To the developers of Chimera: is there any intention of implementing the uploading of imgCIF density maps files? Such files can be generated by RasMol starting from either atomic structures or low-resolution bead models (e.g. SAXS-derived models). Conversely, it would be nice if density maps could be generated within Chimera... Best - Mattia Dr. Mattia Rocco Biopolimeri e Proteomica Istituto Nazionale per la Ricerca sul Cancro (IST) c/o Centro per le Biotecnologie Avanzate (CBA) IST c/o CBA, Largo Rosanna Benzi 10 I-16132 Genova, Italy Phone: +39-0105737-310 Fax: +39-0105737-325 e-mail: mattia.rocco@istge.it ATTENZIONE. Il presente messaggio ed i suoi allegati devono intendersi ad uso esclusivo dei suoi destinatari e sono confidenziali. Persone diverse dal destinatario, anche ai sensi del D.Lgs. n. 196/2003 , non debbono prendere visione dei contenuti, copiare od inoltrare l'e-mail a terzi. Se ricevete questo messaggio per errore, Vi preghiamo di cancellarlo, di distruggerne ogni copia e di informarci immediatamente. La mail non è un protocollo sicuro, pertanto IST declina ogni responsabilità in caso di intercettazione o modifiche del presente messaggio. WARNING. This message and any attachments is intended solely for the use of the intended addressees and is confidential. Any unauthorized review, use, disclosure or distribution is prohibited. If you receive this message in error, please delete it, destroy all copies and immediately notify us. Mail is not a secure protocol, therefore IST will not be liable for interception or amendment of this message.
Dear Mattia, You can make a density map from atomic structures (or their parts) in Chimera using the "molmap" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> For example, commands: open 2gbp molmap ligand 4.5 molmap protein 5 ... would make a map of resolution 4.5 for the ligand part of the structure (glucose) and another map of resolution 5 for the protein part of the structure. You could also specify the whole structure, particular chains, etc. If the SAXS model was in the form of a PDB file with the beads as "atoms," perhaps you could use a similar procedure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 4, 2011, at 7:44 AM, Mattia Rocco wrote:
To the developers of Chimera: is there any intention of implementing the uploading of imgCIF density maps files? Such files can be generated by RasMol starting from either atomic structures or low-resolution bead models (e.g. SAXS-derived models).
Conversely, it would be nice if density maps could be generated within Chimera...
Best - Mattia
Hi Mattia, I put imgCIF support on the Chimera feature request list http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests I don't expect it is likely to get done for several reasons. From what I read on the web imgCIF was developed for recording 2-d x-ray diffraction spot data. Chimera cannot do anything with that kind of data. In 2007 there was some work done to make it handle 3-dimensional density maps and it was included in RasMol for that purpose. There was also some talk of a PyMol plug-in to read the 3-d imgCIF maps but I don't know if anything came of that. It looks like this format is not used by most map display programs. RasMol also uses CCP4 which Chimera reads, as does almost every other map display program. And as Elaine pointed out, Chimera can directly create maps from atomic models. New volume data formats are easy to support in Chimera with Python code. If someone wants to provide and imgCIF reader/writer in Python I could put it into Chimera if the code is well written. Tom
is there any intention of implementing the uploading of imgCIF density maps files? Such files can be generated by RasMol starting from either atomic structures or low-resolution bead models (e.g. SAXS-derived models).
Conversely, it would be nice if density maps could be generated within Chimera...
Hi Tom, many thanks also to you for another fast and very informative answer! I didn't know that RasMol could read ccp4 maps, but at the moment it will not save a generated map in that format. I have recently contacted the RasMol developers, and Dr. Bernstein wrote back to me that he will make a save in ccp4 format option available, so in the end the circle will be hopefully closed... ;-) Best wishes - Mattia At 10.31 04/05/2011 -0700, Tom Goddard wrote:
Hi Mattia,
I put imgCIF support on the Chimera feature request list
http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests
I don't expect it is likely to get done for several reasons. From what I read on the web imgCIF was developed for recording 2-d x-ray diffraction spot data. Chimera cannot do anything with that kind of data. In 2007 there was some work done to make it handle 3-dimensional density maps and it was included in RasMol for that purpose. There was also some talk of a PyMol plug-in to read the 3-d imgCIF maps but I don't know if anything came of that. It looks like this format is not used by most map display programs. RasMol also uses CCP4 which Chimera reads, as does almost every other map display program. And as Elaine pointed out, Chimera can directly create maps from atomic models.
New volume data formats are easy to support in Chimera with Python code. If someone wants to provide and imgCIF reader/writer in Python I could put it into Chimera if the code is well written.
Tom
is there any intention of implementing the uploading of imgCIF density maps files? Such files can be generated by RasMol starting from either atomic structures or low-resolution bead models (e.g. SAXS-derived models).
Conversely, it would be nice if density maps could be generated within Chimera...
participants (3)
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Elaine Meng -
Mattia Rocco -
Tom Goddard