Dear Osvaldo:
Thank you for pointing me to the loadBfacts.py script (
http://www.pymolwiki.org/index.php/Load_new_B-factors). It worked quite
well. I loaded the B-factors into the ancillary file and was able to
obtain a putty representation of the side chain fluctuations. It's pretty
neat. One can see right into the protein channel and determine which of
those side chains are poking into the channel causing the permeant to
perhaps be hindered in some way.
Thanks again.
Kind regards,
Angelo
On Tue, May 12, 2015 at 3:10 PM, Osvaldo Martin <aloctavo...@gmail.com>
wrote:
> HI Angelo,
>
> I used to have a python script to change the b-factors (by reading them
> from a txt file), but now I could not find it. I think you can use this
> script to do that http://www.pymolwiki.org/index.php/Load_new_B-factors
>
> Let me know if that script fit your needs.
>
> As a side note, when replying to the PyMOL mail list try to "reply to all"
> (unless your emails contains private information). This is important
> because the PyMOL list is an archive of questions and aswers and your
> question can be very useful for other people in the future.
>
>
> Cheers,
> Osvaldo
>
>
> On Tue, May 12, 2015 at 3:52 PM, Angelo Rossi <
> angelo.raymond.ro...@gmail.com> wrote:
>
>> Dear Osvaldo:
>>
>> Thank you so much for your response. What you say makes a lot of sense.
>> I had an idea that the algorithm for RMSF used the CA atoms for
>> visualization in Pymol. My problem is now how to add the side chain RMSF
>> to the CA RMSF. I think this would show up nicely as you indicated. I am
>> using CHARMM to compute the RMSF over the trajectory, and the script
>> language computes the RMSF values ok, but it doesn't seem to be flexible
>> enough to allow for adding the side chain RMSF to the CA RMSF.
>>
>> Kind regards,
>>
>> Angelo
>>
>> On Mon, May 11, 2015 at 6:44 PM, Osvaldo Martin <aloctavo...@gmail.com>
>> wrote:
>>
>>> Hi Angelo,
>>>
>>> As far as I understand the putty representation takes the values from
>>> the b-factor of the Ca atom. Probably you should store your fluctuation
>>> values either on the Ca (leaving all the others atoms with 0.0 or any other
>>> value) or just set the same b-factor for all the atoms of a given residue.
>>> Either way you should get what you want.
>>>
>>> I think the error you are getting is because all the Ca have the same
>>> b-factor value is your error something like "invalid putty settings
>>> (division by zero)"? If you want all the Ca having the same b-factor
>>> and use the putty representation anyway you should do the following:
>>>
>>> set cartoon_putty_transform, 2
>>>
>>>
>>> Cheers,
>>> Osvaldo.
>>>
>>>
>>>
>>>
>>> On Mon, May 11, 2015 at 6:35 PM, Angelo Rossi <
>>> angelo.raymond.ro...@gmail.com> wrote:
>>>
>>>> Hello:
>>>>
>>>> I am trying to see the effect of side-chain fluctuation on molecular
>>>> permeation through a transmembrane protein channel.
>>>>
>>>> The idea is create a pdb file with a column of B-values related to the
>>>> RMSF values of the MD trajectory.
>>>>
>>>> What I tried was to set the B-values of all heavy atom main-chain atoms
>>>> to 1.0. Then all the B side-chain values were set equal to the RMSF value
>>>> from the trajectory, using the correct formula relating RMSF fluctuation to
>>>> B-value.
>>>>
>>>> But, the above method blows up in pymol when trying to use the Action
>>>> ---> Preset ---> b factor putty option. I think this is probably due to
>>>> the fact that all main-chain atoms are equal to 1, and the algorithm cannot
>>>> handle this.
>>>>
>>>> Can someone please provide me with a way to clearly see the fluctuation
>>>> of sid-chain atoms in the present of the main-chain atoms?
>>>>
>>>> Thanks so much.
>>>>
>>>> Regards,
>>>>
>>>> Angelo
>>>>
>>>>
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>>>
>>
>
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