Re: [PyMOL] error in loading pdb file
Hi Dong, My guess is (but ofcourse Warren knows best) that pymol chokes in the full pathname, including the spaces. Note that under windows the actual pathname would be D:\DOCUME~1\1LTL.pdb The long pathname is an alias. Cheers, Tsjerk On 6/29/06, LIU Changdong wrote: Dear all: After I install pymol successfully,I load a pdb file,but the progroam give me a error message below.Can you give me any suggestions?My operate system is windows xp sp2. excecutiveprocessPDBfile-error:unableto open file'D:/Documents and settings/1LTL.pdb Function:>(type: < type `instancemethod~>) Arg: ()Traceback£¨inner most last): File"D\Program files\Delano scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line 1747,in _call_ return apply (self.func,args) File"D\Program files\Delano scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line438, in file_open self.cmd.load£¨ofile,quiet=0) File"D\Program files\Delano scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line585,in load if_raising(r):raise pymol.cmdexpception cmdexception:http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net 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
Re: [PyMOL] spheres representation and atomic / ionic radii
Hi Michael, The answer to the second question is: yes alter selection,vdw=1.0 will change the radius of selected atoms to 1.0 angstrom. Cheers, Tsjerk On 6/30/06, Michael Weber wrote: Hi, I have a question concerning the "spheres" representation. According to my rough estimation the spheres drawn for individual atoms/ions don't seem not match experimental atomic/ionic radii if I compare different elements. Is that correct (I quickly checked for oxygen, phosphorus and magnesium2+)? Furthermore, is it possible to manually assign radii to selected atoms? Best regards, Michael. Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net 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
Re: [PyMOL] PyMol question?
Hi Mark: Most likely there is, but I don't know the answer to your question. I'm posting this to the pymol users list (via cc) so hopefully someone else will know the answer. I trust all is going well for you. Bill On Jun 30, 2006, at 8:19 AM, Mark Collins wrote: Hi Bill, I've been looking through the PyMol reference and wiki page and I can't find a command for moving a molecule through a matrix, I would like to move one pdb onto the other using the info below. Is there such a command? ## MATRICES: UX+T is the least-squares superimposition of STRID2 (X) onto STRID1 NR. STRID1 STRID2 U(.,1)U(.,2)U(., 3) T(.) 1: 9506-A 1risU(1,.) -0.230692 -0.010007 -0.972975 50.701385 1: 9506-A 1risU(2,.) 0.443459 0.888979 -0.114287 31.716473 1: 9506-A 1risU(3,.) 0.866098 -0.457839 -0.200643 26.479412 Thanks Mark
Re: [PyMOL] PyMol question?
The easiest way I'm aware of to do this would be to use the ccp4 program pdbset, but there are numerous other ways/programs that will do this (if pymol has this capacity, I'm not aware of it; but someone else will correct me). Pete >> I've been looking through the PyMol reference and wiki page and I can't find a command for moving a molecule through a matrix, I >> would like to move one pdb onto the other using the info below. Is there such a command? >> ## MATRICES: UX+T is the least-squares superimposition of STRID2 (X) onto STRID1 >> NR. STRID1 STRID2 U(.,1)U(.,2)U(., >> 3) T(.) >>1: 9506-A 1risU(1,.) -0.230692 -0.010007 >> -0.972975 50.701385 >>1: 9506-A 1risU(2,.) 0.443459 0.888979 >> -0.114287 31.716473 >>1: 9506-A 1risU(3,.) 0.866098 -0.457839 >> -0.200643 26.479412 Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] Geowall and Mac with Quadro FX 4500
Hi All, We've acquired a geowall system which will likely be attached to a intel Mac tower. Does anyone know if the OS X drivers for the quadro fx 4500 will support the dual monitor clone mode necessary to drive quadbuffered stereo on the geowall? Anyone actually done this? Everything I've found on geowall and pymol has been linux, and I want to try and find out if apple has built in the appropriate support before we drop the cash on the quadro. Thanks! ---Stephen
[PyMOL] Manual updates?
Hi, This is really for Warren. A while ago there was discussion of the ± of updates versus new manuals. The current documentation is now several years out of date. Are their plans to update this? Thanks to all who have worked on Wiki and posted scripts on web sites. Mark --
