjerk A. Wassenaar, M.Sc. > Groningen Biomolecular Sciences and Biotechnology Institute=20 > (GBB) Dept. of Biophysical Chemistry University of Groningen=20 > Nijenborgh 4 9747AG Groningen, The Netherlands > +31 50 363 4336 >=20 >=20 |
From: Tsjerk W. <ts...@gm...> - 2006-04-14 08:29:42
|
Hi Tiger, Nick is largely right. The cause for the link to show up is that pymol just traces through all c-alphas in the object, regardless of chains or distances. So, selecting the linked residues and hiding the trace should solve your problem. Also, creating two files will do the trick. Alternatively, you can create two objects and draw the trace for each of these. Cheers, Tsjerk On 4/13/06, Noinaj <no...@uk...> wrote: > > Tiger, > > I am no expert by far, but can you select the linkage? If so, just selec= t > and hide. Also, you might try just hiding the two residues that are > linked, > this might get rid of the link and you probably wouldn't notice the > missing > residues unless it is a small protein. alternatively, and probably the > best > solution is to edit the pdb file to create two individual files, one for > each dimer (this can be done in any text editor). then open both in Pymo= l > and you should then be able to edit independently. > > The problem may be, and again I remind you that I am no expert, that thes= e > atoms are two close to each other and may be getting mistaken for a > covalent > interaction, can't tell without actually seeing though. > > Hope any or all of this helps. Good Luck! > > > > Cheers, > Nick > > > > > > > ----- Original Message ----- > From: "Geng Tian" <gen...@ho...> > To: <pym...@li...> > Sent: Thursday, April 13, 2006 3:19 PM > Subject: [PyMOL] question about ca trace > > > > Hi, There: > > I have a pdb file for a dimer. only coordinates of alph carbons are in > the > > pdb. In the pymol, I > > set cartoon_trace, 1 > > and > > show cartoon > > each monomer is fine but a weird linkage showed up between the last > > residue of chain a and first residue of chain b. I just can't remove > this > > ugly linkage. Do you have any idea? Thank you. Actually I tried ribbon > > mode and no this weird linkage but I like the figure qualify of the > > cartoon. > > Tiger > > > > _________________________________________________________________ > > Express yourself instantly with MSN Messenger! Download today - it's > FREE! > > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by xPML, a groundbreaking scripting > > language > > that extends applications into web and mobile media. Attend the live > > webcast > > and join the prime developer group breaking into this new coding > > territory! > > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat= =3D121642 > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting > language > that extends applications into web and mobile media. Attend the live > webcast > and join the prime developer group breaking into this new coding > territory! > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat= =3D121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 |
From: Noinaj <no...@uk...> - 2006-04-13 19:28:50
|
Tiger, I am no expert by far, but can you select the linkage? If so, just select and hide. Also, you might try just hiding the two residues that are linked, this might get rid of the link and you probably wouldn't notice the missing residues unless it is a small protein. alternatively, and probably the best solution is to edit the pdb file to create two individual files, one for each dimer (this can be done in any text editor). then open both in Pymol and you should then be able to edit independently. The problem may be, and again I remind you that I am no expert, that these atoms are two close to each other and may be getting mistaken for a covalent interaction, can't tell without actually seeing though. Hope any or all of this helps. Good Luck! Cheers, Nick ----- Original Message ----- From: "Geng Tian" <gen...@ho...> To: <pym...@li...> Sent: Thursday, April 13, 2006 3:19 PM Subject: [PyMOL] question about ca trace > Hi, There: > I have a pdb file for a dimer. only coordinates of alph carbons are in the > pdb. In the pymol, I > set cartoon_trace, 1 > and > show cartoon > each monomer is fine but a weird linkage showed up between the last > residue of chain a and first residue of chain b. I just can't remove this > ugly linkage. Do you have any idea? Thank you. Actually I tried ribbon > mode and no this weird linkage but I like the figure qualify of the > cartoon. > Tiger > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today - it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting > language > that extends applications into web and mobile media. Attend the live > webcast > and join the prime developer group breaking into this new coding > territory! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Geng T. <gen...@ho...> - 2006-04-13 19:19:59
|
Hi, There: I have a pdb file for a dimer. only coordinates of alph carbons are in the pdb. In the pymol, I set cartoon_trace, 1 and show cartoon each monomer is fine but a weird linkage showed up between the last residue of chain a and first residue of chain b. I just can't remove this ugly linkage. Do you have any idea? Thank you. Actually I tried ribbon mode and no this weird linkage but I like the figure qualify of the cartoon. Tiger _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ |
From: Noinaj <no...@uk...> - 2006-04-12 15:34:14
|
Chun, Here is another site to check out. It is Michael Lerner's site, the guy who brings us the APBS PyMol Plugin. He mentions some information about the plugin and also has contact info in case the website doesn't answer your question. http://www-personal.umich.edu/~mlerner/PyMOL/ At a quick glance, it seems to use AMBER force field. I know that the pdb2pqr server has several parameters for you to choose from, so you might check out the plugin and see how Michael sets those to run within PyMOL. You can check that using any text editor such as Notepad. Again, hope this helps. Cheers, Nick ----- Original Message ----- From: "Noinaj" <no...@uk...> To: "Chun Tang" <tcs...@gm...> Sent: Wednesday, April 12, 2006 10:45 AM Subject: Re: [PyMOL] pqr file > Chun, > > You might check out the web site below, it probably contains all > information that you might need and contact information for things not > explained online. > > http://apbs.sourceforge.net/ > > Hope this helps. > > > > Cheers, > Nick > > > > ----- Original Message ----- > From: "Chun Tang" <tcs...@gm...> > To: <pym...@li...> > Sent: Tuesday, April 11, 2006 6:39 PM > Subject: [PyMOL] pqr file > > > Hi there, > > When one uses the APBS plugin of pymol to generate a pqr file, how > dose it assign the partial charges to the atoms, what force field is > it based on? Thank you. > > Chun > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting > language > that extends applications into web and mobile media. Attend the live > webcast > and join the prime developer group breaking into this new coding > territory! > http://sel.as-us.falkag.net/sel?cmd=k&kid0944&bid$1720&dat1642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Chun T. <tcs...@gm...> - 2006-04-12 15:02:06
|
I probably didn't make myself clear in my last email. What I meant is that there is an option in pymol APBS tool that allows one to use pymol to generate pqr file from pdb file, instead of loading an pqr file generated externally. I noticed that the electrostatic potential looks quite different for the pqr file of the same structure generated on pdb2pqr server. My question is how does pymol assign partial charges? I can only find a file called apbs_tools.py under the directory of ./modules/pmg_tk/startup/ that remotely has some information. Chun On 4/11/06, Chun Tang <tcs...@gm...> wrote: > > Hi there, > > When one uses the APBS plugin of pymol to generate a pqr file, how > dose it assign the partial charges to the atoms, what force field is > it based on? Thank you. > > Chun > |
From: Praedor A. <pr...@ya...> - 2006-04-12 12:43:39
|
Yes, this binary works just fine. Thanks again. =20 I am still puzzled/unhappy that I cannot get the source to build on my AMD6= 4. =20 especially given that I've checked and rechecked to make sure the=20 dependencies are met. It isn't just pymol...if any source that SHOULD buil= d=20 fails to build I get unhappy, having to assume that there is something hidd= en=20 "wrong" with my system which limits my capabilities. praedor On Wednesday 12 April 2006 07:36 am, Andrea Spitaleri wrote: > Hi, > this should be a binary, so just installing it should work ... > try also to export the lib path (export or setenv LD_LIBRARY_PATH) > > Regards > > Andrea > > 2006/4/12, Praedor Atrebates <pr...@ya...>: > > Great! Thank you. I've just finished trying and failing to get pymol = to > > build again on my AMD64 Mandriva system. It invariably fails quickly > > with: > > > > layer0/Crystal.c:314:1: error: unterminated argument list invoking macro > > "sprintf" > > layer0/Crystal.c: In function 'CrystalDump': > > layer0/Crystal.c:201: error: syntax error at end of input > > layer0/Crystal.c:201: warning: unused variable '_FBstr' > > layer0/Crystal.c:199: warning: unused variable 'i' > > layer0/Crystal.c:198: warning: unused variable 'G' > > error: command 'gcc' failed with exit status 1 > > > > There must be a lib difference or gcc difference between the Mandriva > > 2006 system and SuSE that apparently allows a 64 bit build to proceed. > > > > praedor > > > > On Wednesday 12 April 2006 04:18 am, Andrea Spitaleri wrote: > > > Hi, > > > few weeks ago I had a problem with pymol-32bit on my laptop 64bit usi= ng > > > slamd Warren built a pymol for 64bit and you can download it from her= e: > > > http://delsci.com/beta/ > > > > > > In my case it worked. > > > Regards > > > > > > andrea > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by xPML, a groundbreaking scripting > > language that extends applications into web and mobile media. Attend the > > live webcast and join the prime developer group breaking into this new > > coding territory! > > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat= =3D121642 > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- > "La conoscenza libera il genere umano dalla superstizione" > J. Watson > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting langua= ge > that extends applications into web and mobile media. Attend the live > webcast and join the prime developer group breaking into this new coding > territory! > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=110944&bid$1720&dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users =2D-=20 The Reichstag fire is to Hitler as 9/11 is to Bush |
From: Andrea S. <and...@gm...> - 2006-04-12 11:36:32
|
Hi, this should be a binary, so just installing it should work ... try also to export the lib path (export or setenv LD_LIBRARY_PATH) Regards Andrea 2006/4/12, Praedor Atrebates <pr...@ya...>: > Great! Thank you. I've just finished trying and failing to get pymol to > build again on my AMD64 Mandriva system. It invariably fails quickly wit= h: > > layer0/Crystal.c:314:1: error: unterminated argument list invoking macro > "sprintf" > layer0/Crystal.c: In function 'CrystalDump': > layer0/Crystal.c:201: error: syntax error at end of input > layer0/Crystal.c:201: warning: unused variable '_FBstr' > layer0/Crystal.c:199: warning: unused variable 'i' > layer0/Crystal.c:198: warning: unused variable 'G' > error: command 'gcc' failed with exit status 1 > > There must be a lib difference or gcc difference between the Mandriva 200= 6 > system and SuSE that apparently allows a 64 bit build to proceed. > > praedor > > On Wednesday 12 April 2006 04:18 am, Andrea Spitaleri wrote: > > Hi, > > few weeks ago I had a problem with pymol-32bit on my laptop 64bit using > > slamd Warren built a pymol for 64bit and you can download it from here: > > http://delsci.com/beta/ > > > > In my case it worked. > > Regards > > > > andrea > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting langua= ge > that extends applications into web and mobile media. Attend the live webc= ast > and join the prime developer group breaking into this new coding territor= y! > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat= =3D121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- "La conoscenza libera il genere umano dalla superstizione" J. Watson |
From: Praedor A. <pr...@ya...> - 2006-04-12 10:23:05
|
Great! Thank you. I've just finished trying and failing to get pymol to build again on my AMD64 Mandriva system. It invariably fails quickly with: layer0/Crystal.c:314:1: error: unterminated argument list invoking macro "sprintf" layer0/Crystal.c: In function 'CrystalDump': layer0/Crystal.c:201: error: syntax error at end of input layer0/Crystal.c:201: warning: unused variable '_FBstr' layer0/Crystal.c:199: warning: unused variable 'i' layer0/Crystal.c:198: warning: unused variable 'G' error: command 'gcc' failed with exit status 1 There must be a lib difference or gcc difference between the Mandriva 2006 system and SuSE that apparently allows a 64 bit build to proceed. praedor On Wednesday 12 April 2006 04:18 am, Andrea Spitaleri wrote: > Hi, > few weeks ago I had a problem with pymol-32bit on my laptop 64bit using > slamd Warren built a pymol for 64bit and you can download it from here: > http://delsci.com/beta/ > > In my case it worked. > Regards > > andrea |
From: Andrea S. <and...@gm...> - 2006-04-12 08:18:09
|
Hi, few weeks ago I had a problem with pymol-32bit on my laptop 64bit using sla= md Warren built a pymol for 64bit and you can download it from here: http://delsci.com/beta/ In my case it worked. Regards andrea 2006/4/11, Florian Haberl <Flo...@ch...>: > hi, > > On Tuesday 11 April 2006 19:59, Praedor Atrebates wrote: > > Is anyone running pymol on an AMD64 system? If so, did you find a preb= uilt > > binary or did you build it yourself? If you built it yourself...HOW DI= D > > YOU DO IT? I'd greatly appreciate help in this regard. > > also the normal 32 bit standalone executebale works for me on em64t cpu. = You > can find it at > > http://delsci.com/rel/099/ > > don`t know if a special 64bit version is necessary if 32 bit version is > running without problems. > Os is Suse 10 for x86_64. > > > > > > Thank you, > > > > praedor > > Greetings, > > Florian > > -- > -------------------------------------------------------------------------= ------ > Florian Haberl > Computer-Chemie-Centrum > Universitaet Erlangen/ Nuernberg > Naegelsbachstr 25 > D-91052 Erlangen > Mailto: florian.haberl AT chemie.uni-erlangen.de > -------------------------------------------------------------------------= ------ > > > -- "La conoscenza libera il genere umano dalla superstizione" J. Watson |
From: Jason V. <jav...@ut...> - 2006-04-12 00:47:26
|
I use PyMol from CVS/SVN -- thus from source. I build and install them by= =20 hand (which is 3 easy commands). Details on the wiki=20 (http://www.pymolwiki.org/index.php/Linux_Install#64-bit_.28x86_64.29). I have two AMD64 machines, both SMP -- PyMol works great on both. =2D- Jason On Tuesday 11 April 2006 13:31, pym...@li...=20 wrote: > Is anyone running pymol on an AMD64 system? =C2=A0If so, did you find a > prebuilt=3D =3D20 > binary or did you build it yourself? =C2=A0If you built it yourself...HOW= DID > YO=3D U=3D20 > DO IT? =C2=A0I'd greatly appreciate help in this regard. > > Thank you, > > praedor =2D-=20 Jason Vertrees BSCB Graduate Student @ UTMB, Galveston jav...@ut... :: http://www.bscb.utmb.edu PyMol Wiki :: http://www.pymolwiki.org Vertrees dot Org :: http://www.vertrees.org |
From: Chun T. <tcs...@gm...> - 2006-04-11 22:39:51
|
Hi there, When one uses the APBS plugin of pymol to generate a pqr file, how dose it assign the partial charges to the atoms, what force field is it based on? Thank you. Chun |
From: Florian H. <Flo...@ch...> - 2006-04-11 19:03:35
|
hi, On Tuesday 11 April 2006 19:59, Praedor Atrebates wrote: > Is anyone running pymol on an AMD64 system? If so, did you find a prebui= lt > binary or did you build it yourself? If you built it yourself...HOW DID > YOU DO IT? I'd greatly appreciate help in this regard. also the normal 32 bit standalone executebale works for me on em64t cpu. Yo= u=20 can find it at http://delsci.com/rel/099/ don`t know if a special 64bit version is necessary if 32 bit version is=20 running without problems. Os is Suse 10 for x86_64. > > Thank you, > > praedor Greetings, =46lorian =2D-=20 =2D------------------------------------------------------------------------= =2D----- Florian Haberl =20 Computer-Chemie-Centrum =20 Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de =2D------------------------------------------------------------------------= =2D----- |
From: Sabuj P. <sab...@va...> - 2006-04-11 18:30:16
|
I use gentoo linux's portage to do all the compile work (emerge pymol). From the ebuild it looks like you need these prerequisites: python, pmw (python library), numeric (python library), tk, libpng, zlib, and glut . Praedor Atrebates wrote: > Is anyone running pymol on an AMD64 system? If so, did you find a prebuilt > binary or did you build it yourself? If you built it yourself...HOW DID YOU > DO IT? I'd greatly appreciate help in this regard. > > Thank you, > > praedor |
From: Praedor A. <pr...@ya...> - 2006-04-11 17:59:56
|
Is anyone running pymol on an AMD64 system? If so, did you find a prebuilt= =20 binary or did you build it yourself? If you built it yourself...HOW DID YO= U=20 DO IT? I'd greatly appreciate help in this regard. Thank you, praedor =2D-=20 The Reichstag fire is to Hitler as 9/11 is to Bush |
From: Noinaj <no...@uk...> - 2006-04-11 17:35:10
|
My dear PyFriends, OKay, I was able to successfully get Pymol up and running on Sony Vaio, = thanks to my new friend Chris Yip! Thanks a million! Hip-Hip Hurray! The cure you ask? Well, as Chris mentioned in his suggestions, I simply = went to the Sony website and downloaded the update driver for the = graphics controller. The funny thing was that, it wasn't nVidia, it was = ATI. So apparently, this driver issue may not be primarily an nVidia = issue. But after I installed updated driver and restarted, Pymol ran = beautifully. Now, I assume we may still run across some bugs in the = future, but for today, we feast on victory! Thanks again Chris and I hope this helps someone else in the future! =20 Cheers, Nick Couple of things that people tried - one was to go to an older PyMol = version (and the corollary - go to the latest beta version). we did try some drivers from the various vendors but that was also hit = and miss... There didn't seem to be a consistent fix Chris On Apr 10, 2006, at 4:47 PM, Noinaj wrote: Thanks Chris for your help. As you have noted and as I have read = online, there seems to be a problem with the graphics drivers, is this = correct? Do you know if updating the drivers remedied the problem? If = not, were you able to work around the problem? Thanks again for your = help! Cheers, Nick ----- Original Message ----- From: Christopher Yip To: Noinaj Sent: Monday, April 10, 2006 4:31 PM Subject: Re: [PyMOL] PymOl INstallation PRoblems A lot of my students ran into the same problem this past fall - = there are a bunch of notes on the list regarding nVidia graphics drivers = that seem to be at the root cause of the problem - you might want to try = a search under WinXP and Pymol... =20 http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4368.html=20 here are some of the links that I found were of use, and posted to = my class list Check here for some info and suggestions: http://delsci.com/beta/ Specifically.. Take a look here: http://sourceforge.net/mailarchive/message.php?msg_id=3D11962703 ++++++ If anyone else is experiencing a non-functional PyMOL with = late-model nVidia drivers on Windows XP or similar, pymol-0_99beta96 contains a = workaround that has been reported to eliminate the problem. http://delsci.com/beta Hopefully the next driver release for Windows will fix this problem = just like it did on Linux... +++++ Some may find this useful too - a Wiki with hints: http://www.pymolwiki.org/index.php/Main_Page http://pymol.sourceforge.net/faq.html http://www.rubor.de/bioinf/pymol_tips.html On Apr 10, 2006, at 4:23 PM, Noinaj wrote: Hi PyWorld, I have been trying to help a friend install PyMol on her laptop = (Sony Vaio) that has Windows XP Home Edition. The installation runs = smooth with no problem at all. But once we try to open the program, its = seems to stall, then crashes, and Windows XP asks if we would like to = send a error report??? I have searched the archives and online for answers, but with no = luck. Therefore, I present to you, my PyFriends, our dilemma and seek a = remedy to our problem. I give you my word, my good friends, that upon = finding the solution, I will not take all the credit for solving this = mystery....just kidding, credit will be duly noted. Thanks in advance for any and all help! Cheers, Nick Christopher M. Yip, Ph.D., P.Eng. Associate Professor - Canada Research Chair in Molecular Imaging Department of Chemical Engineering and Applied Chemistry Department of Biochemistry Institute of Biomaterials and Biomedical Engineering The Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Room 404 160 College St. Toronto, ON, CANADA M5S 3E1 (416) 978-7853 (416) 978-4317 (fax) chr...@ut... http://bigten.med.utoronto.ca Christopher M. Yip, Ph.D., P.Eng. Associate Professor - Canada Research Chair in Molecular Imaging Department of Chemical Engineering and Applied Chemistry Department of Biochemistry Institute of Biomaterials and Biomedical Engineering The Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Room 404 160 College St. Toronto, ON, CANADA M5S 3E1 (416) 978-7853 (416) 978-4317 (fax) chr...@ut... http://bigten.med.utoronto.ca |
From: Peter A. M. <pa...@co...> - 2006-04-11 15:46:49
|
Hi Nick, This sounds vaguely similar to the msvcr71.dll issues that were recently discussed on the list (searching the list archives will give you more info on this, but the quick fix is to search the hd for msvcr71.dll and copy it to the pymol install directory). If that doesn't resolve the problem, then some more details might be useful. Which version of pymol are you running (I'm assuming one of the recent win32 binary distributions)? Are there any error messages, and if so what do they say? Are you starting-up pymol by clicking the start menu icon (if so, try opening a dos window, going to the pymol directory, and starting from the dos prompt...this probably won't fix the problem, but will probably give more detailed error messages)? The quickest resolution (assuming msvcr71.dll isn't the problem) might be to install a slightly older version. Hope this helps, Pete > Hi PyWorld, > > > I have been trying to help a friend install PyMol on her laptop (Sony Vaio) that has Windows XP Home Edition. The installation runs smooth with > no problem at all. But once we try to open the program, its seems to stall, then crashes, and Windows XP asks if we would like to send a error > report??? > > I have searched the archives and online for answers, but with no luck. Therefore, I present to you, my PyFriends, our dilemma and seek a remedy to our problem. I give you my word, my good friends, that upon finding the solution, I will not take all the credit for solving this > mystery....just kidding, credit will be duly noted. > > Thanks in advance for any and all help! > > > Cheers, > Nick > > > Pete Meyer Fu Lab BMCB grad student Cornell University |
From: Noinaj <no...@uk...> - 2006-04-10 20:23:34
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Hi PyWorld, I have been trying to help a friend install PyMol on her laptop (Sony = Vaio) that has Windows XP Home Edition. The installation runs smooth = with no problem at all. But once we try to open the program, its seems = to stall, then crashes, and Windows XP asks if we would like to send a = error report??? I have searched the archives and online for answers, but with no luck. = Therefore, I present to you, my PyFriends, our dilemma and seek a remedy = to our problem. I give you my word, my good friends, that upon finding = the solution, I will not take all the credit for solving this = mystery....just kidding, credit will be duly noted. Thanks in advance for any and all help! Cheers, Nick |