[PyMOL] Re: New spectral color pallette
how can i get 300 dpi image or picture of higher resolution from pymol On 1/5/06, Robert Campbell r...@post.queensu.ca wrote: Alexander, * alexander.paut...@bc.boehringer-ingelheim.com wrote: I would like to color my protein according to B-factor with a self-defined spectral palette (In this case I have put sequence conservation into the Bfactor this column). I found that spectrum b, blue_white_red, minimum=0, maximum=100 would do part of the job with a predefined pallette - I could not find out how to define my own new color palette like white_red. - Is there a way to visualize the color palettes before applying it to an object? * Seth Harris set...@gmail.com [2005-12-31 09:54] wrote: This is more half an answer than the real deal, but when I had the same issue I opted for the quick work around of setting the range from -100 to 100 for the blue-white-red palette which effectively made 0-100 correspond to white to red only since there were no negative B factors/conservation scores. e.g. spectrum b, blue_white_red, minimum=-100, maximum=100 I am curious for better answers, as you are, but haven't delved into the code to look for it myself, either. But perhaps this or some fine tuning of the range or other pre-defined palettes will get done what you desire. I have a script, color_b.py, available on my website that allows one to colour based on the value of the B-factor or occupancy columns. It currently has the following colour gradients: 'bgr': blue - green - red 'rgb': red - green - blue 'bwr': blue - white - red 'rwb': red - white - blue 'bmr': blue - magenta - red 'rmb': red - magenta - blue 'rw' : red - white 'wr' : white - red 'gw' : green - white 'wg' : white - green 'bw' : blue - white 'wb' : white - blue 'gy' : green - yellow 'yg' : yellow - green 'gray' : black - white 'reversegray' : white - black It isn't too difficult to add more gradients by following the recipes in the make_gradient function in that script. It is also possible to set the minimum and maximum values to tune the exact gradient limits as well as to set the saturation and brightness (value) of the colours, via the command options. Hope this helps. Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Ms. DIVYA DUBE Junior Research Fellow C/O Dr.R.Ravishankar MSB Division CDRI Lucknow,INDIA
Re: [PyMOL] Re: New spectral color pallette
Alexander, * alexander.paut...@bc.boehringer-ingelheim.com wrote: I would like to color my protein according to B-factor with a self-defined spectral palette (In this case I have put sequence conservation into the Bfactor this column). I found that spectrum b, blue_white_red, minimum=0, maximum=100 would do part of the job with a predefined pallette - I could not find out how to define my own new color palette like white_red. - Is there a way to visualize the color palettes before applying it to an object? * Seth Harris set...@gmail.com [2005-12-31 09:54] wrote: This is more half an answer than the real deal, but when I had the same issue I opted for the quick work around of setting the range from -100 to 100 for the blue-white-red palette which effectively made 0-100 correspond to white to red only since there were no negative B factors/conservation scores. e.g. spectrum b, blue_white_red, minimum=-100, maximum=100 I am curious for better answers, as you are, but haven't delved into the code to look for it myself, either. But perhaps this or some fine tuning of the range or other pre-defined palettes will get done what you desire. I have a script, color_b.py, available on my website that allows one to colour based on the value of the B-factor or occupancy columns. It currently has the following colour gradients: 'bgr': blue - green - red 'rgb': red - green - blue 'bwr': blue - white - red 'rwb': red - white - blue 'bmr': blue - magenta - red 'rmb': red - magenta - blue 'rw' : red - white 'wr' : white - red 'gw' : green - white 'wg' : white - green 'bw' : blue - white 'wb' : white - blue 'gy' : green - yellow 'yg' : yellow - green 'gray' : black - white 'reversegray' : white - black It isn't too difficult to add more gradients by following the recipes in the make_gradient function in that script. It is also possible to set the minimum and maximum values to tune the exact gradient limits as well as to set the saturation and brightness (value) of the colours, via the command options. Hope this helps. Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
[PyMOL] Re: New spectral color pallette
This is more half an answer than the real deal, but when I had the same issue I opted for the quick work around of setting the range from -100 to 100 for the blue-white-red palette which effectively made 0-100 correspond to white to red only since there were no negative B factors/conservation scores. e.g. spectrum b, blue_white_red, minimum=-100, maximum=100 I am curious for better answers, as you are, but haven't delved into the code to look for it myself, either. But perhaps this or some fine tuning of the range or other pre-defined palettes will get done what you desire. Cheers, Seth Message: 1 From: alexander.paut...@bc.boehringer-ingelheim.com To: pymol-users@lists.sourceforge.net Date: Fri, 30 Dec 2005 10:24:10 +0100 Subject: [PyMOL] new spectral color palette This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --_=_NextPart_001_01C60D22.CA0F1A47 Content-Type: text/plain Content-Transfer-Encoding: 7bit Hi I would like to color my protein according to B-factor with a self-defined spectral palette (In this case I have put sequence conservation into the Bfactor this column). I found that spectrum b, blue_white_red, minimum=0, maximum=100 would do part of the job with a predefined pallette - I could not find out how to define my own new color palette like white_red. - Is there a way to visualize the color palettes before applying it to an object? Thanks for any help. alex Dr. Alexander Pautsch Protein Crystallography /Structural Research Boehringer Ingelheim Pharma GmbH Co. KG Deutschland Birkendorferstrasse 65 88400 BIBERACH, Germany tel. +49 - (0)7351 - 54 4683 fax. +49 - (0)7351 - 83 4683 email alexander.paut...@bc.boehringer-ingelheim.com
