Re: [ccp4bb] Visualisation software supporting ChromaDepth
Hi Jan, Chromadepth is actually in Open-Source PyMOL since version 2.2. I see the ChangeLog only mentions "Graphics refactoring, ported from Incentive PyMOL". I'll fix the related documentation. Cheers, Thomas > On Mar 7, 2019, at 12:38 PM, Jan Gebauer wrote: > > Dear all, > > I know it's not quite the topic of this list, but hopefully related enough. > > I am looking for a free software,able to render PDB structures in ChromaDepth > colours (Meaning from blue to red based on the distance from the viewer - > https://en.wikipedia.org/wiki/ChromaDepth). I'd like to print some structure > for an "open-day" of our faculty. > > I found that the incentive version of PyMol supports it, but this is a little > bit to expensive. > > Is there any free software out there? Or potentially a plugin? If not is > there a function to determine distances of atoms from the viewer in Chimera > -- I could write my own python script then... > > Thanks for all help, > > Jan Gebauer > -- > Dr. Jan Gebauer > Structural Biologist > px.uni-koeln.de / c2f.uni-koeln.de / pipc.uni-koeln.de > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] pymol fonts on gui
Hi Amir, This looks like missing shader support, which is unexpected on modern Mac hardware. Can you try to set the "use_shaders" setting? PyMOL> set use_shaders, 1 If this fixes it, then please check your ~/.pymolrc file if the use_shaders setting is wrongly disabled there (File > Edit pymolrc). Cheers, Thomas > On Mar 8, 2018, at 11:05 AM, Amir Khan <amirr...@tcd.ie> wrote: > > Hi > > Apologies for the non-CCP4 question, I can’t find help on other forums. > > I’ve got extremely small fonts on Pymol graphical window, can’t see the > options (A, SA, H ,L etc) or the primary sequence without a magnifying glass. > > Running Pymol 2.0.7 on Mac 10.12.6, I’ve attached an image showing the > problem. > > Any ideas? > > Thanks > Amir > > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] RMSD between superposed structures without moving
Just use the "rms_cur" command instead of "align". https://pymolwiki.org/index.php/rms_cur Cheers, Thomas > On Aug 28, 2017, at 10:04 AM, Johannes Sommerkamp > <155b9e78396e-dmarc-requ...@jiscmail.ac.uk> wrote: > > Thanks a lot for your answers and the PyMOL mailing list hint. I didnt had in > mind this list. > > I read the Pymol Wiki. The commands > align moving, target, cycles=0, transform=0 > > align moving, target, cycles=0 > > give identical values for RMSD. So, the only difference is, that the moving > structure is not moved in the graphical output. Additionally the RMSD with > the argument cycles=0 can't be the RMSD before any movement because the > values differ for the super and the align command. I think its just without > refinement. > Since the two structure I want to compare are already aligned based on the > central beta sheet CA atoms, I want to calculate the RMSD without any > movement. > > > Regards > Johannes > > > > On 27/08/17 19:18, Folmer Fredslund wrote: >> Hi Johannes, >> >> Did you read the PymoWIKI entry on the align command? >> >> https://pymolwiki.org/index.php/Align#RMSD >> >> I think this should give you what you want within PyMOL. >> >> Btw, there is a nice dedicated PyMOL mailing list >> https://pymolwiki.org/index.php/PyMOL_mailing_list >> It is rather low traffic, but the replies are generally from the developers >> or very knowledgeable users. >> >> Hope this helps, >> Folmer Fredslund >> >> On 2017-08-27 13:09, Johannes Sommerkamp wrote: >>> Hello everybody, >>> I have superposed two structures based on the central beta-sheet CA atoms >>> with the "super" command in Pymol. >>> Now, I want to calculate the RMSD between ALL atoms or ALL CA atoms without >>> moving the structures again. The rms_cur command in Pymol would do that, >>> but only works if all atom identifiers match. Adding "transform=0" to the >>> super, oder align command still does the alignment and moves the structure >>> but does not show the movement. >>> >>> Is there an easy way to just calculate the all atom RMSD between two >>> already superposed structures in pymol or any other programm? >>> >>> Thanks in advance! >>> Johannes >>> > > -- > Johannes Sommerkamp > Ruhr-Universität Bochum > AG Röntgenstrukturanalyse an Proteinen, LS Biophysik, ND04/396 > Universitätsstraße 150 > 44801 Bochum > Tel: +49-(0)234/32-25754 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] PyMOL question
Hi Lindsey,
The following should work:
select sele, obj1 and not (obj1 like obj2)
or to match all identifiers, not only resi/name:
select sele, obj1 and not (obj1 in obj2)
There are also actual "diff" and "symdiff" commands available from PSICO
(https://pymolwiki.org/index.php/Psico). Try this:
run
https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/selecting.py
symdiff obj1, obj2
Hope that helps.
Cheers,
Thomas
On 23 Jan 2017, at 14:00, L. Doyle <ldo...@fhcrc.org> wrote:
> Hello!
> Does anyone know how to select residues in object 1 that are different from
> object 2? I know how to select residues that are similar ("select name, obj1
> like obj2") but can't figure out how to do the opposite. I am running PyMOL
> on a Mac.
> Thank you,
> Lindsey
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
Re: [ccp4bb] Residues are missing in cartoon mode when dealing with virus capsid-like proteins in Pymol
Hi Didi, Does the PDB file have unique chain identifiers, or is this a concatenation of multiple chains which us the same identifier? If that's the case, try this: PyMOL> set retain_order See also: https://pymolwiki.org/index.php/retain_order Hope that helps. Cheers, Thomas On 11 Nov 2016, at 16:30, Didi He <bosipop...@gmail.com> wrote: > Hi all, > > I want to use PyMOL to draw an image of a big protein complex with a virus > capsid-like protein shell and an enclosed enzyme. But it only works in line > mode. If I show it in cartoon mode, most residues went missing. Did anyone > come across the same problem and could you give me some suggestions? > > Thanks very much! > Best wishes, > Didi -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] PyMOL v. Coot map 'level'
in Coot looks more like a 0.5 level in PyMOL. Does anyone have insight they could share about the difference between how Coot and PyMOL loads maps? Maybe the PyMOL 'level' is not a rmsd? is there some other normalization factor in PyMOL that I should set? Or, perhaps there is a mailing list post out there that I've missed, to which you could point me. :-) Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of the 2Fo-Fc map, contoured at 1.0 about a 3-residue-long 'selection' like so: isomesh map, My_2Fo-Fc.map, 1.0, selection, carve=2.0, and after hiding everything but the selection, I have a nice picture ... but with a map at a level I cannot interpret in PyMOL relative to Coot :-/ Regards, Emily. -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlVo1L4ACgkQU5C0gGfAG10YkwCfROYPVXBK/pDS4z/zi5MNY1D+ nHIAnjOFiAkb6JbuIGWRWkBFDG5Xgc2K =hrPT -END PGP SIGNATURE- -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] PyMOL v. Coot map 'level'
Hi James, carving and normalization in PyMOL are really independent things. Normalization happens during map loading (if normalize_ccp4_maps is on). Carving happens during mesh generation (it's an argument of the isomesh command) and is really just a way to limit mesh display to an area of interest. You can do a simple test and create a mesh of an entire map, and a carved mesh around a ligand or residue, and both should match perfectly. Example: fetch 1rx1, async=0 fetch 1rx1, async=0, type=2fofc isomesh meshfull, 1rx1_2fofc, 1.0 isomesh meshcarve, 1rx1_2fofc, 1.0, organic, 2.0, 1, 2.0 set grid_mode disable 1rx1 set_view (\ 0.929457247,0.368711948,0.012666196,\ -0.360624999,0.900760233,0.242035180,\ 0.077831753, -0.229529440,0.970184207,\ 0.16911,0.72468, -31.454853058,\ 26.290172577, 59.373352051, 15.045225143,\ 29.803743362, 33.103614807, -20.0 ) Expanding the map also happens during mesh generation and does nothing to the data, except replicating it. Using your tool of choice to normalize a map before loading into PyMOL is for sure a good practice and solves the issue that PyMOL doesn't normalize across the asymmetric unit, but the raw data (if raw data != integral number of asymmetric units). Cheers, Thomas On 03 Jun 2015, at 14:14, James Holton jmhol...@lbl.gov wrote: I have never trusted Pymol's normalization of maps, because it has never been clear to me if it does the normalization before or after the carve. If it is after, then you have a serious interpretation problem: the 1 sigma level will be MUCH lower than if the rest of the map were not set to zero. In this situation if you set the carve right the map will look a LOT more like the coordinates than it should. In fact, if you normalize a map using anything but an integral number of asymmetric units your 1 sigma level will not be the same as if it were done properly. With pymol you usually have to extend the map to cover the protein of interest, and this extended map is seldom an integral number of asymmetric units. So, I have always taken to normalizing the map myself (using mapmask) with a single ASU or single cell as the map extent, and THEN extending the map to cover the PDB (using a completely different run of mapmask) and only then load it into pymol. I always turn off map normalization in pymol. I have also never used carve, as my thesis adviser strongly disapproved of the practice. Mostly because of the potential for bias mentioned above. Do you really have to carve for your density to be clear? -James Holton MAD Scientist On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote: Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (http://sourceforge.net/p/pymol/mailman/message/26496806/ and http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions about how to fix the problem are not working for me, and I cannot figure out why. Perhaps someone here can help: I'd like to display (for beauty's sake) a selection of a model with the map about this selection. I've fetched the model from the PDB, downloaded its 2mFo-DFc CCP4 map, loaded both the map and model into both PyMOL (student version) and Coot (0.8.2-pre EL (revision 5592)), and decided that I would use PyMOL to make the figure. I notice, though, that the map 'level' in PyMOL is not equivalent to the rmsd level in Coot, even when I set normalization off in PyMOL. I expected that a 1.0 rmsd level in Coot would look identical to a 1.0 level in PyMOL, but it does not; rather, a 1.0 rmsd level in Coot looks more like a 0.5 level in PyMOL. Does anyone have insight they could share about the difference between how Coot and PyMOL loads maps? Maybe the PyMOL 'level' is not a rmsd? is there some other normalization factor in PyMOL that I should set? Or, perhaps there is a mailing list post out there that I've missed, to which you could point me. :-) Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of the 2Fo-Fc map, contoured at 1.0 about a 3-residue-long 'selection' like so: isomesh map, My_2Fo-Fc.map, 1.0, selection, carve=2.0, and after hiding everything but the selection, I have a nice picture ... but with a map at a level I cannot interpret in PyMOL relative to Coot :-/ Regards, Emily. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] PyMOL v. Coot map 'level'
Hi Emilia et al., I tried to figure out the PyMOL vs. Coot normalization discrepancy a while ago. As far as I remember, PyMOL normalizes on the raw data array, while Coot normalizes across the unit cell. So if the data doesn't exactly cover the cell, the results might be different. Cheers, Thomas On 01 Jun 2015, at 11:37, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: One cannot understand what is going on without knowing how this map was calculated. Maps calculated by the Electron Density Server have density in units of electron/A^3 if I recall, or at least its best effort to do so. This is what I was looking for! (i.e. what the units are) Thanks. :-) Yes, I'd downloaded the 2mFo-DFc map from the EDS, and got the same Coot v. PyMOL discrepancy whether or not I turned off the PyMOL map normalization feature. If you load the same map into Pymol and ask it to normalize the density values you should set your contour level to Coot's rmsd level. If you don't normalize you should use Coot's e/A^3 level. It is quite possible that they could differ by a factor of two. This was exactly the case. The map e/A^3 level (not the rmsd level) in Coot matched very well, visually, the map 'level' in PyMOL; they were roughly off by a factor of 2. I did end up also generating a 2mFo-DFc map using phenix, which fetched the structure factors of the model in which I was interested. The result was the same (i.e. PyMOL 'level' = Coot e/A^3 level ~ = 1/2 Coot's rmsd level) whether I used the CCP4 map downloaded from the EDS, or generated from the structure factors with phenix. Thanks All. Emily. Dale Tronrud On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote: Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (http://sourceforge.net/p/pymol/mailman/message/26496806/ and http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions about how to fix the problem are not working for me, and I cannot figure out why. Perhaps someone here can help: I'd like to display (for beauty's sake) a selection of a model with the map about this selection. I've fetched the model from the PDB, downloaded its 2mFo-DFc CCP4 map, loaded both the map and model into both PyMOL (student version) and Coot (0.8.2-pre EL (revision 5592)), and decided that I would use PyMOL to make the figure. I notice, though, that the map 'level' in PyMOL is not equivalent to the rmsd level in Coot, even when I set normalization off in PyMOL. I expected that a 1.0 rmsd level in Coot would look identical to a 1.0 level in PyMOL, but it does not; rather, a 1.0 rmsd level in Coot looks more like a 0.5 level in PyMOL. Does anyone have insight they could share about the difference between how Coot and PyMOL loads maps? Maybe the PyMOL 'level' is not a rmsd? is there some other normalization factor in PyMOL that I should set? Or, perhaps there is a mailing list post out there that I've missed, to which you could point me. :-) Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of the 2Fo-Fc map, contoured at 1.0 about a 3-residue-long 'selection' like so: isomesh map, My_2Fo-Fc.map, 1.0, selection, carve=2.0, and after hiding everything but the selection, I have a nice picture ... but with a map at a level I cannot interpret in PyMOL relative to Coot :-/ Regards, Emily. -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlVo1L4ACgkQU5C0gGfAG10YkwCfROYPVXBK/pDS4z/zi5MNY1D+ nHIAnjOFiAkb6JbuIGWRWkBFDG5Xgc2K =hrPT -END PGP SIGNATURE- -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] off topic: measuring angle between two nucleic acid helices
Hi Almudena, you can do it with PyMOL, using PSICO's angle_between_helices with the cafit method. Example: run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/orientation.py fetch 3pt6, async=0 as cartoon angle_between_helices chain D+J, chain I+C, cafit Hope that helps. Cheers, Thomas On 04 Mar 2015, at 13:04, Almudena Ponce Salvatierra maps.fa...@gmail.com wrote: Hi everyone, I would like to ask if any of you know how to measure the angle between two nucleic acid helices? I am trying with pymol, but have not found a solution to it yet. Any ideas? Thanks a lot. Best, Almudena. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] RMSD of dimers
Hi Dan, gaps/insertions should be no problem for PyMOL's rms_cur command, as long as chain identifiers match (and all other atomic identifiers!). See http://pymolwiki.org/index.php/Fit for a description of the matchmaker argument. Cheers, Thomas On 24 Feb 2015, at 16:30, D Bonsor dbon...@ihv.umaryland.edu wrote: I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have superimposed using Chain A. Several programs will produce the RMSD of Chain A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain B2, B3, B4... to Chain B1 when I have superimposed the structures relative to Chain A. I have tried using Pymol though there are gaps/insertions so rms/rms_cur will not work. Does anyone else have any other suggestions? Thanks in advance, Dan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] CCP4BB Digest - 6 Aug 2014 to 7 Aug 2014 (#2014-213)
Hi Remie, PyMOL by default sorts atoms based on their identifiers (segment, chain, residue number). Could it be that your file has segment identifiers? Try this after loading your file: PyMOLalter all, segi= PyMOLsort Cheers, Thomas On 07 Aug 2014, at 19:08, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: Date:Thu, 7 Aug 2014 11:19:42 -0400 From:Remie Fawaz-Touma remiefa...@gmail.com Subject: Chains view Hi everyone, Does anyone know how to rearrange chains when looking at a structure in PyMol (maybe it has to be done in coot, don’t know). I have the ligand first now in PyMol and would like to see the sequence of the protein first, then ligand. It is worth mentioning that I did reorder the chains in coot: Extensions Modelling Reorder chains, and chain A is my protein, B is the ligand and C are the waters. So why don’t I see the same order in PyMol and how do I fix that? Thanks for any help, Remie -- Thomas Holder PyMOL Developer Schrödinger, Inc.
Re: [ccp4bb] [PyMOL] Farewell
Dear Jason, thank you so much for you deep commitment and your invaluable contributions to PyMOL and the PyMOL community. You assumed responsibility for PyMOL and managed to give it a new home at Schrödinger. We are sorry to see you leave and will truly miss you here. To me personally, you have been a great mentor and guide and I can hardly enumerate what I learned from you. I owe you deep gratitude. It is my honour to now take the lead on PyMOL and serve the community and our sponsors as best as I can. The PyMOL team at Schrödinger is strongly dedicated to continuously improve PyMOL and keep the PyMOL spirit alive. Cheers, Thomas On 24 Apr 2014, at 05:00, Jason Vertrees jason.vertr...@gmail.com wrote: Greetings PyMOLers and CCP4ers worldwide, It has been my great pleasure to serve the PyMOL community both in a volunteer and professional capacity for the past decade. I have recently been given an offer I can't refuse—to follow one of my dreams—helping lead technology and science at a new startup. March 30th marked my last day at Schrödinger and supporting PyMOL. Because of my great fondness for PyMOL and its community, I will continue to operate the PyMOLWiki until I find it a suitable home. I started the PyMOLWiki in 2005 and since then it's been visited over 15,289,590 times! (If you would like to sponsor or host the wiki feel free to email me.) Now I can't imagine the PyMOL community without it. Last, I am truly humbled to have followed in the footsteps of Warren DeLano. He was an amazing man whose ideas and actions have touched the lives of millions, whether they know it or not. He is missed. It's been great fun. I wish you all the best. Cheers, -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.com (o) +1 (603) 374-7120 -- Thomas Holder PyMOL Developer Schrödinger, Inc.
Re: [ccp4bb] pymol multiple transparent surfaces
Hi Matthias, you can switch to multi-layer transparency: PyMOL set transparency_mode, 1 This works for ray-tracing. In real-time (OpenGL) rendering, it currently depends on which object was enabled first. So try to toggle the back object off and on in the object menu panel. Cheers, Thomas Subject: [ccp4bb] pymol multiple transparent surfaces Date: Mon, 24 Feb 2014 22:25:39 + From: Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.de Reply-To: matth...@strubi.ox.ac.uk To: CCP4BB@JISCMAIL.AC.UK Dear BB-lers, I want to draw in pymol 2 objects, which are behind each other, as transparent surfaces. The surface at the back gets simply deleted. This would be correct (save some rendering time) if the object at the front was not see-thru. What wheel do I need to turn to get the surface of my object in the back drawn? Thanks a lot, Matthias -- - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk - -- Thomas Holder PyMOL Developer Schrödinger, Inc.
Re: [ccp4bb] Tool for calculating RMSD
Hi Claudia, this is very convenient with PyMOL: http://pymolwiki.org/index.php/Rms_cur Cheers, Thomas On 06/19/2012 05:04 PM, Claudia Millán Nebot wrote: Hello everyone :) I would like to know if it exist some tool that allows to calculate RMSD between 2 pdbs that are identic, but just displaced in space. It should not make a superposition, beause if this is the case it will just say that RMSD is 0 . I know is not such a difficult problem in terms of scripting, but i was wondering if there are tools already. Claudia Millán (cmn...@ibmb.csic.es mailto:cmn...@ibmb.csic.es) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] Finding N-term to C-term Distances
There is a separate problem with Thomas' script, though. Many structures do not have an OXT atom at the C-terminus of their polypeptide chains. It is probably safer to select the C-terminus with: sele_c = 'last (chain %s and name O and polymer) % chain I'm aware of that. But I think the more serious problem for such a statistic is that many PDB files do not contain the full-length protein and the last O atom is not actually the C-terminus (same with first N atom). Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] Server or software for B factor analysis
Hi Dialing,
if you know some python you can use PyMOL.
# get C-alpha b-factors as list
from pymol import cmd, stored
stored.bfactors = []
cmd.iterate('name CA', 'stored.bfactors.append((b,resv))')
# min/max b-factors with residue number
print min(stored.bfactors)
print max(stored.bfactors)
# data for plotting
x = [resv for (b,resv) in stored.bfactors]
y = [bfor (b,resv) in stored.bfactors]
# plot to a pdf file with matplotlib
from matplotlib.pyplot import figure
from matplotlib.backends.backend_pdf import PdfPages
fig = figure()
sub = fig.add_subplot(111)
sub.plot(x, y)
pp = PdfPages('bfactors.pdf')
fig.savefig(pp, format='pdf')
pp.close()
Hope that helps.
Cheers,
Thomas
On 02/22/2012 05:04 AM, Dialing Pretty wrote:
Dear All,
Will you please tell me a server of software which can draw a curve for
the B factor of the atoms in a protein PDB file from the first residue
to the residue?Or a server or software by which we can easily order the
B factors of the atoms in the PDB file according to the B factor in
decrease or in increase? Or to get the residues with the highest B
factor and the lowest B factor?
Cheers,
Dialing
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
Re: [ccp4bb] residuewise rmsd for multiple chain superposition
Dear Sreetama, theseus can superpose multiple structures and reports RMSD per residue. http://www.theseus3d.org/ If your sequences are not identical and you want least squares superposition, run it like this: theseus_align -l -f *.pdb This will produce several output files. The file theseus_variances.txt contains the RMSD per residue. Cheers, Thomas On 02/21/2012 10:33 AM, sreetama das wrote: Dear all, Is there any software which will print the RMSDs (residue wise, and not chain wise) for more-than-2 chains (having similar/same sequences) superposed together? Thanks in advance, sreetama -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] PyMol plugin
On 08/15/2011 12:15 AM, Yuri Pompeu wrote: ... I then installed cctbx+Python bundle from http://cci.lbl.gov/cctbx_build/ and sourced it. I still get the same result in PyMol though.. Does anyone know what to do? You need to launch PyMOL with the python executable that was installed by cctbx. For example my PyMOL+cctbx launcher looks like this: #!/bin/sh cctbx.python /opt/pymol-svn/modules/pymol/__init__.py $@ You could also symlink cctbx.python to python, like described here: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/cctbx/ Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] Symmetry Related molecules
On 08/05/2011 05:22 AM, Albert Guskov wrote: have a look at SuperSym plugin for pymol http://www.pymolwiki.org/index.php/SuperSym Or the Supercell script. It has less features than SuperSym but does not require cctbx module. http://pymolwiki.org/index.php/Supercell Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] print cmd.align in PYMOL
The numbers are: 1) RMSD after refinement 2) Number of aligned atoms after refinement 3) Number of refinement cycles 4) RMSD before refinement (raw sequence alignment) 5) Number of aligned atoms before refinement 6) Raw alignment score 7) Number of residues aligned The refinement drops outliers, if you don't want refinement set cycles=0. Cheers, Thomas On 08/02/2011 05:10 PM, G Y wrote: Dear all, A question for PYMOL. The command print cmd.align will align two pdbs and print out some informations like: (3.7496898174285889, 42, 1, 3.7496898174285889, 42, 20.0, 2) My question is what are the meaning of those number? which one is RMSD? Many thanks! G -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] Influence of symmetry related molecules on a protomer conformation in crystal structures
this is of course possible with PyMOL, try this:
pdbid, chain = '1a00', 'A'
cmd.fetch(pdbid, async=0)
cmd.symexp('__neighbors', pdbid, pdbid + ' and chain ' + chain, 5.0)
print 'Number:', len(cmd.get_object_list('(__neighbors*)'))
cmd.delete('__neighbors*')
cmd.delete(pdbid)
Cheers,
Thomas
On 07/14/2011 01:48 PM, sukanta mondal wrote:
I know, in PyMOL using 'symexp' possible to generate symmetry related
molecules for a given crystal structure. But I'm looking for some
program/software (for batch) by which I can find out the number
of symmetry related molecules (distance cutoff= 5A) interacting with
a given chain in a crystal structure.
Thanking you,
suku
NIBIO, Osaka
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
Re: [ccp4bb] generate large symmetry model
You can do this with PyMOL with the supercell script: http://pymolwiki.org/index.php/Supercell Cheers, Thomas On 06/30/2011 02:52 PM, Hargreaves, David wrote: Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave *David Hargreaves* Associate Principal Scientist -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] mutation and minimization
Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. PyMOL has a Mutagenesis wizard but you have to pick the best rotamer yourself. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] PDB data mining
Jason, that was pretty fast! You delivered the script before someone else could even suggest PyMOL ;) If you use from chempy import cpv cpv.distance(aa.coord, bb.coord) instead of cmd.get_distance( index %s % aa.index, index %s % bb.index) it will be significantly faster. Cheers, Thomas On Mar 9, 2011, at 7:43 AM, Jason Vertrees wrote: Hi Cale, For any given structure in the PDB, I want to identify all the Histidine ND1 atoms. I then want to consider these atoms in pairs, measure the distance in Angstroms between the ND1 atoms in each pair, and compile these distances (along with residue numbers of the pair) in a table. I then want to repeat this procedure for each unique structure in the PDB and generate a table containing all occurrences of HisND1 pairs with their corresponding separation distance. Amongst other things, I want e.g. generate a histogram from this table and determine e.g. the shortest HisND1 pair distance observed and the structure in which this happens. Does anyone have any suggestions for any tools I might be able to use to perform this search? This looked like a fun little PyMOL task. So, I wrote a script to do it. This will iterate over all the PDBs in a given directory and calculate the non-redundant distances of all HIS ND1s. A table is written to pre_hist.csv. Use R or something similar to create the histogram and do the numerical analysis. To use this, first, you'll need a prepared copy of the PDB, suitable for this task, downloaded locally in pdb_path. You will need to set pdb_path in the script below to wherever your PDBs are. (The other kind folks on this list already pointed you to resources for mirroring the PDB, if you haven't done it already.) To run the script below just save it to disk as his.py and launch it with: # from Linux pymol -cq his.py # or, from Mac /Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL -cq his.py If you're a Linux/Mac user, when the script finishes, just type: sort -n -k8 pre_hist.csv | head -2 into your BASH shell to get the shortest distance. For my example PDB it was: $ sort -n -k8 pre_hist.csv | head -2 PDBCHAINRESIATOM-ACHAINRESIATOM-BDISTANCE 5rla B187 3729 C312 7075 2.838208 To view the shortest distance use the ATOM-A and ATOM-B fields from the output file. From my example above I would need to fetch the protein and create a distance from index 3729 to index 7075. Here's how: # fetch the protein fetch 5rla, async=0 # show the distance distance index 3729, index 7075 # zoom on the new distance zoom dist01 Here's the Python script that does the work: import glob, os, pymol, sys from pymol import cmd the_pdb=/Users/vertrees/small_pdb files = glob.glob(the_pdb+os.sep+*.pdb) if not len(files): print Please set 'the_pdb' variable to a valid path containing PDB files. sys.exit(1) else: print Processing %d files. % len(files) s, outFile = resn HIS and name ND1, pre_hist.csv f = open(outFile, 'wb') # write the header f.write(PDB\tCHAIN\tRESI\tATOM-A\tCHAIN\tRESI\tATOM-B\tDISTANCE\n) # for each file in the mirror for x in files: cmd.load(x,finish=1) n = cmd.get_names()[0] m = cmd.get_model(s).atom # pairwise for each atom for aa in m: for bb in m: # avoid duplicates if aa.index==bb.index: continue f.write( %s\t%s\t%s\t%s\t%s\t%s\t%d\t%f\n % (n, aa.chain, aa.resi, aa.index, bb.chain, bb.resi, bb.index, cmd.get_distance( index %s % aa.index, index %s % bb.index))) cmd.delete(n) f.close() print Processed %d files. Please see %s for results. % (len(files), outFile) Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] rmsd calculation for all atoms.
Hello Mike, I would recommend PyMOL. Consider this example: # get structures from PDB fetch 2j0s, async=0 fetch 2j0u, async=0 # remove alternative configurations remove not alt +A # select conformers with c-alpha atoms select conf1, 2j0s and chain A and name CA select conf2, 2j0u and chain A and name CA # select domains select dom1, resi 69-239 select dom2, resi 250-411 # superimpose on dom1 and calculate RMSD for dom2 fit (conf1 like conf2) and dom1, (conf2 like conf1) and dom1 rms_cur (conf1 like conf2) and dom2, (conf2 like conf1) and dom2 Cheers, Thomas On Wed, 2010-12-29 at 13:52 +, Michael Swan wrote: Dear all, I am having a bit of trouble finding a program to do an rmsd calculation and give me the differences between all the atoms in the structures. I have two structures which are identical in the sense that one is the apo protein and one is the bound structure. I would like to superimpose them using only one domain then output the rmsd values for all the atoms or at least individual residues. The structures are not completely identical as some extra residues were visible in the bound structure so I hope there is a program that can ignore those differences. If anyone knows of a program that will do this calculation I would much appreciate hearing about it. There seem to be many programs that will give an average rmsd over the whole structure or just the region used for alignment but I haven't found anything that will give me distances between atoms or residues that were not used in the alignment. Thanks, Mike. -- Thomas Holder AG Jekely MPI for Developmental Biology Spemannstr. 35 D-72076 Tuebingen
