Re: [PyMOL] Odd issue with control and shift keys in pymol
Hi Paul and Adam, I can confirm this. The problem comes with two patches that Fedora applies to freeglut (freeglut_xinput.c). I don't know why they do this, but if I compile freeglut without those, PyMOL works fine. Paul, that 1.4.1 version of PyMOL and also Coot, are those linked to the system glut library (/usr/lib64/libglut.so.3.9.0 on my Fedora 18) or is there any other glut installation? Incentive builds of PyMOL 1.6 ship with a working glut library. It's only used as a fallback if there is no system glut (determined by setup.sh). So if you are on Fedora 18, just move "pymol/ext/libextra/libglut.so.3" to "pymol/ext/lib/" to give it priority over the broken system glut. Cheers, Thomas Adam Middleton wrote, On 06/26/13 12:14: > Hi Paul, > > I have the same problem. I am using Fedora 18 and PyMOL v.1.5 (from > the repository). > > It is annoying. Right now I have to use another computer if I want to > use the more 'advanced' functions of PyMOL. > > I found one other person with the same problem who posted to the > Fedora forum, and got no response: > http://www.forum.fedoraforum.org/showthread.php?t=287005 > > No explanations here. > > Adam > > On Wed, Jun 26, 2013 at 3:08 AM, Paul Paukstelis wrote: >> I've found that all recent versions (1.5, 1.6, non-incentive) of Pymol >> on my laptop running updated Fedora 18 (nvidia drivers) don't allow me >> to use the control or shift keys for selection or editing in the gui. I >> dug out an older version (1.4.1) and it behaved properly. It appears to >> be pymol specific as coot and other programs work fine. Has anyone seen >> this before or have some sort of explanation? >> >> Thanks, >> >> --paul -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Odd issue with control and shift keys in pymol
Hi Thomas, Thanks for the info. I don't have the 1.4 version of Pymol handy at the moment, but Coot does use the system libglut without problems. --p On 07/01/2013 05:36 AM, Thomas Holder wrote: > Hi Paul and Adam, > > I can confirm this. The problem comes with two patches that Fedora > applies to freeglut (freeglut_xinput.c). I don't know why they do this, > but if I compile freeglut without those, PyMOL works fine. > > Paul, that 1.4.1 version of PyMOL and also Coot, are those linked to the > system glut library (/usr/lib64/libglut.so.3.9.0 on my Fedora 18) or is > there any other glut installation? > > Incentive builds of PyMOL 1.6 ship with a working glut library. It's > only used as a fallback if there is no system glut (determined by > setup.sh). So if you are on Fedora 18, just move > "pymol/ext/libextra/libglut.so.3" to "pymol/ext/lib/" to give it > priority over the broken system glut. > > Cheers, >Thomas > > Adam Middleton wrote, On 06/26/13 12:14: >> Hi Paul, >> >> I have the same problem. I am using Fedora 18 and PyMOL v.1.5 (from >> the repository). >> >> It is annoying. Right now I have to use another computer if I want to >> use the more 'advanced' functions of PyMOL. >> >> I found one other person with the same problem who posted to the >> Fedora forum, and got no response: >> http://www.forum.fedoraforum.org/showthread.php?t=287005 >> >> No explanations here. >> >> Adam >> >> On Wed, Jun 26, 2013 at 3:08 AM, Paul Paukstelis wrote: >>> I've found that all recent versions (1.5, 1.6, non-incentive) of Pymol >>> on my laptop running updated Fedora 18 (nvidia drivers) don't allow me >>> to use the control or shift keys for selection or editing in the gui. I >>> dug out an older version (1.4.1) and it behaved properly. It appears to >>> be pymol specific as coot and other programs work fine. Has anyone seen >>> this before or have some sort of explanation? >>> >>> Thanks, >>> >>> --paul -- Paul Paukstelis, Ph.D Assistant Professor University of Maryland Chemistry & Biochemistry Dept. Center for Biomolecular Structure & Organization pauks...@umd.edu 301-405-9933 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] cut protein in half
Hi Yeping, The technique will differ depending on the structure you have. Can you send me a copy and I can try to put something together for you? If it's a homodimer, usually we can just disable one unit and show the open channel. Also, see http://hollow.sourceforge.net/channel.html and http://www.pymolwiki.org/index.php/Biochemistry_student_intro#Movie_of_Epidermal_Growth_Factor . Cheers, -- Jason On Fri, Jun 28, 2013 at 2:14 AM, wrote: > > > > > Dear pymol users, > > I want to make a cross-section on a ion tunnel protein to cut it in half > and observe the intenal characters of the tunnel. According to materials on > web, I runed the following commands: > > hide all > show surfaceset ray_trace_mode, 0set two_sided_lighting, offset > ray_interior_color, grey50 > > > > But I didn't see any obvious change on the structure except that the protein > became dim. Could you help me with that? > > Tnanks in advance! > > > > Yeping Sun > > > > -- > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] 2013 PyMOL Open Source Fellowship–Request for Applications
Greetings PyMOLers, We have pushed back the deadline for the 2013 PyMOL Open Source Fellowship program to July 8th for those wishing to participate. If you like PyMOL, science, programming, and open-source here's your chance to give back. Students and postdocs are especially welcome to apply. For more information on the stipend, application rules, terms, etc., please see the main fellowship page on our website: http://pymol.org/fellowship. Cheers, -- Jason On Thu, Apr 25, 2013 at 9:31 AM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Greetings, > > I am delighted to announce that the 2013 PyMOL Open Source Fellowship > program is now accepting applications. Due to the success of the > program, we have two open spots this year. > > Application instructions and deadlines for the 2013 PyMOL Open Source > Fellowship have been posted here http://pymol.org/fellowship. > Interested applicants, please review the instructions before applying. > > The application deadline is July 1, 2013. > > Good luck! > > Cheers, > > -- Jason > > -- > Jason Vertrees, PhD > Director of Core Modeling Products > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] restricting selection to the current frame
Hi, Is it possible to force a selection to only apply to the specific frame rather then across frames? I'm running in to a problem where I have some (~40) frames from an explicit solvent MD that I want to look at. What I want to do is look at water molecules around a specific residue at each frame, but when I do something like, 'sele wats, byres resn WAT in within 6 of ', it ends up a majority of the waters in the system. I think that what it is doing is finding all waters that are with 6 A of the residue of interest in ALL frames, then selecting them in the current frame. Which is not the expected behavior. From what I can tell, there isn't a selection syntax for selecting the frame. Perhaps there is a setting for this that I couldn't find. Any help would be appreciated including solutions involving VMD or custom scripts. Thanks, Matt -- -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] restricting selection to the current frame
I know you have asked for frames, but I assume that each frame is mapped to a
state. The selection logic allows for you to specify the state.
So if the waters of interest are in state 1,40:
python
for i in range(1,41):
cmd.select("wat_"+i,"byres in within 6 of
",state=i)
python end
J
> 'sele wats, byres res
> WAT in within 6 of
> ',
On Jul 1, 2013, at 12:42 PM, Matthew Baumgartner wrote:
> Hi,
> Is it possible to force a selection to only apply to the specific frame
> rather then across frames?
> I'm running in to a problem where I have some (~40) frames from an
> explicit solvent MD that I want to look at. What I want to do is look at
> water molecules around a specific residue at each frame, but when I do
> something like, 'sele wats, byres resn WAT in within 6 of
> ', it ends up a majority of the waters in the
> system. I think that what it is doing is finding all waters that are
> with 6 A of the residue of interest in ALL frames, then selecting them
> in the current frame. Which is not the expected behavior.
>
> From what I can tell, there isn't a selection syntax for selecting the
> frame. Perhaps there is a setting for this that I couldn't find.
>
> Any help would be appreciated including solutions involving VMD or
> custom scripts.
>
> Thanks,
> Matt
>
> --
>
>
> --
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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Re: [PyMOL] Label problems (PyMOL ver. 1.6)
Hi Yoshitaka, did you get the source code from SVN? On June 13 (after 1.6.0.0 release) we pushed a label related fix to SVN, does that fix your issue? Can you also check if it's related to shaders and if yes, tell us what graphics card you have? PyMOL> set use_shaders, 0 PyMOL> set use_shaders, 1 PyMOL> print cmd.get_renderer() Cheers, Thomas Yoshitaka MORIWAKI wrote, On 06/25/13 07:27: > Dear Pymol Users, > > I have installed PyMOL 1.6 built from source code on Ubuntu and > Windows on June 23, 2013. I've noticed that the label of distance (or > angle) is not shown properly. > > I describe the steps to reproduce: 1. load a PDB file. 2. select two > atoms by clicking the middle button on the PyMOL Viewer (pushing a > wheel of a computer mouse). 3. type ">dist" to create a distance > object (dist01). > > Then, a yellow broken line was produced between the selected atoms. > However, the label of distance (i.e. 2.2 Å) was not shown though the > older versions (including v1.6-beta2) correctly showed. Label of > angle is the same. It is also ineffective to select "Show -> label" > of object "dist01" from PyMOL Viewer. > > Please help me. > > Thanks, Yoshitaka -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] restricting selection to the current frame
Yes, sorry, the frames are mapped to states. Ah, yes, that is what I
needed, that 'state' keyword argument was not listed in the wiki page.
For posterity's sake, a couple of minor modifications were required in
the code you provided.
python
for i in range(1,41):
cmd.select("wat_" + str(i),"resn WAT in within 6 of
", state=i)
python end
I removed the byres command because I have more then 1 water
molecules in my system and the residue ID's were rolling over and waters
far from the residue of interest were being selected.
If anyone has a suggestion on this, please let me know, I would like to
select whole water molecules for making figures.
Thanks,
Matt
On 07/01/2013 02:10 PM, Jordan Willis wrote:
> I know you have asked for frames, but I assume that each frame is mapped to a
> state. The selection logic allows for you to specify the state.
>
> So if the waters of interest are in state 1,40:
>
> python
> for i in range(1,41):
> cmd.select("wat_"+i,"byres in within 6 of
> ",state=i)
> python end
>
> J
>
>
>> 'sele wats, byres res
>> WAT in within 6 of
>> ',
>
>
> On Jul 1, 2013, at 12:42 PM, Matthew Baumgartner wrote:
>
>> Hi,
>> Is it possible to force a selection to only apply to the specific frame
>> rather then across frames?
>> I'm running in to a problem where I have some (~40) frames from an
>> explicit solvent MD that I want to look at. What I want to do is look at
>> water molecules around a specific residue at each frame, but when I do
>> something like, 'sele wats, byres resn WAT in within 6 of
>> ', it ends up a majority of the waters in the
>> system. I think that what it is doing is finding all waters that are
>> with 6 A of the residue of interest in ALL frames, then selecting them
>> in the current frame. Which is not the expected behavior.
>>
>> From what I can tell, there isn't a selection syntax for selecting the
>> frame. Perhaps there is a setting for this that I couldn't find.
>>
>> Any help would be appreciated including solutions involving VMD or
>> custom scripts.
>>
>> Thanks,
>> Matt
>>
>> --
>>
>>
>> --
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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Re: [PyMOL] restricting selection to the current frame
Matthew Baumgartner wrote, On 07/01/13 21:34: > I removed the byres command because I have more then 1 water > molecules in my system and the residue ID's were rolling over and waters > far from the residue of interest were being selected. > If anyone has a suggestion on this, please let me know, I would like to > select whole water molecules for making figures. use "bymol". Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Accessing progress bar
Hi, My google-fu didn't find anything, but is it possible to access the progress bar in pymol (the one that comes up when ray tracing) in a script? I have a script that is a little long running and it would benefit from giving users feedback on progress. Thanks, Matt -- -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
