Re: [PyMOL] pymol in the background
Thanks to all, redirecting didn't work but it seems fine now after restarting kde. Don't know what's different though. On 20/09/2007, DeLano Scientific wrote: > > Try redirecting stderr and stdout to a file -- the process may be getting > suspended by the shell due to output. > > csh/tcsh: > > pymol -qc script.pml >& pymol.log > > sh/bash: > > pymol -qc script.pml > pymol.log 2>&1 > > > > -- > *From:* pymol-users-boun...@lists.sourceforge.net [mailto: > pymol-users-boun...@lists.sourceforge.net] *On Behalf Of *Gordon Wells > *Sent:* Thursday, September 20, 2007 10:11 AM > *To:* pymol-users@lists.sourceforge.net > *Subject:* [PyMOL] pymol in the background > > Hi > > I seem to be having trouble running pymol (v1.0, gentoo) in the background > from a terminal, neither appending "&" nor "ctrl+z" followed "bg" is doing > the trick. In both cases pymol freezes during certain operations, eg opening > pdbs, drawing cartoon. The window controls themselves respond. Don't want to > have to change directory in pymol all the time. Any ideas? > > > -- > I think perhaps the most important problem is that we are trying to > understand the fundamental workings of the universe via a language devised > for telling one another when the best fruit is. > > -- Terry Pratchett, alt.fan.pratchett > -- > > Gordon Wells > Bioinformatics and Computational Biology Unit > Department of Biochemistry > University of Pretoria > > -- I think perhaps the most important problem is that we are trying to understand the fundamental workings of the universe via a language devised for telling one another when the best fruit is. -- Terry Pratchett, alt.fan.pratchett -- Gordon Wells Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria
[PyMOL] Pymol apbs problem
With a certain file 1za1 from pdb when I try to run apbs I get the errors below. Other files are OK. Any suggestions? error: 1 ValueError Exception in Tk callback Function: at 0x182892b0> (type: ) Args: () Traceback (innermost last): File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/ Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/ Pmw_1_2/lib/PmwDialog.py", line 153, in command=lambda self=self, name=name: self._doCommand(name)) File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/ Pmw_1_2/lib/PmwDialog.py", line 132, in _doCommand return command(name) File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/ pmg_tk/startup/apbs_tools.py", line , in execute self.runPsize() File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/ pmg_tk/startup/apbs_tools.py", line 1155, in runPsize size.runPsize(pdb_filename) File "/sw/share/xtal/bin/psize.py", line 267, in runPsize self.parseInput(filename) File "/sw/share/xtal/bin/psize.py", line 102, in parseInput self.parseLines(file.readlines()) File "/sw/share/xtal/bin/psize.py", line 116, in parseLines self.q = self.q + float(words[3]) ValueError: invalid literal for float(): 1.00101.59 --- Evan R. Kantrowitz, Ph.D evan.kantrow...@bc.edu Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/ ~kantrow Chestnut Hill, MA 02467 ---
Re: [PyMOL] Pymol apbs problem
Evan, This appears to be a problem with file format incompatibility between PyMOL and the psize.py script. I suspect that rounding off the atom coordinates will eliminate it: alter_state 1, all, (x,y,z)=(int(x*1000)/1000.0, int(y*1000)/1000.0, int(z*1000)/1000.0) Cheers, Warren _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Evan Kantrowitz Sent: Friday, September 21, 2007 7:28 AM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] Pymol apbs problem With a certain file 1za1 from pdb when I try to run apbs I get the errors below. Other files are OK. Any suggestions? error: 1 ValueError Exception in Tk callback Function: at 0x182892b0> (type: ) Args: () Traceback (innermost last): File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw Base.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw Dialog.py", line 153, in command=lambda self=self, name=name: self._doCommand(name)) File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw Dialog.py", line 132, in _doCommand return command(name) File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs _tools.py", line , in execute self.runPsize() File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs _tools.py", line 1155, in runPsize size.runPsize(pdb_filename) File "/sw/share/xtal/bin/psize.py", line 267, in runPsize self.parseInput(filename) File "/sw/share/xtal/bin/psize.py", line 102, in parseInput self.parseLines(file.readlines()) File "/sw/share/xtal/bin/psize.py", line 116, in parseLines self.q = self.q + float(words[3]) ValueError: invalid literal for float(): 1.00101.59 --- Evan R. Kantrowitz, Ph.D evan.kantrow...@bc.edu Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow Chestnut Hill, MA 02467 ---
Re: [PyMOL] Per residue rms
Per, No, looking through the code, there doesn't seem to be anything like this available yet, other than 3D visualization of the alignment (lines drawn between atom centers). What you are presumably looking for is the length of those lines. hmm... Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Per Larsson > Sent: Wednesday, September 19, 2007 8:56 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Per residue rms > > Dear people > > Is there somewhere in pymol an option that will allow me to > see the per-residue rms-values when doing a structural > alignment with align? > > Regards > /Per Larsson > > -- > --- > This SF.net email is sponsored by: Microsoft Defy all > challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Mutagenesis wizard
> However, step 6. (apply) results in this: > > Selector-Error: invalid model "and". > ( ( Model and _mutate_sel ) )<-- > > Anyone with any ideas? Unfortunately, "model" is a PyMOL selection language keyword. Everyone, please avoid naming your models "model", if possible -- that will save you some confusion. > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Mitchell J Stanton-Cook > Sent: Thursday, September 20, 2007 9:04 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Mutagenesis wizard > > Hi, > > To perform the mutations I have followed the steps as per: > http://www.pymolwiki.org/index.php/Mutagenesis > > > However, step 6. (apply) results in this: > > Selector-Error: invalid model "and". > ( ( Model and _mutate_sel ) )<-- > > Anyone with any ideas? > > Cheers > > Mitch > > -- > Mitchell Jon Stanton-Cook > PhD Student > Biomolecular modelling group > University of Queensland > > m.stantonc...@uq.edu.au > http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Mitchel > l_Stanton-Cook > > > -- > --- > This SF.net email is sponsored by: Microsoft Defy all > challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Pymol apbs problem
Hi Evan: I ran pdb2pqr by hand and I think the Zn and CTP is problematic: REMARK 5 WARNING: PDB2PQR was unable to assign charges REMARK 5 to the following atoms (omitted below): REMARK 5 7220 ZN in ZN 154 REMARK 5 7221 ZN in ZN 154 REMARK 5 7222 N1 in CTP 901 REMARK 5 7223 C2 in CTP 901 REMARK 5 7224 N3 in CTP 901 REMARK 5 7225 C4 in CTP 901 REMARK 5 7226 C5 in CTP 901 REMARK 5 7227 C6 in CTP 901 REMARK 5 7228 O2 in CTP 901 REMARK 5 7229 N4 in CTP 901 REMARK 5 7230 C1' in CTP 901 REMARK 5 7231 C2' in CTP 901 REMARK 5 7232 O2' in CTP 901 REMARK 5 7233 C3' in CTP 901 REMARK 5 7234 C4' in CTP 901 REMARK 5 7235 O4' in CTP 901 REMARK 5 7236 O3' in CTP 901 REMARK 5 7237 C5' in CTP 901 REMARK 5 7238 O5' in CTP 901 REMARK 5 7239 PA in CTP 901 REMARK 5 7240 O1A in CTP 901 REMARK 5 7241 O2A in CTP 901 REMARK 5 7242 O3A in CTP 901 REMARK 5 7243 PB in CTP 901 REMARK 5 7244 O1B in CTP 901 REMARK 5 7245 O2B in CTP 901 REMARK 5 7246 O3B in CTP 901 REMARK 5 7247 PG in CTP 901 REMARK 5 7248 O1G in CTP 901 REMARK 5 7249 O2G in CTP 901 REMARK 5 7250 O3G in CTP 901 REMARK 5 7251 N1 in CTP 902 REMARK 5 7252 C2 in CTP 902 REMARK 5 7253 N3 in CTP 902 REMARK 5 7254 C4 in CTP 902 REMARK 5 7255 C5 in CTP 902 REMARK 5 7256 C6 in CTP 902 REMARK 5 7257 O2 in CTP 902 REMARK 5 7258 N4 in CTP 902 REMARK 5 7259 C1' in CTP 902 REMARK 5 7260 C2' in CTP 902 REMARK 5 7261 O2' in CTP 902 REMARK 5 7262 C3' in CTP 902 REMARK 5 7263 C4' in CTP 902 REMARK 5 7264 O4' in CTP 902 REMARK 5 7265 O3' in CTP 902 REMARK 5 7266 C5' in CTP 902 REMARK 5 7267 O5' in CTP 902 REMARK 5 7268 PA in CTP 902 REMARK 5 7269 O1A in CTP 902 REMARK 5 7270 O2A in CTP 902 REMARK 5 7271 O3A in CTP 902 REMARK 5 7272 PB in CTP 902 REMARK 5 7273 O1B in CTP 902 REMARK 5 7274 O2B in CTP 902 REMARK 5 7275 O3B in CTP 902 REMARK 5 7276 PG in CTP 902 REMARK 5 7277 O1G in CTP 902 REMARK 5 7278 O2G in CTP 902 REMARK 5 7279 O3G in CTP 902 REMARK 5 REMARK 6 Total charge on this protein: -10. e REMARK 6 Bill On Fri, 21 Sep 2007 08:46:43 -0700 "DeLano Scientific" wrote: Evan, This appears to be a problem with file format incompatibility between PyMOL and the psize.py script. I suspect that rounding off the atom coordinates will eliminate it: alter_state 1, all, (x,y,z)=(int(x*1000)/1000.0, int(y*1000)/1000.0, int(z*1000)/1000.0) Cheers, Warren _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Evan Kantrowitz Sent: Friday, September 21, 2007 7:28 AM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] Pymol apbs problem With a certain file 1za1 from pdb when I try to run apbs I get the errors below. Other files are OK. Any suggestions? error: 1 ValueError Exception in Tk callback Function: at 0x182892b0> (type: ) Args: () Traceback (innermost last): File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw Base.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw Dialog.py", line 153, in command=lambda self=self, name=name: self._doCommand(name)) File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw Dialog.py", line 132, in _doCommand return command(name) File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs _tools.py", line , in execute self.runPsize() File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs _tools.py", line 1155, in runPsize size.runPsize(pdb_filename) File "/sw/share/xtal/bin/psize.py", line 267, in runPsize self.parseInput(filename) File "/sw/share/xtal/bin/psize.py", line 102, in parseInput self.parseLines(file.readlines()) File "/sw/share/xtal/bin/psize.py", line 116, in parseLines self.q = self.
