Dear Orly,
I just remembered that your question has been answered a few years ago
on here by Nat Echols:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1004&L=CCP4BB&O=D&P=269798
His python script doesn't take care of possible integer unit cell
translations. so you'd still need to deal with that.
Regards,
Rob
On 13/01/2020 08:54, orly avraham wrote:
Hi Tristan,
Thank you very much!!
I will continue with my exploration and I am grateful for all the
assistance.
Best regards,
Orly
On Sun, Jan 12, 2020 at 11:18 PM Tristan Croll <ti...@cam.ac.uk
<mailto:ti...@cam.ac.uk>> wrote:
(sending again because it seems the message board server gets a
little
confused by Python files as attachments).
Hi Orly,
Turns out I didn't have a pre-baked method for this specific task,
but
the method defined in the attached file works - although you'll
undoubtedly want to adapt it to your specific purposes. To play
around
with it, download and install ChimeraX 0.91, then install Clipper
with
"toolshed install clipper" on its command line. Then, you can open
the
ChimeraX interactive Python shell with Tools/General/Shell. This
comes
with the top-level ChimeraX session object pre-loaded with the
variable
name "session". Copy-paste the method definition in to that, and
you'll
be ready to explore. You can also run Python files with "open
xxx.py" on
the command line or on starting ChimeraX with "chimerax xxx.py" - in
either case, these will also have the session object automatically
available.
Best regards,
Tristan
On 2020-01-12 19:54, orly avraham wrote:
> Hi Tristan,
>
> I am looking into all the options listed, yet would still highly
> appreciate any additional resources!
> If you would be kind enough to share an example script that would be
> great.
>
> Best,
> Orly
>
> On Sun, Jan 12, 2020 at 9:12 PM Tristan Croll <ti...@cam.ac.uk
<mailto:ti...@cam.ac.uk>> wrote:
>
>> Just to add to the already-excellent list of replies, this can also
>> be done quite straightforwardly with the Clipper plugin in
ChimeraX.
>> I’d be happy to provide an example script if you want one.
>>
>> Best regards,
>>
>> Tristan
>>
>> On 12 Jan 2020, at 18:54, orly avraham
>> <orly.levin...@mail.huji.ac.il
<mailto:orly.levin...@mail.huji.ac.il>> wrote:
>>
>> Hi Marcin,
>>
>> Thank you very much for your detailed reply!
>> You pointed out many special cases that I wouldn't have thought of.
>> Indeed an existing solution is highly preferred, and I appreciate
>> you pointing out several available libraries. I came across Gemmi
>> and I will give it another look, and I will examine the additional
>> resources you mentioned as well.
>>
>> Best regards,
>> Orly Avraham
>>
>> On Sun, Jan 12, 2020 at 5:59 PM Marcin Wojdyr <woj...@gmail.com
<mailto:woj...@gmail.com>>
>> wrote:
>> Hi Zhijie,
>>
>> it's good and instructive to implement such things from the ground
>> up,
>> but there are many special cases that one would be discovering
while
>> testing this procedure, so if the time is limited it may be better
>> to
>> use an existing solution.
>>
>> For instance, here one may find out that using the SCALE1 record
>> doesn't give the sufficient accuracy. In the example in your script
>> you have 6 significant digits in the unit cell lengths in CRYST1,
>> but
>> only 4 significant digits in SCALE1. (The accuracy of SCALE1 is
>> problematic in general; sometimes it needs to be manually removed
>> when
>> a program reads it in preference to CRYST1.)
>>
>> Then one may find out that the 3x3x3 supercell is not
sufficient. If
>> the molecule is far from the origin, symmetry operations send
it far
>> away. For example, 5M3H annotates (in the mmCIF format) hydrogen
>> bond
>> between 1_555 and 2_11516 - the symmetry mate is shifted 16 unit
>> cells
>> in the z direction. Since you already use fractional coordinates in
>> your script you could tell directly from the center-of-mass
>> coordinates how many unit cells it should be shifted. Say, you have
>> x=3.1, so to shift it near the origin you shift it by 3 unit cells
>> along x.
>>
>> But even if all the molecules are shifted near the origin, the
3x3x3
>> cell is still not sufficient to find contacts.
>> See 3NWH – a homo-4-mer in P2 (4 x 2 chains per unit cell). Here
>> it in
>> its unit cell, colored by the chain id:
>> https://gemmi.readthedocs.io/en/latest/_images/3nwh.png
>> Or 5XG2 – a monomer in P21. Two copies of the chain are
>> rainbow-colored here:
>> https://gemmi.readthedocs.io/en/latest/_images/5xg2.png
>> These chains span over more than 4 unit cells in one direction. One
>> could use big enough supercell, but it'd be slow. I suppose that
>> even
>> using a 3x3x3 supercell is slow. The alternative is to do the
>> distance
>> calculation in fractional coordinates modulo 1.
>>
>> Then you needs to consider atoms on special positions. If you apply
>> symmetry operations to an atom on a 4-fold symmetry axis you get 4
>> atoms in the same place. So this needs to be handled. The atom may
>> not
>> be exactly on the axis, because the refinement program may not
>> constrain its position. So the symmetry operations should
produce, I
>> think, 4 alternative locations of the same atom. But you could also
>> have an atom near the symmetry axis bonded to its symmetry mate -
>> then
>> the symmetry operations should produce different atoms. So the
>> procedure requires a cut-off distance or a heuristics to
distinguish
>> the two cases.
>>
>> Then, if you'd like to expand non-crystallographic symmetry
from the
>> MTRIX records - this is another complication. And so on...
>>
>> So I'd recommend using one of many available programs for finding
>> contacts or interactions. If none of them is suitable - then try
>> crystallographic libraries.
>> I didn't document yet how to find the contacts using gemmi, but
I'll
>> do it in the coming weeks (or months). Cctbx and clipper are other
>> (more mature) libraries worth checking.
>>
>> Best wishes,
>> Marcin
>>
>> On Sat, 11 Jan 2020 at 02:11, Zhijie Li <zhijie...@utoronto.ca
<mailto:zhijie...@utoronto.ca>>
>> wrote:
>>>
>>> Hi Orly,
>>>
>>> REMARK 290 should be the easiest way for generating symmetry
>> mates. Other routes are just going to give you the same results. As
>> Jonathan already pointed out, the symm ops do not garantee that the
>> symm copies are close to each other. The most simple-minded
>> solution to this problem would be simply generating 3x3x3 unit
cells
>> so that the unit cell in center will be complete. An upgrade to
this
>> is to compute the center of mass of the symmetry copies in each of
>> the 3x3c3 cells and find which one is closest to the orignal 1555
>> copy. Just for fun, I wrote a little python script that does this
>> (attached). In this script for unit cell translation and
calculating
>> center-center distances, I converted the Cartesian coordinates to
>> fractional coords first. Then after the translation,I used the
>> inverse of the SCALE1 matrix to get the shifted Cartesian coords.
>> This way I don't need to read wikipedia on geometry . But as noted
>> in the script the distances should better be calculated in
>> Cartesian.
>>>
>>> Zhijie
>>>
>>> ________________________________
>>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of
>> orly avraham <orly.levin...@mail.huji.ac.il
<mailto:orly.levin...@mail.huji.ac.il>>
>>> Sent: Friday, January 10, 2020 3:30 PM
>>> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
<CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>>
>>> Subject: [ccp4bb] Generating symmetry mates using python
>>>
>>> Hi all,
>>>
>>> I am a crystallographer currently employing computational methods
>> as well as experimental crystallography.
>>> I am trying to generate symmetry mates in python (working with
>> pandas dataframes), in order to analyze inter-sub-unit
interactions.
>> To do so I am trying to use the info in "REMARK 290
CRYSTALLOGRAPHIC
>> SYMMETRY" and manually (using numpy) perform a matrix
multiplication
>> with the relevant translation (xyz*rotation + translation).
>>> For some reason this doesn't work consistently and I feel I need
>> to use the info in CRYST1 to obtain the unit cell and
multiplication
>> matrix. Here I ran into trouble with extracting the correct
symmetry
>> operations based on each space group. I found spglib but it doesn't
>> quite solve the problem.
>>> I also tried opening PyMol through the command and generating
>> symmetry mates this way. It worked on a few files but failed quite
>> quickly (segmentation fault) and was also very slow.
>>> Can anyone suggest a useful solution, preferably clear to use
>> and/or well documented? Or even have a python script/code they can
>> share for this?
>>>
>>> Best regards,
>>> Orly
>>>
>>> --
>>>
>>> Orly Avraham, Ph.D.
>>> Postdoctoral fellow
>>> The lab of Prof. Oded Livnah
>>> and the lab of Prof. Ora Schueler-Furman
>>> The Hebrew University of Jerusalem
>>> Israel
>>>
>>>
>>> ________________________________
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>>
>>>
>>> ________________________________
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>>
>
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>>
>> --
>>
>> Orly Avraham, Ph.D.
>> Postdoctoral fellow
>> The lab of Prof. Oded Livnah
>> and the lab of Prof. Ora Schueler-Furman
>> The Hebrew University of Jerusalem
>> Israel
>>
>> -------------------------
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> --
>
> Orly Avraham, Ph.D.
> Postdoctoral fellow
> The lab of Prof. Oded Livnah
> and the lab of Prof. Ora Schueler-Furman
> The Hebrew University of Jerusalem
> Israel
--
Orly Avraham, Ph.D.
Postdoctoral fellow
The lab of Prof. Oded Livnah
and the lab of Prof. Ora Schueler-Furman
The Hebrew University of Jerusalem
Israel
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--
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
The Keith Peters Building
Hills Road
Cambridge CB2 0XY
www.cimr.cam.ac.uk/investigators/read/index.html
tel: +44(0)1223 763234
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