Re: [PyMOL] regarding show_bumps

2016-01-28 Thread Thomas Holder 
Hi Spencer & Priyan,

I've updated the show_bumps script to work with multi-state objects. Please 
re-download.

Cheers,
  Thomas

On 28 Jan 2016, at 06:15, Spencer Bliven  wrote:

> You can automate generating the bump objects:
> 
> split_states *,prefix=split_
> for n in cmd.get_object_list("(split_*)"): show_bumps(n, "bump_"+n);
> 
> However, unfortunately the bump cgo objects don't seem to be able to be 
> combined into a multi-state object (e.g. with `for n in 
> cmd.get_object_list("(split_*)"): 
> cmd.create("bumps","bump_"+n,target_state=-1)`). Thus you might have to 
> generate your movie using some python loops to enable/disable the bumps for 
> each frame, if you want to automate it.
> 
> -Spencer
> 
> On Thu, Jan 28, 2016 at 11:25 AM, ccp4 pymol  wrote:
> Dear Spencer
> 
> Thank you for the suggestion. Well, I actually wanted to do it as a part of 
> making a movie, so would have liked some automation.
> 
> Thank you.
> 
> Best Regards
> Priyan 
> 
> On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven  
> wrote:
> Priyan–
> 
> You can use the split_states command to divide it into multiple objects, then 
> run the script on each state individually.
> 
> -Spencer
> 
> On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol  wrote:
> Hi
> 
> I have a multi-state object loaded in PyMOL which represents transition of a 
> domain from one orientation to the other. I tried using "show_bumps.py" to 
> bring up clashes during the transition but the cgo that is written out shows 
> clashes only for the first state. Am I doing something wrong or should we 
> pass additional commands to show clashes for all states. Kindly post your 
> replies with help/suggestions in this regard.
> 
> Thank you
> 
> Best Regards
> Priyan

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] regarding show_bumps

2016-01-28 Thread ccp4 pymol 
Dear Spencer

Thank you for the suggestion. Well, I actually wanted to do it as a part of
making a movie, so would have liked some automation.

Thank you.

Best Regards
Priyan

On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven 
wrote:

> Priyan–
>
> You can use the split_states 
> command to divide it into multiple objects, then run the script on each
> state individually.
>
> -Spencer
>
> On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol  wrote:
>
>> Hi
>>
>> I have a multi-state object loaded in PyMOL which represents transition
>> of a domain from one orientation to the other. I tried using
>> "show_bumps.py" to bring up clashes during the transition but the cgo that
>> is written out shows clashes only for the first state. Am I doing something
>> wrong or should we pass additional commands to show clashes for all states.
>> Kindly post your replies with help/suggestions in this regard.
>>
>> Thank you
>>
>> Best Regards
>> Priyan
>>
>>
>> --
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
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>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
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Re: [PyMOL] regarding show_bumps

2016-01-28 Thread Spencer Bliven 
You can automate generating the bump objects:

split_states *,prefix=split_
for n in cmd.get_object_list("(split_*)"): show_bumps(n, "bump_"+n);

However, unfortunately the bump cgo objects don't seem to be able to be
combined into a multi-state object (e.g. with `for n in
cmd.get_object_list("(split_*)"):
cmd.create("bumps","bump_"+n,target_state=-1)`). Thus you might have to
generate your movie using some python loops to enable/disable the bumps for
each frame, if you want to automate it.

-Spencer

On Thu, Jan 28, 2016 at 11:25 AM, ccp4 pymol  wrote:

> Dear Spencer
>
> Thank you for the suggestion. Well, I actually wanted to do it as a part
> of making a movie, so would have liked some automation.
>
> Thank you.
>
> Best Regards
> Priyan
>
> On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven 
> wrote:
>
>> Priyan–
>>
>> You can use the split_states
>>  command to divide it into
>> multiple objects, then run the script on each state individually.
>>
>> -Spencer
>>
>> On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol  wrote:
>>
>>> Hi
>>>
>>> I have a multi-state object loaded in PyMOL which represents transition
>>> of a domain from one orientation to the other. I tried using
>>> "show_bumps.py" to bring up clashes during the transition but the cgo that
>>> is written out shows clashes only for the first state. Am I doing something
>>> wrong or should we pass additional commands to show clashes for all states.
>>> Kindly post your replies with help/suggestions in this regard.
>>>
>>> Thank you
>>>
>>> Best Regards
>>> Priyan
>>>
>>>
>>> --
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311=/4140
>>> ___
>>> 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] regarding show_bumps

2016-01-28 Thread ccp4 pymol 
Dear Thomas

Thank you very much!!

Best Regards
Priyan

On Fri, Jan 29, 2016 at 5:13 AM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Spencer & Priyan,
>
> I've updated the show_bumps script to work with multi-state objects.
> Please re-download.
>
> Cheers,
>   Thomas
>
> On 28 Jan 2016, at 06:15, Spencer Bliven  wrote:
>
> > You can automate generating the bump objects:
> >
> > split_states *,prefix=split_
> > for n in cmd.get_object_list("(split_*)"): show_bumps(n, "bump_"+n);
> >
> > However, unfortunately the bump cgo objects don't seem to be able to be
> combined into a multi-state object (e.g. with `for n in
> cmd.get_object_list("(split_*)"):
> cmd.create("bumps","bump_"+n,target_state=-1)`). Thus you might have to
> generate your movie using some python loops to enable/disable the bumps for
> each frame, if you want to automate it.
> >
> > -Spencer
> >
> > On Thu, Jan 28, 2016 at 11:25 AM, ccp4 pymol 
> wrote:
> > Dear Spencer
> >
> > Thank you for the suggestion. Well, I actually wanted to do it as a part
> of making a movie, so would have liked some automation.
> >
> > Thank you.
> >
> > Best Regards
> > Priyan
> >
> > On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven <
> spencer.bli...@gmail.com> wrote:
> > Priyan–
> >
> > You can use the split_states command to divide it into multiple objects,
> then run the script on each state individually.
> >
> > -Spencer
> >
> > On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol 
> wrote:
> > Hi
> >
> > I have a multi-state object loaded in PyMOL which represents transition
> of a domain from one orientation to the other. I tried using
> "show_bumps.py" to bring up clashes during the transition but the cgo that
> is written out shows clashes only for the first state. Am I doing something
> wrong or should we pass additional commands to show clashes for all states.
> Kindly post your replies with help/suggestions in this regard.
> >
> > Thank you
> >
> > Best Regards
> > Priyan
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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