From: Daniel R. <dr...@li...> - 2008-10-09 10:22:37
Attachments:
incomplete_cartoon.png
|
Dear all I've just extracted a region of B sheet from a structure to produce a session for teaching purposes. To my surprise, when I created an object from the four distinct stretches making up the sheet, PyMOL redrew the previously complete strands in a very incomplete way (attached). When I colour by secondary structure I can see that they are all defined as 'beta'. Why will cartoon not draw complete arrows for me? I looked for settings that might be relevant but couldn't see any. I'm on 0.99rc6, if that makes any difference. Thanks in advance for your help Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. |
From: DeLano S. <de...@de...> - 2008-10-09 16:06:57
|
Daniel, This is just a guess, but I suspect that there is a problem with identifiers and/or residue ordering in the structure which may be confusing PyMOL. A command like label name ca, segi+"-"+chain+"-"+resi may help reveal what is going on. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:su...@de... -----Original Message----- From: Daniel Rigden [mailto:dr...@li...] Sent: Thursday, October 09, 2008 3:20 AM To: pym...@li... Subject: [PyMOL] incompletely drawn cartoon strands Dear all I've just extracted a region of B sheet from a structure to produce a session for teaching purposes. To my surprise, when I created an object from the four distinct stretches making up the sheet, PyMOL redrew the previously complete strands in a very incomplete way (attached). When I colour by secondary structure I can see that they are all defined as 'beta'. Why will cartoon not draw complete arrows for me? I looked for settings that might be relevant but couldn't see any. I'm on 0.99rc6, if that makes any difference. Thanks in advance for your help Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. |
From: Daniel R. <dr...@li...> - 2008-10-10 08:30:19
|
Dear all Thanks for the replies. After a few minutes testing it seems that the problem is only caused when I create an object which, unintentionally (carelessly), selects from across different molecules. If load 1jqd through PDB loader then do create parallel, resid 111-116 or resid 82-88 or resid 53-59 or resid 136-142 no problem. However, if I make duplicate objects then issue the same create command I see incomplete strands. The artifacts are worse if there are two duplicates than if there is one. So, I don't know why this should PyMOL a problem, but the lesson seems to be to take more care with object creation. Incidentally, I could also get round the problem by saving the object 'parallel' and reloading it, but this workaround seems unnecessary. Cheers Daniel On Thu, 2008-10-09 at 08:21 -0700, DeLano Scientific wrote: > Daniel, > > This is just a guess, but I suspect that there is a problem with identifiers and/or residue ordering in the structure which may be confusing PyMOL. A command like > > label name ca, segi+"-"+chain+"-"+resi > > may help reveal what is going on. > > Cheers, > Warren > > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:su...@de... > > > -----Original Message----- > From: Daniel Rigden [mailto:dr...@li...] > Sent: Thursday, October 09, 2008 3:20 AM > To: pym...@li... > Subject: [PyMOL] incompletely drawn cartoon strands > > Dear all > > I've just extracted a region of B sheet from a structure to produce a session for teaching purposes. To my surprise, when I created an object from the four distinct stretches making up the sheet, PyMOL redrew the previously complete strands in a very incomplete way (attached). When I colour by secondary structure I can see that they are all defined as 'beta'. Why will cartoon not draw complete arrows for me? I looked for settings that might be relevant but couldn't see any. I'm on 0.99rc6, if that makes any difference. > > Thanks in advance for your help > > Daniel > -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. |
From: H. A. S. <ad...@st...> - 2009-01-06 19:25:05
|
I just had the same problem, it seems to happen when parts of the cartoon from one of the objects overlaps with similar parts of a cartoon from the second object. Daniel Rigden wrote: > Dear all > > Thanks for the replies. After a few minutes testing it seems that the > problem is only caused when I create an object which, unintentionally > (carelessly), selects from across different molecules. If load 1jqd > through PDB loader then do > > create parallel, resid 111-116 or resid 82-88 or resid 53-59 or resid > 136-142 > > no problem. > > However, if I make duplicate objects then issue the same create command > I see incomplete strands. The artifacts are worse if there are two > duplicates than if there is one. > > So, I don't know why this should PyMOL a problem, but the lesson seems > to be to take more care with object creation. Incidentally, I could > also get round the problem by saving the object 'parallel' and reloading > it, but this workaround seems unnecessary. > > Cheers > > Daniel > > On Thu, 2008-10-09 at 08:21 -0700, DeLano Scientific wrote: > >> Daniel, >> >> This is just a guess, but I suspect that there is a problem with identifiers and/or residue ordering in the structure which may be confusing PyMOL. A command like >> >> label name ca, segi+"-"+chain+"-"+resi >> >> may help reveal what is going on. >> >> Cheers, >> Warren >> >> -- >> DeLano Scientific LLC >> Subscriber Support Services >> mailto:su...@de... >> >> >> -----Original Message----- >> From: Daniel Rigden [mailto:dr...@li...] >> Sent: Thursday, October 09, 2008 3:20 AM >> To: pym...@li... >> Subject: [PyMOL] incompletely drawn cartoon strands >> >> Dear all >> >> I've just extracted a region of B sheet from a structure to produce a session for teaching purposes. To my surprise, when I created an object from the four distinct stretches making up the sheet, PyMOL redrew the previously complete strands in a very incomplete way (attached). When I colour by secondary structure I can see that they are all defined as 'beta'. Why will cartoon not draw complete arrows for me? I looked for settings that might be relevant but couldn't see any. I'm on 0.99rc6, if that makes any difference. >> >> Thanks in advance for your help >> >> Daniel >> >> -- _______________________________________ H. Adam Steinberg Artist, Scientist <http://adam.steinbergs.us> Information Technology and Media Center Department of Biochemistry University of Wisconsin-Madison 433 Babcock Drive Madison, WI 53706 608/265-4982 _______________________________________ |