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At 2014-05-22 00:08:55, [email protected] wrote:
>Send PyMOL-users mailing list submissions to
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>
>Today's Topics:
>
> 1. Re: morph command questions (Thomas Holder)
> 2. Re: disable all screen output (Osvaldo Martin)
> 3. Re: Bugfix release 1.7.0.5 (Abhinav Kumar)
> 4. Re: Bugfix release 1.7.0.5 (Abhinav Kumar)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 20 May 2014 17:04:27 -0400
>From: Thomas Holder <[email protected]>
>Subject: Re: [PyMOL] morph command questions
>To: "Dr. Mark Mayer" <[email protected]>
>Cc: [email protected]
>Message-ID: <[email protected]>
>Content-Type: text/plain; charset=iso-8859-1
>
>Hi Mark,
>
>both the labels and the distance lines should be visible in all states. Here a
>working example, tested with 1.7.0.0 and 1.7.0.5:
>
>fetch 1akeA 4akeA, async=0
>align 1akeA, 4akeA
>morph mobj, 1akeA, 4akeA
>as ribbon
>enable 1akeA
>select sele1, resi 148 & guide
>label sele1, resi
>distance dobj, mobj & sele1, 1akeA & sele1
>mplay
>
>Feel free to share your script (if possible), then we can figure out if there
>is a problem.
>
>Cheers,
> Thomas
>
>On 20 May 2014, at 16:14, Dr. Mark Mayer <[email protected]> wrote:
>
>> I have two questions about the morph command in PyMOL 1.7
>>
>> 1) Is it possible to keep atom label text displayed throughout the
>> morph? I've run a script morphing from mol1 to mol2 with text
>> associated with mol1, but the label disappears at the start of the
>> morph.
>>
>> 2) Is it possible to have the distance vector between identical atom
>> selections in mol1 and mol2
>> displayed to indicate the change in distance during the morph. I've
>> run a script morphing from mol1 to mol2 with text associated with
>> mol1, but the line disappears at the start of the morph.
>>
>> Thanks,
>>
>> Mark
>
>--
>Thomas Holder
>PyMOL Developer
>Schr?dinger, Inc.
>
>
>
>
>------------------------------
>
>Message: 2
>Date: Tue, 20 May 2014 18:16:17 -0300
>From: Osvaldo Martin <[email protected]>
>Subject: Re: [PyMOL] disable all screen output
>To: Thomas Holder <[email protected]>
>Cc: "[email protected]"
> <[email protected]>
>Message-ID:
> <cagmh68uaf2j4a4ssflwwh958mzwq+uak+-rnf+n23snnphe...@mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Thanks Thomas,
>
>You are right. I just have added a couple of links to the "suspend_updates"
>setting in the wiki to make that option easier to find.
>
>Cheers,
>Osvaldo.
>
>
>On Tue, May 20, 2014 at 5:46 PM, Thomas Holder <
>[email protected]> wrote:
>
>> Hi Osvaldo,
>>
>> I think you are looking for the "suspend_updates" setting.
>>
>> Cheers,
>> Thomas
>>
>> On 19 May 2014, at 15:10, Osvaldo Martin <[email protected]> wrote:
>>
>> > Hello everyone!
>> >
>> > I working on a PyMOL plugin that performs a lot of selections and
>> operations. I would like to avoid updating the screen until the script
>> finish (mainly to increase the performance of the plugin)
>> >
>> > I tried with something like this
>> >
>> > cmd.disable('all')
>> > "Some code"
>> > cmd.enable('all')
>> >
>> > The problem is that the "disable" command only toggles off the display
>> of the currently visible representations of an object. If "Some code"
>> creates a new object then this new object will be visible. On possible
>> solution will be to repeat the "cmd.disable('all')" command any time a new
>> object is created, but I will prefer a cleaner solution (if possible).
>> >
>> > Thanks in advance,
>> >
>> > Osvaldo.
>>
>> --
>> Thomas Holder
>> PyMOL Developer
>> Schr?dinger, Inc.
>>
>>
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>------------------------------
>
>Message: 3
>Date: Wed, 21 May 2014 08:26:47 -0700
>From: Abhinav Kumar <[email protected]>
>Subject: Re: [PyMOL] Bugfix release 1.7.0.5
>To: <[email protected]>
>Message-ID: <[email protected]>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi,
>
>I installed pymol ( pymol-v1.7.0.5-Linux-x86_64.tar.bz2) on my ubuntu
>(12.04 LTS) desktop and this was working fine.
>Later, I upgraded my Ubuntu to 14.04 LTS and now pymol has become
>extremely sluggish. Even rotating a small molecule like ATP takes a while.
>
>Any suggestions on how to fix this?
>
>Coot and rasmol are not affected by this Ubuntu upgrade.
>
>Thanks,
>Abhinav
>______________________________________
>Abhinav Kumar, Ph.D.
>The Joint Center for Structural Genomics
>MS99, SLAC National Accelerator Laboratory
>2575 Sand Hill Rd, Menlo Park, CA 94025
>(650) 926-2992
>
>
>On 05/13/2014 10:43 AM, Thomas Holder wrote:
>> Greetings,
>>
>> We'd like to announce the release of Incentive PyMOL 1.7.0.5, which is a
>> bugfix release. Applicable bugfixes have also been pushed to the sourceforge
>> SVN repository as Open-Source PyMOL 1.7.1.3 (SVN rev 4076).
>>
>> Fixed bugs include:
>>
>> Incentive PyMOL (for licensed users):
>> - don't disable all shaders if geometry shaders are not available
>> - many z-depth issues for labels and connectors in immediate, shader, and
>> ray tracing (all renderings should now look almost exactly the same)
>> - background in front of text with use_shaders=0
>> - label picking broken with use_shaders=0
>> - character rendering in ray tracing
>> - clipped text in multi-line labels (shader on and off)
>>
>> Open Source and Incentive PyMOL:
>> - cartoon memory leak
>> - CGO colors ignored with ALPHA
>> - hidden groups flash in scene based movies
>> - "A > find > polar contact > just intra-side chain" broken
>> - "scene auto, update" broken
>> - small solvent_radius crashes Surface generation
>> - grid_mode support for volumes
>>
>> Some of these changes have been in the SVN repository for a couple of weeks.
>>
>> Download:
>> Installers for Incentive PyMOL: http://pymol.org/dsc/ip/
>> Open Source: http://sourceforge.net/p/pymol/
>>
>> Cheers,
>> The PyMOL Team at Schr?dinger
>>
>
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>
>------------------------------
>
>Message: 4
>Date: Wed, 21 May 2014 09:08:27 -0700
>From: Abhinav Kumar <[email protected]>
>Subject: Re: [PyMOL] Bugfix release 1.7.0.5
>To: Clotilde LowKam <[email protected]>, pymol-users
> <[email protected]>
>Message-ID: <[email protected]>
>Content-Type: text/plain; charset="utf-8"
>
>Thanks Clotilde again.
>
>I switched the graphics card driver and it has fixed the problem.
>The switch I made was from Nouveau display driver to Nvidia dreiver.
>
>Thanks,
>Abhinav
>______________________________________
>Abhinav Kumar, Ph.D.
>The Joint Center for Structural Genomics
>MS99, SLAC National Accelerator Laboratory
>2575 Sand Hill Rd, Menlo Park, CA 94025
>(650) 926-2992
>
>
>On 05/21/2014 08:44 AM, Clotilde LowKam wrote:
>> Hello,
>> probably a driver/graphic card problem. Maybe trying the legacy driver
>> for your card could help.
>> Clotilde
>>
>>
>> 2014-05-21 11:26 GMT-04:00 Abhinav Kumar <[email protected]
>> <mailto:[email protected]>>:
>>
>> Hi,
>>
>> I installed pymol ( pymol-v1.7.0.5-Linux-x86_64.tar.bz2) on my
>> ubuntu (12.04 LTS) desktop and this was working fine.
>> Later, I upgraded my Ubuntu to 14.04 LTS and now pymol has become
>> extremely sluggish. Even rotating a small molecule like ATP takes
>> a while.
>>
>> Any suggestions on how to fix this?
>>
>> Coot and rasmol are not affected by this Ubuntu upgrade.
>>
>> Thanks,
>> Abhinav
>> ______________________________________
>> Abhinav Kumar, Ph.D.
>> The Joint Center for Structural Genomics
>> MS99, SLAC National Accelerator Laboratory
>> 2575 Sand Hill Rd, Menlo Park, CA 94025
>> (650) 926-2992 <tel:%28650%29%20926-2992>
>>
>>
>> On 05/13/2014 10:43 AM, Thomas Holder wrote:
>>> Greetings,
>>>
>>> We'd like to announce the release of Incentive PyMOL 1.7.0.5, which is
>>> a bugfix release. Applicable bugfixes have also been pushed to the
>>> sourceforge SVN repository as Open-Source PyMOL 1.7.1.3 (SVN rev 4076).
>>>
>>> Fixed bugs include:
>>>
>>> Incentive PyMOL (for licensed users):
>>> - don't disable all shaders if geometry shaders are not available
>>> - many z-depth issues for labels and connectors in immediate, shader,
>>> and
>>> ray tracing (all renderings should now look almost exactly the same)
>>> - background in front of text with use_shaders=0
>>> - label picking broken with use_shaders=0
>>> - character rendering in ray tracing
>>> - clipped text in multi-line labels (shader on and off)
>>>
>>> Open Source and Incentive PyMOL:
>>> - cartoon memory leak
>>> - CGO colors ignored with ALPHA
>>> - hidden groups flash in scene based movies
>>> - "A > find > polar contact > just intra-side chain" broken
>>> - "scene auto, update" broken
>>> - small solvent_radius crashes Surface generation
>>> - grid_mode support for volumes
>>>
>>> Some of these changes have been in the SVN repository for a couple of
>>> weeks.
>>>
>>> Download:
>>> Installers for Incentive PyMOL:http://pymol.org/dsc/ip/
>>> Open Source:http://sourceforge.net/p/pymol/
>>>
>>> Cheers,
>>> The PyMOL Team at Schr?dinger
>>>
>>
>>
>>
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>> <mailto:[email protected]>)
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>>
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