VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Wed May 24 2017 - 12:21:17 CDT

By direct cuttoff I mean if the actual value in the map is below that
threshold value, it will not be included in the calculation.

On Wed, May 24, 2017 at 12:10 PM Karol KASZUBA <karol.kaszuba_at_ist.ac.at>
wrote:

> Hi,
>
> By "direct cutoff for voxel values" you mean: you cut density within X A
> of any atom of a residue, where X would be a treshold?
>
> I will try with mdff ccc. This would be very informative.
>
> By weird I mean: I have a residue, which is definitely not in the density
> (at least in coot), but still the cc score is +0.43, which should not be.
>
> thanks!
> ------------------------------
> *From:* Ryan McGreevy [ryanmcgreevy_at_ks.uiuc.edu]
> *Sent:* Wednesday, May 24, 2017 6:07 PM
>
> *To:* Karol KASZUBA; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: MDFF time line ccc score
> I have never used coot, so I can't say for sure. For the "mdffi" and
> "Timeline" calculations, the threshold is not in sigmas, but instead is a
> direct cutoff for voxel values. "mdff ccc" is, however, in sigmas.
>
> What do you mean by "weird" scores? If the per-residue correlations are
> not looking as you expected them to, it is probably because of the
> resolution of the map. 4-5A is not quite good enough to really see
> side-chains, so the correlations for individual residues may be misleading.
> Also, because each residue contributes density to its neighbors, it is hard
> to get a clear correlation because it is hard to separate the contribution
> from the surrounding area. This is another reason we don't generally do
> per-residue correlations.
>
> On Wed, May 24, 2017 at 10:52 AM Karol KASZUBA <karol.kaszuba_at_ist.ac.at>
> wrote:
>
>> Hello again,
>>
>> Can you tell me, which treshold value would correspond to sigma=6 in coot?
>> Map resolution 4-5A.
>>
>> I am asking since I am getting some weird scores.
>>
>> thanks
>> ------------------------------
>> *From:* Karol KASZUBA
>> *Sent:* Wednesday, May 24, 2017 5:22 PM
>> *To:* Ryan McGreevy; vmd-l_at_ks.uiuc.edu
>> *Subject:* RE: vmd-l: MDFF time line ccc score
>>
>> OK.
>>
>> thanks
>> ------------------------------
>> *From:* Ryan McGreevy [ryanmcgreevy_at_ks.uiuc.edu]
>> *Sent:* Wednesday, May 24, 2017 5:11 PM
>> *To:* Karol KASZUBA; vmd-l_at_ks.uiuc.edu
>> *Subject:* Re: vmd-l: MDFF time line ccc score
>>
>> Just to be clear, you said you had tried "mdff ccc" which is different
>> from the "mdffi cc" that I am proposing you use. "mdffi cc" uses exactly
>> the same algorithm as Timeline and will give you exactly the same results,
>> whereas "mdff ccc" will not (and will also be much slower).
>>
>> On Wed, May 24, 2017 at 10:09 AM Karol KASZUBA <karol.kaszuba_at_ist.ac.at>
>> wrote:
>>
>>> Hi,
>>>
>>> Yes. Exactly, I want to do it for a single frame.
>>> Using mdffi cc was my plan from the very beginning, but as I said, the
>>> ones computed with Time Line appear to be more reliable. However, to be
>>> sure I need to run additional tests. I will keep you posted
>>>
>>> thanks!
>>> ------------------------------
>>> *From:* Ryan McGreevy [ryanmcgreevy_at_ks.uiuc.edu]
>>> *Sent:* Wednesday, May 24, 2017 5:03 PM
>>>
>>> *To:* Karol KASZUBA; vmd-l_at_ks.uiuc.edu
>>> *Subject:* Re: vmd-l: MDFF time line ccc score
>>> Timeline wasn't really designed to give a per-residue cross correlation
>>> because (a) calculating the correlation for each residue for an entire
>>> trajectory is very computationally heavy, even with the fast algorithm
>>> Timeline uses and (b) most cryo-em maps are too low resolution for
>>> per-residue calculations to make sense.
>>>
>>> If you really want to do this though, you can write a fairly simple
>>> script using the "mdffi cc" command. "mdffi" (note the 'i' at the end) is
>>> the newer, faster algorithm that both Timeline and "mdff check" uses,
>>> versus the older, slower "mdff ccc" command (though mdff ccc too will be
>>> changed in the future, once all the bugs are worked out). Using this, you
>>> can just calculate the mdffi cc for each residue you want in a tcl loop. I
>>> would recommend only doing this for a single frame, however, and not an
>>> entire trajectory if you have one.
>>>
>>> On Wed, May 24, 2017 at 9:42 AM Karol KASZUBA <karol.kaszuba_at_ist.ac.at>
>>> wrote:
>>>
>>>> Hi Ryan,
>>>>
>>>> Thank you for your prompt reply.
>>>>
>>>> This is cryo-em model and in certain places there is no density at all,
>>>> which would explain these low negative values.
>>>>
>>>> (1) Actually, I played with treshold a bit and now the values are quite
>>>> nice, between 0.5-0.78.
>>>> The value of treshold corresponds to the sigma values I use. So,
>>>> it looks good now.
>>>>
>>>> (2) I also found that Timeline cc gives a much more reasonable score
>>>> than mdff ccc.
>>>>
>>>> I played quite a lot with selection in Timeline. Can you tell me what
>>>> would be the proper selection to get a per-residue score for a given
>>>> segment of residues. For example, when I try {segname PRT1 and resid 1 to
>>>> 29} it returns one number, most likely treating selection between {} as one
>>>> segment. However, what I need is per-residue score.
>>>> I have a big structure, so typing {resid 1} {resid 2} and so on will
>>>> not work for me.
>>>>
>>>> thank you very much
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>> *From:* Ryan McGreevy [ryanmcgreevy_at_ks.uiuc.edu]
>>>> *Sent:* Wednesday, May 24, 2017 4:16 PM
>>>> *To:* Karol KASZUBA; vmd-l_at_ks.uiuc.edu
>>>> *Subject:* Re: vmd-l: MDFF time line ccc score
>>>>
>>>> (1) In general those values are pretty low. Having a high of .35 is not
>>>> very good. The extremely low negative values are most likely due to pieces
>>>> of the structure that are sticking out of the map significantly, where
>>>> correlation is undefined. You could also try using the "threshold" option
>>>> in the Timeline cross correlation parameters (try 0.1 for example) which
>>>> will remove some of the excess noise around your structure from the
>>>> calculation. Is your structure that you are analyzing the result of a
>>>> fitting, like MDFF? Without actually seeing the map and model it is hard to
>>>> say anything more concrete.
>>>>
>>>> (2) It is okay that Timeline and mdff ccc do not give exactly the same
>>>> results. First, if you ran Timeline with default options, the correlations
>>>> are calculated on sections of contiguous secondary structure, not
>>>> per-residue, so the CC's are not being calculated on exactly the same
>>>> parts. Second, the algorithms used by the Timeline and mdff ccc are not
>>>> exactly the same, so there will be small discrepancies, but shouldn't be
>>>> more than a few hundredth.
>>>>
>>>> On Wed, May 24, 2017 at 2:50 AM Karol KASZUBA <karol.kaszuba_at_ist.ac.at>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am trying to calculate the cross-correlation score between my map
>>>>> and a model. The map is in .mrc format.
>>>>>
>>>>> (1) At first I used time line plugin and "calculate cc" option.
>>>>> So, I got the scores. They make sense, but what I am worried is the
>>>>> scale: it starts from -100 and finishes at 0.35. Is it normal?
>>>>>
>>>>> I would expect a score from 0 to 1, where low values would correspond
>>>>> to poor density fit, while higher (positive) values would denote a good
>>>>> match.
>>>>>
>>>>> (2) I also calculated cc using "mdff ccc" command in tcl console. I
>>>>> just choose one residue to see whether the cc score calculated in
>>>>> time line and from command line. will be the same. These were not.
>>>>>
>>>>>
>>>>> Please let me know what do you think
>>>>> thanks
>>>>> Karol
>>>>>
>>>>>